Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

Rachel Gilroy; Anuradha Ravi; Maria Getino; Isabella Pursley; Daniel L Horton; Nabil-Fareed Alikhan; Dave Baker; Karim Gharbi; Neil Hall; Mick Watson; Evelien M Adriaenssens; Ebenezer Foster-Nyarko; Sheikh Jarju; Arss Secka; Martin Antonio; Aharon Oren; Roy R Chaudhuri; Roberto La Ragione; Falk Hildebrand; Mark J Pallen

doi:10.7717/peerj.10941

. 2021 Apr 6;9:e10941. doi: 10.7717/peerj.10941

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

Rachel Gilroy ¹, Anuradha Ravi ¹, Maria Getino ², Isabella Pursley ², Daniel L Horton ², Nabil-Fareed Alikhan ¹, Dave Baker ¹, Karim Gharbi ³, Neil Hall ^3,⁴, Mick Watson ⁵, Evelien M Adriaenssens ¹, Ebenezer Foster-Nyarko ¹, Sheikh Jarju ⁶, Arss Secka ⁷, Martin Antonio ⁶, Aharon Oren ⁸, Roy R Chaudhuri ⁹, Roberto La Ragione ², Falk Hildebrand ^1,^3,^✉, Mark J Pallen ^1,^2,^4,^✉

Editor: Timothy Driscoll

PMCID: PMC8035907 PMID: 33868800

Abstract

Background

The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community.

Results

We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii.

Conclusions

Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.

Keywords: Chickens, Gut microbiome, Biodiversity, Metagenomics, Metagenome-assembled genome, Bacterial nomenclature, Uncultured bacteria, Candidatus

Introduction

The domestic chicken is the most abundant bird and most abundant food animal on Earth, accounting for a larger fraction of the planet’s biomass than all species of wild birds combined (Bennett et al., 2018). Consumption of chicken meat is growing faster than any other type of meat and is seen as a cheaper, healthier, low-carbon alternative to meat from mammalian livestock (Eshel et al., 2014; Willett et al., 2019). Chicken eggs remain a nutritious, affordable food across the globe (Réhault-Godbert, Guyot & Nys, 2019).

The chicken gastrointestinal tract is home to a complex community of microbes and their genes—the chicken gut microbiome—that underpins links between diet, health and productivity in poultry, as evidenced by the ability of antibiotics to promote growth in chicks (Bedford, 2000). This microbial community also acts as a source of pathogens associated with disease in birds or in humans—including Campylobacter, Salmonella, and Escherichia coli—as well as providing a reservoir of antimicrobial resistance genes (Florez-Cuadrado et al., 2018; Jørgensen et al., 2019; Hermans et al., 2012).

Previous studies of this community have documented a rich variety of microorganisms (dominated by bacteria, but including viruses, archaea and microbial eukaryotes) and have shown that the taxonomic composition of this community varies with age, breed and disease status (Shang et al., 2018; Rychlik, 2020). However, these earlier efforts have largely relied on analyses of molecular barcodes (in particular short 16S rRNA gene sequences), which fail to provide species-level resolution, are unable to detect viruses and reveal nothing about the genome sequences, population structures or functional repertoires of microbial species (Hillmann et al., 2018).

Two strategies have proven productive for exploring taxonomic and functional diversity in complex microbial communities (Almeida et al., 2019; Forster et al., 2019). Culture-independent approaches rely on shotgun metagenomic sequencing of DNA extracted from relevant samples, followed by bioinformatics-based community profiling and analysis (Glendinning et al., 2020; Sergeant et al., 2014). Culture-dependent approaches combine large-scale isolation of microorganisms in pure culture with whole-genome sequencing and phylogenomic analysis (Medvecky et al., 2018). To explore taxonomic novelty in the chicken gut microbiome, we generated phylogenetic profiles to document known and unknown diversity and then exploited culture-dependent and culture-independent approaches to create an unprecedented high-quality reference collection of microbial genes and genomes from the chicken gut, revealing and naming hundreds of new candidate species from this commonplace but important ecological setting.

Materials and Methods

Sample collection and storage

Faecal samples were collected in South-East England from adult Lohmann Brown laying hens and adult Silkie hens in 2018. Birds were housed in a large outdoor run with a substrate of stone chippings and small turf enrichment beds during the day and kept in a coop overnight. They were fed a commercial layer feed, Farmgate Layer pellets and mash (ForFarmers UK Limited, Rougham, Bury St Edmunds), according to the manufacturer’s instructions and no antibiotics were used. Faecal sampling was approved by the University of Surrey’s NASPA ethics committee.

Sixty faecal samples were collected from the Lohmann Brown laying hens and thirty samples from the Silkie hens (six and three samples per day, respectively, for 10 days). Freshly evacuated faeces from individual birds were collected in sterile containers and immediately stored at −20 °C. Samples were then transferred to the laboratory for culture and/or DNA extraction. DNA was extracted using DNeasy PowerSoil kit (Qiagen, Hilden, Germany), following manufacturer’s instructions and then stored at −20 °C.

Sequencing and subsequent workflow

Workflow from this point forward is summarised in Fig. 1.The fifty samples yielding >20 ng DNA were processed according to the Low Input, Transpose Enabled (LITE) library construction pipeline (Perez-Sepulveda et al., 2020) before being subjected to paired-end (2 × 150 bp) metagenomic sequencing on the Illumina Novaseq 6000 platform. Bioinformatics analyses were performed on the Earlham Institute’s High Performance Computing cluster and on the Cloud Infrastructure for Microbial Bioinformatics (Connor et al., 2016). Sequences were assessed for quality using FastQC Version 0.11.8 and trimmed using Trimmomatic Version 0.36, configured to a minimum read length of 40, ‘leading’ and ‘trailing’ settings of 3 (SLIDINGWINDOW:4:20) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc; Bolger, Lohse & Usadel, 2014). Metagenomic sequences for all samples have been uploaded to the Sequence Read Archive under Bioproject ID PRJNA543206.

An asterisk (*) indicates read numbers are detailed post-filtering of diet and host associated reads.

Reference-based metagenomic analysis

An initial analysis of our chicken faecal sequences using the Kraken 2 taxonomic classifier (Wood, Lu & Langmead, 2019) was performed on custom databases representing the domestic chicken genome (GenBank assembly accession GCF_000002315.6) and the food plants Triticum aestivum (wheat), Aegilops tauschii (diploid progenitor of the D genome of hexaploid wheat) and Glycine max (soy bean): GenBank assembly accessions GCF_001957025.1, GCA_900519105.1, GCF_000004515.5. Kraken 2 revealed that 8% of reads originated from the chicken and at least 16% originated from the diet. These sequences were filtered from our dataset and excluded from subsequent analyses by keeping only reads ‘Unclassified’ by Kraken 2 after comparison with each database in turn.

The remaining dataset underwent taxonomic profiling using Kraken 2 against a microbial database built from all complete/representative archaeal, bacterial, fungal, protozoan, viral and UniVec_Core sequences in RefSeq (O’Leary et al., 2016) in January 2020. Bracken (Lu et al., 2017) was used to estimate taxon abundance from the Kraken 2 profiles, accepting only those taxa with ≥1,000 assigned reads. Bracken-database files were generated using ‘bracken-build’ on our microbial database and visualised using Pavian (Breitwieser & Salzberg, 2016).

Metagenomic assembly

We searched the NCBI BioProjects database (https://www.ncbi.nlm.nih.gov/bioproject/) in November 2019 with the term ‘chicken gut microbiome’ and then selected nine publicly available projects that contained at least one metagenomic sequence dataset >1 GByte in size: PRJEB33338, PRJNA193217, PRJNA291299, PRJNA375762, PRJNA415593, PRJNA417359, PRJEB22062, PRJNA543206, PRJNA417359, PRJNA385038, PRJNA616250. Only four of these studies were linked to research publications at the time of publication (Glendinning et al., 2020; Sergeant et al., 2014; Foster-Nyarko et al., 2020; Luiken et al., 2020)

All shotgun metagenomic reads were quality-filtered by removing reads shorter than 70% of the maximum expected read length (100 bp, 250 bp for MiSeq data), an estimated accumulated error >2.5 with a probability of ≥0.01 (Puente-Sánchez, Aguirre & Parro, 2016) or with an observed accumulated error >2, or >1 ambiguous position to assist assembly. If base quality dropped below 20 in a window of 15 bases at the 3′ end, or if the accumulated error exceeded 2, reads were trimmed. All these filter steps are integrated in sdm (Hildebrand et al., 2014). Reads mapping to the chicken genome and diet were removed from the metagenomic data as described previously, classifying reads with Kraken 2 against custom databases built on the aforementioned genomes.

Sequence datasets from our fifty samples—together with 582 samples from the selected BioProjects—were assembled using MegaHIT (Li et al., 2016) under the option ‘--k-list 25,43,67,87,101,127’. To avoid artefacts that sometimes result from co-assembly of sequences from different samples and different sources, we performed individual assemblies on each sample, with the exception of BioProject PRJNA417359. For that BioProject, as multiple metagenomic samples had been sourced from different tissues of the same individual bird, we co-assembled reads from the 120 BioSamples from that project.

Bacteriophage identification and characterisation

Contig sequences from the MegaHIT assemblies of our 50 samples that were ≥10 kb were analysed with VirSorter v1.0.5 with the ‘-db 2’ option to identify viral genomes (Roux et al., 2015). VirSorter Category 1 and 2 contig sequences were collapsed at 95% nucleotide identity over 70% of the sequence length using CD-Hit Est v4.6.1 (Fu et al., 2012). Classification of bacteriophage sequences relied on nucleotide searches using BLASTN against the NCBI NT database (Completed April 2020) and protein searches using Kaiju Version 1.7.3 against the RefSeq database (Completed April 2020) (Menzel, Ng & Krogh, 2016). Only bacteriophage genomes with BLASTN hit E-Value < 0.05, percentage identity >70% and query covering >50% were selected as reliable hits.

A taxonomic assignment was drawn from the highest scoring BLASTN (or in rare cases BLASTP) hit ranked by query cover and percentage ID. Synteny between predicted coliphages and their respective reference genomes were visualised using EasyFig (Sullivan, Petty & Beatson, 2011). Escherichia bacteriophage coverage per sample was determined using Anvi’o v6.1 (Eren et al., 2015) using default parameters and visualised in R using the Pheatmap package (https://www.rdocumentation.org/packages/pheatmap). Remaining viral genomes were filtered for completeness, retaining those that were circular and encoded a complete terminase gene (as predicted by VirSorter). Taxonomic assignments to the level of family were performed on viral genomes using Demovir (https://github.com/feargalr/Demovir).

Gene catalogue

Complete genes identified by Prodigal v2.6.1 (Hyatt et al., 2010) were clustered at 95% nucleotide identity using CD-HIT-Est v4.6.1 (Fu et al., 2012). Incomplete genes were then mapped to this complete gene list using Bowtie2 v 2.3.4.1 (Langmead & Salzberg, 2012) and any mapping at 95% nucleotide identity were incorporated into the relevant gene clusters. Finally, genes representing the 40 conserved marker genes defined by Mende et al. (2013) were clustered separately and then merged with the existing set of gene clusters. We thus obtained a gene catalogue of >20 million genes, defined as non-redundant at 95% average nucleotide identity (ANI). The final gene catalogue was uploaded to FigShare (https://doi.org/10.6084/m9.figshare.13116809.v4)

Abundance estimates of contigs and genes

Prodigal (Hyatt et al., 2010) was applied in metagenome-mode to all contigs from the MegaHIT assemblies. Unfiltered reads from each sample were mapped against their respective assembly to provide an estimate of contig and gene abundance using Bowtie2 (Langmead & Salzberg, 2012) with the options ‘--no-unal--end-to-end -score-min L, −0.6,−0.6’. Samtools 1.3.1 was used to sort and index all resulting Bam files (Li et al., 2009). Only reads with mapping quality >20, >95% nucleotide identity and >75% overall alignment length were retained. BEDTools v2.21.0 (Quinlan, 2014) was used to create depth profiles from the Bam files. These depth profiles were then translated with rdCover (https://github.com/hildebra/rdCover) into average coverage (in a 50 bp window) per contig or per gene predicted from each contig. Bam files were translated to abundances using the ‘jgi_summarize_bam_contig_depths’ script from the MetaBAT 2 package (Kang et al., 2019).

Gene abundances were linked to their respective gene clusters and originating samples. Redundant genes representing the same orthologue were removed.

Binning

We identified metagenomic species (MGSs) using the combinatorial approach described by Hildebrand et al. (2019), incorporating single-assembly binning in the creation of metagenome-assembled genomes (MAGs), gene catalogue binning in the creation of canopy clusters (Nielsen et al., 2014) and hierarchical clustering of candidate genes using the R function hclust, method = complete. To start with, we used MetaBAT 2 v2.15 (Kang et al., 2019) to bin contigs ≥400 bp. These were quality filtered using CheckM v1.0.11 (Parks et al., 2015) to obtain 5,595 bins at >80% completeness and <5% contamination.

Species-level clusters were formed using a combination of two distinct approaches. One approach removed redundancy between samples by pre-clustering bins if ≥30% of their genes overlapped with a higher-quality bin to create a set of pre-MGS bins. Lower-quality bins (>60% completeness and <10% contamination) were also included in the analysis but were not used to form new species clusters. To recover prokaryotic species usually obscured using single-sample assemblies and conventional binning techniques, we refined all species bins into ‘hcl-clusters’ using gene correlations and hierarchical clustering, as described by Hildebrand et al. (2019). We chose genes occurring in ≥10% of all associated MAGs as representatives for each pre-MGS bin and used these to fish for additional co-occurring genes from the gene catalogue, using a threshold of >0.75 Pearson correlation and >0.85 spearman rho to identify gene co-occurrences within this core gene set. We then merged MetaBAT 2 bins, canopy bins and co-occurring genes into our species bins. We used the presence of 40 known single-copy marker genes, without duplicates, as a quality criterion in selection of sub-clusters, before extracting the final set of MGS gene representatives using MATAFILER (https://github.com/hildebra/MATAFILER). The final collection of MGS bins (canopy clusters + hcl-clusters) was re-assessed for contamination and completeness using CheckM (Parks et al., 2015), so that we could be confident that each bin represents a single species.

A second approach de-replicated all MAGs at 95% ANI (species-level) and 99% ANI (strain-level) using dRep Version 2.0 (Olm et al., 2017) and only species not identified in approach one were added to the resulting non-redundant species catalogue. The minimum aligned fraction used during ANI genome alignment was 60%. A single representative MAG for each novel species cluster was uploaded to NCBI SRA under BioProject PRJNA543206 and all MAGs generated were uploaded to FigShare (https://doi.org/10.6084/m9.figshare.13116809.v4.). CompareM Version0.1.1 (https://github.com/dparks1134/CompareM) was used to calculate average amino acid identity (AAI) when identifying novel genera, using a cut-off of 60% for the percentage identity and 70% for the minimum alignment length used to delineate genus boundaries.

Taxonomy of metagenomic species

We used the Genome Taxonomy Database Toolkit (GTDB-Tk Release 95) to perform taxonomic assignments on strain-level dereplicated MAGs (Chaumeil et al., 2019). In addition, genes from each MGS were analysed through GTDB-Tk (Release 95), proGenomes resource (Mende et al., 2017) and underwent k-mer-based taxonomic profiling using Kraken 2. In assigning taxonomy, we allowed GTDB assignments to take precedence—only when no GTDB taxonomy was available would we adopt taxonomies assigned by ProGenomes and Kraken 2 and, then, only where genus and family assignments from these sources matched. When exploiting the taxonomy assigned according genes from metagenomic species, we applied a least-common-ancestor approach to unplaced taxa at higher taxonomic levels. Species distribution analyses were conducted using the Vegan package in R (R-Core-Team, 2018), before visualisation using ggplot2 (Wickham, 2016) and Pheatmap R packages (https://www.rdocumentation.org/packages/pheatmap). Pan-genome analysis was conducted using Roary v3.11.2 and visualised using the roary2svg.pl script (Page et al., 2015). Comparison of our derived metagenomes with those of Glendinning et al. (2020) was performed at 95% ANI using dRep and visualised using web-tool BioVenn (Hulsen, De Vlieg & Alkema, 2008).

Bacterial culture

To estimate species richness and diversity, the Phyloseq package of R (R-Core-Team, 2018) was applied to the output from Bracken (Lu et al., 2017) on all of our chicken faecal metagenomic datasets. The six faecal samples that showed highest species richness and taxonomic diversity were selected for culture-based studies. Frozen faecal samples were thawed, vortexed and two 0.5 g aliquots (once processed aerobically, the other anaerobically) from each sample were suspended in 5 ml PBS. Each aliquot was vortexed until homogenised, before performing serial dilutions in duplicate down to 1 × 10⁻⁵. Processing of samples for aerobic and anaerobic culture was identical, except that, for anaerobic culture, all culture media, diluent and consumables were pre-reduced to anaerobic conditions for at least 24 h before faecal samples were processed in a Whitley A95TG workstation.

For dilutions 10⁻³–10⁵, 200 µl was plated directly on to a set of three agar plates for each culture medium (Brain Heart Infusion, Colombia Blood Agar, Yeast extract, casitone and fatty acid) with or without vancomycin supplementation at a concentration of 6 µg/ml (Table S1). Cultures were incubated at 37 °C for 72 h in their respective conditions before assessment of colony growth. Well-isolated colonies were picked according to colonial morphotype distinctive in colour, shape and size, before being re-streaked on to the growth medium from which they were sourced to confirm purity. Individual colonies were subsequently used to inoculate 2 ml of broth based on the source culture medium, incubated at 37 °C for a further 24 h before bacterial DNA extraction. All isolates were archived at −80 °C in glycerol at 20% concentration.

Genome sequencing and analysis

Genomic DNA was extracted using a DNeasy UltraClean DNA isolation kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany). DNA was quantified using a Qubit^® fluorometer (Invitrogen, Carlsbad, CA, USA) high-sensitivity assay, before dilution to the required concentration in RNase-free water and purification on AMPure XP beads (Beckman Coulter, Brea, CA, USA). Sequencing libraries were prepared from 0.5 ng/µl of RNA free genomic DNA. A total of 282 isolates were included for genomic sequencing using the Nextera-XT DNA sample preparation kit (Illumina, San Diego, CA, USA) and whole-genome sequencing performed using the Illumina NextSeq sequencing platform, generating paired-end reads (2 × 150 bp).

Paired-end reads were quality-assessed and trimmed using FastQC and Trimmomatic as described above. Trimmed reads were assembled into contigs using SPAdes version 3.13.1 (Bankevich et al., 2012). Contigs shorter than 500 bp were discarded from analysis. Genome contamination and completeness was assessed using CheckM version 1.0.13. To confirm assembly quality, only genomes conforming to all the following criteria were included in further analysis: (i) contig N50 of >20 kbp (ii) 90% of assembled bases at >5× read coverage (iii) completeness of >95% (iv) contamination of <5% (v) complete 16S rRNA gene sequence.

Genome sequence taxonomic assignment

Barrnap Version 0.9 (https://github.com/tseemann/barrnap) was applied to all genomes that passed the quality filters to extract full-length 16S rRNA gene sequences. These were then compared to NCBI 16S rRNA gene sequences from RefSeq genomes using the NCBI’s web-based BLASTN facility (Altschul et al., 1990). 16S rRNA gene sequences that showed an identity of <98.7% to known sequences were assigned to novel species, using the conservative approach in proposed minimal standards (Chun et al., 2018). We used ReferenceSeeker Version 1.6.2 (Schwengers et al., 2019) to determine ANI and conserved DNA values compared to RefSeq bacterial genomes (Completed March 2020) (O’Leary et al., 2016). Genomes that showed ANI ≤95% and conserved DNA ≤69% to the closest relative were designated novel species. The Genome Taxonomy Database Toolkit (GTDB-Tk Release 95) was used to perform taxonomic assignments on isolate genomes (Chaumeil et al., 2019). Genomes were clustered at 95% and 99% ANI before selection of a single representative isolate per species using dRep (Olm et al., 2017). Where a genome previously designated as novel clustered with a genome of assigned taxonomy, this taxonomy was then applied to the previously designated ‘novel’ genome. Final taxonomic assignments were based on genome-based ANI values derived from RefSeq and GTDB—with GTDB assignments taking precedence. A single representative genome for each novel or renamed species cluster was uploaded to NCBI SRA under BioProject PRJNA543206 and all genomes alongside respective 16S rRNA gene sequences generated were uploaded to FigShare (https://doi.org/10.6084/m9.figshare.13234556).

Phylogenetic analysis

For phylogenetic analysis of all MGS and genome sequenced isolates we used PhyloPhlAn v3.0.58 (Asnicar et al., 2020) with the ‘diversity high’ and a proteome input predicted from all genome sequences using Prodigal v2.6.1 (Hyatt et al., 2010). Diamond v0.9.34 (Buchfink, Xie & Huson, 2015) was used to perform a search against 400 universal PhyloPhlAn markers. MAFFT v.7.271 (Katoh et al., 2002) was used to perform multiple sequence alignment before refinement with trimAl v.1.4 (Capella-Gutiérrez, Silla-Martínez & Gabaldón, 2009) and reconstruction into trees using FastTree v2.1 and RAxML v. 8.2.12 (Price, Dehal & Arkin, 2010; Stamatakis, 2014). All trees were visualised and annotated manually using the online iTOLv5.7 platform (Letunic & Bork, 2016). Trees were scrutinised to confirm that species and genera were monophyletic. Phylogeny for all cultured genomes unassigned at species level was confirmed as previously described against all available reference proteomes of that respective genus downloaded from NCBI.

To investigate the phylogenetic placement of cultured isolates designated as Escherichia marmotae and Escherichia sp001660175 by GTDB, we constructed a core genome phylogenetic tree. The genomes from cultured isolates were compared to genomes representing the full diversity of the genus Escherichia. Three Salmonella genomes were included as an outgroup. The genome sequences were aligned using Mugsy (Angiuoli & Salzberg, 2011), and alignment blocks conserved across all genomes were concatenated to produce a core genome alignment. A phylogenetic tree was constructed by maximum likelihood with 100 rapid bootstrap replicates, using the general time reversible model of nucleotide substitution with gamma correction for rate heterogeneity, as implemented in RAxML version 8.2.12 (Stamatakis, 2014).

Results

Reference-based profiling documents novel diversity

We collected faecal samples from 90 chickens reared in the UK belonging to two breeds: Lohman Browns (n = 60) and Silkies (n = 30). Short-read sequencing of 50 of these faecal samples generated a metagenomic dataset in excess of a billion paired-end reads or three hundred billion base pairs (Table S2).

We initially analysed the faecal samples using the k-mer-based programme Kraken 2, followed by refined phylogenetic analysis using the allied programme Bracken (Lu et al., 2017) (Table S3). Unsurprisingly, these programmes assigned sequence reads from the faecal samples to all three domains of life, as well as to viruses (Table S4), although relative abundance assignments show that bacteria predominate in this environment. Sequences were assigned to a wide range of bacterial phyla, including the three expected as predominant in the vertebrate gut (Bacteroidetes, Firmicutes, Proteobacteria), but also including over twenty additional phyla. Searches of the PubMed database with each phylum name and the term ‘chicken’ reveal that round half of these have been previously documented in the chicken gut. However, at least a dozen appear to be novel in this setting, including the Aquificae, Balneolaeota, Calditrichaeota, Chlorobi, Dictyoglomi, Fibrobacteres, Gemmatimonadetes, Ignavibacteriae, Kiritimatiellaeota, Lentisphaerae, Nitrospirae, and the Thermodesulfobacteria.

When we rank-ordered the species identified by Bracken according to maximum abundance in any one sample, we found, as expected, that species from the family Lactobacillaceae dominated among the top 20 most abundant organisms. However, we found that two species of Escherichia— Escherichia coli and Escherichia marmotae—accounted for ≥5% of reads in nearly half of the samples (22/50) and in two samples, accounted for more than 50%. Such monodominance of the gut microbiome by bacterial species has been described in diseased humans (Hildebrand et al., 2019; Ravi et al., 2019), but is surprising in the context of poultry reported as apparently healthy by their handlers. We also noted a high relative abundance of the recently described chicken pathogen Gallibacterium anatis (Narasinakuppe Krishnegowda et al., 2020) in most birds (with four birds showing >5% reads assigned to this organism), despite their healthy status. Similarly, Fusobacterium mortiferum—an opportunistic pathogen of humans (Almohaya et al., 2020)—accounted for >10% of sequences in 11 birds, corroborating a recent report of high abundance of 16S rRNA gene sequences from this organism obtained from the chicken caecum (Kollarcikova et al., 2019).

Bracken assigned sequences to over a hundred bacteriophage genomes, predominately phages infecting members of the Enterobacteriaceae assigned to the families Myoviridae and Podoviridae. Particularly noteworthy was the high abundance of reads in some samples from two distinct bacteriophages that prey on E. coli: phiEcoM-GJ1—a lytic bacteriophage isolated in Canada from pig sewage (Jamalludeen et al., 2008)—which accounted for 6.5% reads in a single sample and phAPEC8—a lytic bacteriophage with a large 147 kb genome, isolated from a Belgian poultry farm—which accounted for 10% of reads in a single sample and for >1% of reads in three others (Tsonos et al., 2012).

Although these k-mer-based analyses can provide interesting insights into taxonomic diversity within the chicken gut, we quickly realised that they provide an incomplete and misleading picture of this important microbiome for several reasons: (1) they often report the presence of highly implausible organisms—for example, Kraken 2 reported the presence of human pathogens such as Shigella flexneri and Plasmodium falciparum that are simply not credible in this context on clinical grounds; (2) as with studies on 16S rRNA gene sequences, they fail to provide genomic data or insights into the functional diversity or population structure of the microbial species that they identify and; (3) they rely on a reference database and so can only report previously known organisms and can never uncover ‘unknown unknowns’.

The scale of the problem of unknown diversity is clear from the observation that nearly three quarters (73%) of sequence reads from our chicken samples cannot be confidently classified by Kraken 2 to species level and more than half of the reads (52%) cannot be classified at all and are simply designated as ‘Unassigned’. We therefore sought to extend our understanding of this community through two powerful reference-free approaches: assembly-based metagenome analyses and high-throughput culture.

Metagenomic assembly uncovers a wealth of viral diversity

Assembly of metagenomic sequences is a reference-free approach that involves aligning and merging short sequence reads into long contiguous sequences (contigs) contigs.

To confirm the presence of bacteriophages inferred through the reference-based analysis and to identify novel viral genomes, we assembled sequence reads from our fifty chicken faecal samples into contigs. Contigs ≥10 kb were analysed with VirSorter—a programme designed to detect viral signals in microbial sequence data to find novel viruses (Roux et al., 2015).

VirSorter identified 184 of our chicken faecal contigs as Category 1 (‘most confident’) bacteriophage sequences and identified an additional 1,840 contigs as Category 2 (‘likely’) bacteriophage sequences. This was de-replicated to 1,455 genomes using similarity thresholds of 95% ANI over 70% of the genome (Table S5). BLASTN analysis revealed only 10 of these bacteriophage genomes showed high similarity (percentage identity > 70%; query covering > 50%) to known phages at the nucleotide level (Table S6). These included close relatives of the two phages (phiEcoM-GJ1 and phAPEC8) found highly abundant in the Bracken analyses (Fig. 2). Interestingly, more than one genus of coliphage (e.g. Jilinvirus, Phapecoctavirus, or Gamaleyavirus) was often detected in the same sample, along with an abundance of reads from their predicted prey (Escherichia) suggesting interesting dynamics in phage-host and phage-phage interactions (Fig. 3; Table S7).

Synteny plots comparing four novel coliphage genomes recovered from chicken faecal metagenomes (in red) to closest reference genomes. The figure was generated using EasyFig.

Coverage of four coliphages and of putative host bacterial species. Only samples in which at least one genome had ≥1× coverage are shown (n = 29). All coverage values have been Log₁₀ transformed with blue depicting low abundance and red high abundance.

Of the remaining 1,445 unclassified bacteriophage genomes, nearly 600 encoded either an obvious terminase region or were circular and as such were suggested as being near-complete. Classification of these genomes revealed all genomes were predicted to belong to the order Caudovirales of tailed phages, with the majority belonging to the family Siphoviridae (n = 429), but we also found representatives from the Myoviridae (n = 87) and Podoviridae (n = 27), plus some bacteriophages unclassified at family level (n = 28) (Table S8).

Remarkable microbial genome diversity in the chicken gut

Next, we subjected our samples to computational binning—a process of grouping contigs on the basis of sequence composition and depth of coverage into discrete population bins representing metagenome-assembled genomes (MAGs). However, to carry out a definitive survey of bacterial and archaeal diversity in the chicken gut microbiome—in addition to analysing the fifty faecal samples mentioned and before we started the binning—we retrieved all publicly available chicken gut metagenomic datasets, to create an expansive dataset representing >630 samples, drawn from ten studies and twelve countries (Belgium, China, France, Germany, Italy, Malaysia, Netherlands, Poland, Spain, The Gambia, UK, USA) (Figs. S1A and S1B; Table S9).

Sequence assembly and binning on all these samples generated 5,595 MAGs that passed our quality threshold of ≥80% completion and ≤5% contamination (Fig. S1C). Of these 3,131 could be considered high-quality draft genomes, with >90% completion and <5% contamination, as judged by recently published criteria (Table S10) (Bowers et al., 2017). Genome sizes of the MAGs ranged from ~0.4 to 6.8 Mbp, while GC content ranged from 24% to 73%.

Then, we grouped the MAGs into metagenomic species (MGSs). Initially, this involved de-replicating MAGs at the widely accepted 95% average nucleotide identity (ANI) for defining bacterial and archaeal species and 99% ANI for defining bacterial and archaeal strains (Jain et al., 2018; Luo, Rodriguez-R & Konstantinidis, 2014). De-replication of MAGs at 95% ANI resulted in 846 clusters representing bacterial and archaeal species, while de-replication at 99% ANI resulted in 2182 clusters, representing strains. However, to improve recovery of MAGs, MGSs and associated gene sets, we used gene correlations to identify species-representative genes and then applied hierarchical clustering to co-occurring genes across the samples. This allowed us to identify additional genes from the core genome of a species, even when they show divergent nucleotide compositions (such as genes from genomic islands and plasmids) (Hildebrand et al., 2019). Similarly, using canopy clustering (Nielsen et al., 2014), we could identify commonly occurring species of low abundance. Using these approaches, we were able to identify an additional seven MGSs (Table S11). These MGS were prevalent at >1× coverage in 53% of all analysed samples spanning at least 4 different BioProjects.

Analysis of bacterial metagenomic species, primarily using the Genome Taxonomy Database (GTDB) taxonomy (Parks et al., 2020), confirmed and extended the taxonomic novelty uncovered by reference-based community profiling (Fig. 4), recovering species spanning nineteen of the bacterial phyla defined by GTDB (Table S12). These include Cyanobacteria (12 species; 32 strains); Deferribacterota (1 species; 1 strain) Synergistota (2 species; 5 strains) and the Verrucomicrobiota (7 species; 8 strains).

Phylum, generally as assigned by GTDB, is indicated by colour range. Data symbols in the outer layers have been used to describe further characteristics for each draft genomes. Triangles indicate sequence novelty and status of binomial designation within publicly available databases or published research with filled symbols indicating novel species assigned a binomial as part of this research, hollow symbol indicated a known species assigned a binomial as part of this research and no symbol indicated a known species with a well-formed binomial already assigned. Stars are used to indicate isolation source, with filled symbols indicating isolation of species in both culture and metagenomic assembly and hollow symbols indicating isolation in culture alone. Tree branches have been collapsed where duplicate species have been identified by different methodologies. The tree was reconstructed using PhyloPhlAn 3.0.58 against 400 marker genes before reconstruction using FastTree and RAxML of a MAFFT sequence alignment and visualised using the online iTOLv5.7 tool including provision of a heat map according to individual genome length.

Of the 853 de-replicated bacterial metagenomic species, 321 represented previously delineated species catalogued in publicly available databases (Table S13). Following direct comparison, a further 165 metagenomic species had been previously identified by Glendinning et al. (2020), with these sequences not currently available in public archives. However, only 158 of our metagenomic species possess validly published names based on Latin binomials.

We performed a search of PubMed with the species name and ‘chicken’, leaving aside the 33 species named by Glendinning et al. (2020). This suggested that our study provides the first-evidence-in-chickens for the majority (81/125) of these species (Table S14). Examples include: Jeotgalicoccus halophilus, first isolated from the traditional fermented seafood, Jeotgal (Yoon et al., 2003) and present in 197 chicken samples; Aliicoccus persicus, first isolated from a hypersaline lake (Amoozegar et al., 2014) and present in 241 chicken samples; and Bacteroides reticulotermitis, first isolated from the gut of a termite (Sakamoto & Ohkuma, 2013) and present in 39 chicken samples.

We found that 309 of our metagenomic species could be assigned a taxonomy only at the level of genus and so represent novel candidate species. A further 56 species could be assigned a taxonomy only at the level of family and, after AAI clustering at 60%, were assigned to 36 novel candidate genera. One candidate bacterial species could be assigned a taxonomy only at the level of order (Oscillospirales) and so represent a new family.

Three MAGs were assigned to the domain Archaea. One represents the species Methanobrevibacter woesei—which is already known to inhabit the chicken gut (Saengkerdsub et al., 2007)—while the other two represent novel species within the genera Methanocorpusculum and UBA71, which we have renamed Candidatus Methanospyradousia.

Linnaean binomials for hundreds of new candidate species

Linnaeus first proposed the assignment of Latin binomials to provide a universal nomenclature for biological species (Linnaeus, 1759). The International Code of Nomenclature of Prokaryotes (ICNP) sets the rules for naming prokaryotic species (Parker, Tindall & Garrity, 2019), but currently precludes the valid publication of names of uncultivated organisms, represented by MAGs or other sequences. Furthermore, high-throughput generation of MAGs and of sequence-based taxonomies for bacteria, such as the GTDB (Parks et al., 2020) is often assumed to preclude the detailed attention usually given to one-by-one construction of Linnaean binomials. As a result, most uncultured taxa, as well as many taxa defined on sequence-based criteria, have been assigned unstable, confusing and hard to-remember alphanumerical identifiers.

To provide a stable, clear and memorable nomenclature for novel and/or previously unnamed bacterial and archaeal species from the chicken gut, we exploited the provision within the ICNP for naming uncultivated taxa via Candidatus assignments, which, although provisional, provide the scientific community with well-formed Latin binomials (Oren, 2017; Oren et al., 2020). However, this prompted us into an unprecedented effort to create hundreds of new names for the purpose of this single research study—an effort that required us to devise a scalable combinatorial system for the creation of binomials. Here, we made extensive combinatorial use of several dozen Latin and Greek roots pertaining to poultry (avi-, galli-, pulli-, alektryo, ptero, kotto-, ornitho-), intestines (intestini- entero-), faeces (faec-, kakke, merd-, kopro-, excrement-) or microbial life (-monas, -bacterium, -microbium, -coccus, -bacillus, -bium, -cola)—twinned with addition of these roots (singly or in tandem) and/or prefixes (allo, hetero, meta-, para-, crypto-) to existing genus names—to create over 150 Candidatus genus names. For genera with alphanumeric designations in GTDB Release 05-RS95 (Parks et al., 2020) known to occur also in gut microbiomes of other animals, we adopted a similar combinatorial approach, but avoided roots pertaining to poultry and stuck instead with combinations that simply meant ‘gut or faecal microbe’, for example Fimicola, Caccocola. An additional source of diversity stemmed from repetitive use of around forty Candidatus species epithets built from similar roots, which when combined with genus names gave us a total of over 650 distinctive binomials for new Candidatus species (Table 1; Table S15).

Table 1. Protologues for new Candidatus taxa identified from metagenomic analysis of chicken gut samples.

Description of Candidatus Acetatifactor stercoripullorum sp. nov.

Candidatus Acetatifactor stercoripullorum (ster.co.ri.pul.lo’rum. L. neut. n. stercus dung; L. masc. n. pullus a young chicken; N.L. gen. n. stercoripullorum of the faceces of young chickens)

Description of Candidatus Acinetobacter avistercoris sp. nov.

Candidatus Acinetobacter avistercoris (a.vi.ster’co.ris. L. fem. n. avis bird; L. neut. n. stercus dung; N.L. gen. n. avistercoris of bird faeces)

Description of Candidatus Acutalibacter ornithocaccae sp. nov.

Candidatus Acutalibacter ornithocaccae (or.ni.tho.cac’cae. Gr. masc. or fem. n. ornis, ornithos bird; Gr. fem. n. kakke faeces; N.L. gen. n. ornithocaccae of bird faeces)

Description of Candidatus Acutalibacter pullicola sp. nov.

Candidatus Acutalibacter pullicola (pul.li’co.la. L. masc. n. pullus a young chicken; L. suff. -cola inhabitant of; N.L. n. pullicola an inhabitant of young chickens)

Description of Candidatus Acutalibacter pullistercoris sp. nov.

Candidatus Acutalibacter pullistercoris (pul.li.ster’co.ris. L. masc. n. pullus a young chicken; L. neut. n. stercus dung; N.L. gen. n. pullistercoris of young chicken faeces)

Description of Candidatus Acutalibacter stercoravium sp. nov.

Candidatus Acutalibacter stercoravium (ster.cor.a’vi.um. L. neut. n. stercus dung; L. fem. n. avis bird; N.L. gen. n. stercoravium of bird faeces)

Description of Candidatus Acutalibacter stercorigallinarum sp. nov.

Candidatus Acutalibacter stercorigallinarum (ster.co.ri.gal.li.na’rum. L. neut. n. stercus dung; L. fem. n. gallina hen; N.L. gen. n. stercorigallinarum of hen faeces)

Description of Candidatus Agathobaculum intestinigallinarum sp. nov.

Candidatus Agathobaculum intestinigallinarum (in.tes.ti.ni.gal.li.na’rum. L. neut. n. intestinum gut; L. fem. n. gallina hen; N.L. gen. n. intestinigallinarum of the gut of the hens)

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Description of Candidatus Agathobaculum intestinipullorum sp. nov.

Candidatus Agathobaculum intestinipullorum (in.tes.ti.ni.pul.lo’rum. L. neut. n. intestinum gut; L. masc. n. pullus a young chicken; N.L. gen. n. intestinipullorum of the gut of young chickens)

Description of Candidatus Agathobaculum merdavium sp. nov.

Candidatus Agathobaculum merdavium (merd.a’vi.um. L. fem. n. merda faeces; L. fem. n. avis bird; N.L. gen. n. merdavium of bird faeces)

Description of Candidatus Agathobaculum merdigallinarum sp. nov.

Candidatus Agathobaculum merdigallinarum (mer.di.gal.li.na’rum. L. fem. n. merda faeces; L. fem. n. gallina hen; N.L. gen. n. merdigallinarum of hen faeces)

Description of Candidatus Agathobaculum merdipullorum sp. nov.

Candidatus Agathobaculum merdipullorum (mer.di.pul.lo’rum. L. fem. n. merda faeces; L. masc. n. pullus a young chicken; N.L. gen. n. merdipullorum of the faeces of young chickens)

Description of Candidatus Agathobaculum pullicola sp. nov.

Candidatus Agathobaculum pullicola (pul.li’co.la. L. masc. n. pullus a young chicken; L. suff. -cola inhabitant of; N.L. n. pullicola an inhabitant of young chickens)

Description of Candidatus Agathobaculum pullistercoris sp. nov.

Candidatus Agathobaculum pullistercoris (pul.li.ster’co.ris. L. masc. n. pullus a young chicken; L. neut. n. stercus dung; N.L. gen. n. pullistercoris of young chicken faeces)

Description of Candidatus Agathobaculum stercoravium sp. nov.

Candidatus Agathobaculum stercoravium (ster.cor.a’vi.um. L. neut. n. stercus dung; L. fem. n. avis bird; N.L. gen. n. stercoravium of bird faeces)

Description of Candidatus Agrococcus pullicola sp. nov.

Candidatus Agrococcus pullicola (pul.li’co.la. L. masc. n. pullus a young chicken; L. suff. -cola inhabitant of; N.L. n. pullicola an inhabitant of young chickens)

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Description of Candidatus Akkermansia intestinavium sp. nov.

Candidatus Akkermansia intestinavium (in.tes.tin.a’vi.um. L. neut. n. intestinum gut; L. fem. n. avis bird; N.L. gen. n. intestinavium of the gut of birds)

Description of Candidatus Akkermansia intestinigallinarum sp. nov.

Candidatus Akkermansia intestinigallinarum (in.tes.ti.ni.gal.li.na’rum. L. neut. n. intestinum gut; L. fem. n. gallina hen; N.L. gen. n. intestinigallinarum of the gut of the hens)

Description of Candidatus Alectryobacillus gen. nov.

Candidatus Alectryobacillus (A.lec.try.o.ba.cil’lus. Gr. neut. n. alektryon chicken; L. masc. n. bacillus a rod; N.L. masc. n. Alectryobacillus a bacillus found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Alectryobacillus merdavium. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order RFN20 and to the family CAG-826.

Description of Candidatus Alectryobacillus merdavium sp. nov.

Candidatus Alectryobacillus merdavium (merd.a’vi.um. L. fem. n. merda faeces; L. fem. n. avis bird; N.L. gen. n. merdavium of bird faeces)

Description of Candidatus Alectryocaccobium gen. nov.

Candidatus Alectryocaccobium (A.lec.try.o.cac.co’bi.um. Gr. neut. n. alektryon chicken; Gr. fem. n. kakke faeces; Gr. masc. n. bios life; N.L. neut. n. Alectryocaccobium A life form found in chicken faceces)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Alectryocaccobium stercorigallinarum. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Lachnospirales and to the family Lachnospiraceae.

Description of Candidatus Alectryocaccobium stercorigallinarum sp. nov.

Candidatus Alectryocaccobium stercorigallinarum (ster.co.ri.gal.li.na’rum. L. neut. n. stercus dung; L. fem. n. gallina hen; N.L. gen. n. stercorigallinarum of hen faeces)

Description of Candidatus Alectryocaccomicrobium gen. nov.

Candidatus Alectryocaccomicrobium (A.lec.try.o.cac.co.mi.cro’bi.um. Gr. neut. n. alektryon chicken; Gr. fem. n. kakke faeces; N.L. neut. n. microbium a microbe; N.L. neut. n. Alectryocaccomicrobium A microbe found in chicken faceces)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Alectryocaccomicrobium excrementavium. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Christensenellales and to the family CAG-74.

Description of Candidatus Alectryocaccomicrobium excrementavium sp. nov.

Candidatus Alectryocaccomicrobium excrementavium (ex.cre.ment.a’vi.um. L. neut. n. excrementum excrement; L. fem. n. avis bird; N.L. gen. n. excrementavium of bird excrement)

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Description of Candidatus Alistipes avicola sp. nov.

Candidatus Alistipes avicola (a.vi’co.la. L. fem. n. avis bird; L. suff. -cola inhabitant of; N.L. n. avicola inhabitant of birds)

Description of Candidatus Alistipes avistercoris sp. nov.

Candidatus Alistipes avistercoris (a.vi.ster’co.ris. L. fem. n. avis bird; L. neut. n. stercus dung; N.L. gen. n. avistercoris of bird faeces)

Description of Candidatus Alistipes cottocaccae sp. nov.

Candidatus Alistipes cottocaccae (cot.to.cac’cae. Gr. masc. n. kottos chicken Gr. fem. n. kakke faeces; N.L. gen. n. cottocaccae of chicken faeces)

Description of Candidatus Alistipes excrementavium sp. nov.

Candidatus Alistipes excrementavium (ex.cre.ment.a’vi.um. L. neut. n. excrementum excrement; L. fem. n. avis bird; N.L. gen. n. excrementavium of bird excrement)

Description of Candidatus Alistipes excrementigallinarum sp. nov.

Candidatus Alistipes excrementigallinarum (ex.cre.men.ti.gal.li.na’rum. L. neut. n. excrementum excrement; L. fem. n. gallina hen; N.L. gen. n. excrementigallinarum of hen excrement)

Description of Candidatus Alistipes excrementipullorum sp. nov.

Candidatus Alistipes excrementipullorum (ex.cre.men.ti.pul.lo’rum. L. neut. n. excrementum excrement; L. masc. n. pullus a young chicken; N.L. gen. n. excrementipullorum of young chicken excrement)

Description of Candidatus Alistipes faecavium sp. nov.

Candidatus Alistipes faecavium (faec.a’vi.um. L. fem. n. faex, faecis excrement; L. fem. n. avis bird; N.L. gen. n. faecavium of bird faeces)

Description of Candidatus Alistipes faecigallinarum sp. nov.

Candidatus Alistipes faecigallinarum (fae.ci.gal.li.na’rum. L. fem. n. faex, faecis excrement; L. fem. n. gallina hen; N.L. gen. n. faecigallinarum of chicken faeces)

Description of Candidatus Alistipes intestinigallinarum sp. nov.

Candidatus Alistipes intestinigallinarum (in.tes.ti.ni.gal.li.na’rum. L. neut. n. intestinum gut; L. fem. n. gallina hen; N.L. gen. n. intestinigallinarum of the gut of the hens)

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Description of Candidatus Alistipes intestinipullorum sp. nov.

Candidatus Alistipes intestinipullorum (in.tes.ti.ni.pul.lo’rum. L. neut. n. intestinum gut; L. masc. n. pullus a young chicken; N.L. gen. n. intestinipullorum of the gut of young chickens)

Description of Candidatus Alistipes merdavium sp. nov.

Candidatus Alistipes merdavium (merd.a’vi.um. L. fem. n. merda faeces; L. fem. n. avis bird; N.L. gen. n. merdavium of bird faeces)

Description of Candidatus Alistipes merdigallinarum sp. nov.

Candidatus Alistipes merdigallinarum (mer.di.gal.li.na’rum. L. fem. n. merda faeces; L. fem. n. gallina hen; N.L. gen. n. merdigallinarum of hen faeces)

A bacterial species identified by metagenomic analyses. This species includes all bacteria with genomes that show ≥95% average nucleotide identity (ANI) to the type genome, which has been assigned the MAG ID 2432 and which is available via NCBI BioSample SAMN15816893. Although GTDB has assigned this species to the genus it calls Alistipes_A, this genus designation cannot be incorporated into a well-formed binomial, so in naming this species, we have used the current validly published name for the genus. The GC content of the type genome is 49.96% and the genome length is 2.2 Mbp.

Description of Candidatus Alistipes merdipullorum sp. nov.

Candidatus Alistipes merdipullorum (mer.di.pul.lo’rum. L. fem. n. merda faeces; L. masc. n. pullus a young chicken; N.L. gen. n. merdipullorum of the faeces of young chickens)

Description of Candidatus Alistipes pullicola sp. nov.

Candidatus Alistipes pullicola (pul.li’co.la. L. masc. n. pullus a young chicken; L. suff. -cola inhabitant of; N.L. n. pullicola an inhabitant of young chickens)

A bacterial species identified by metagenomic analyses. This species includes all bacteria with genomes that show ≥95% average nucleotide identity (ANI) to the type genome, which has been assigned the MAG ID ChiHjej10B9-11434 and which is available via NCBI BioSample SAMN15816929. This is a new name for the alphanumeric GTDB species sp900546005. Although GTDB has assigned this species to the genus it calls Alistipes_A, this genus designation cannot be incorporated into a well-formed binomial, so in naming this species, we have used the current validly published name for the genus. The GC content of the type genome is 52.02% and the genome length is 1.9 Mbp.

Description of Candidatus Alistipes pullistercoris sp. nov.

Candidatus Alistipes pullistercoris (pul.li.ster’co.ris. L. masc. n. pullus a young chicken; L. neut. n. stercus dung; N.L. gen. n. pullistercoris of young chicken faeces)

A bacterial species identified by metagenomic analyses. This species includes all bacteria with genomes that show ≥95% average nucleotide identity (ANI) to the type genome, which has been assigned the MAG ID 3244 and which is available via NCBI BioSample SAMN15816930. This is a new name for the alphanumeric GTDB species sp900240235. Although GTDB has assigned this species to the genus it calls Alistipes_A, this genus designation cannot be incorporated into a well-formed binomial, so in naming this species, we have used the current validly published name for the genus. The GC content of the type genome is 56.88% and the genome length is 2.0 Mbp.

Description of Candidatus Alistipes stercoravium sp. nov.

Candidatus Alistipes stercoravium (ster.cor.a’vi.um. L. neut. n. stercus dung; L. fem. n. avis bird; N.L. gen. n. stercoravium of bird faeces)

Description of Candidatus Alistipes stercorigallinarum sp. nov.

Candidatus Alistipes stercorigallinarum (ster.co.ri.gal.li.na’rum. L. neut. n. stercus dung; L. fem. n. gallina hen; N.L. gen. n. stercorigallinarum of hen faeces)

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Description of Candidatus Alistipes stercoripullorum sp. nov.

Candidatus Alistipes stercoripullorum (ster.co.ri.pul.lo’rum. L. neut. n. stercus dung; L. masc. n. pullus a young chicken; N.L. gen. n. stercoripullorum of the faceces of young chickens)

Description of Candidatus Anaerobiospirillum merdipullorum sp. nov.

Candidatus Anaerobiospirillum merdipullorum (mer.di.pul.lo’rum. L. fem. n. merda faeces; L. masc. n. pullus a young chicken; N.L. gen. n. merdipullorum of the faeces of young chickens)

A bacterial species identified by metagenomic analyses. This species includes all bacteria with genomes that show ≥95% average nucleotide identity (ANI) to the type genome, which has been assigned the MAG ID 687 and which is available via NCBI BioSample SAMN15816911. Although GTDB has assigned this species to the genus it calls Anaerobiospirillum_A, this genus designation cannot be incorporated into a well-formed binomial, so in naming this species, we have used the current validly published name for the genus. The GC content of the type genome is 49.84% and the genome length is 2.0 Mbp.

Description of Candidatus Anaerobiospirillum pullicola sp. nov.

Candidatus Anaerobiospirillum pullicola (pul.li’co.la. L. masc. n. pullus a young chicken; L. suff. -cola inhabitant of; N.L. n. pullicola an inhabitant of young chickens)

Description of Candidatus Anaerobiospirillum pullistercoris sp. nov.

Candidatus Anaerobiospirillum pullistercoris (pul.li.ster’co.ris. L. masc. n. pullus a young chicken; L. neut. n. stercus dung; N.L. gen. n. pullistercoris of young chicken faeces)

Description of Candidatus Anaerobiospirillum stercoravium sp. nov.

Candidatus Anaerobiospirillum stercoravium (ster.cor.a’vi.um. L. neut. n. stercus dung; L. fem. n. avis bird; N.L. gen. n. stercoravium of bird faeces)

Description of Candidatus Anaerobutyricum avicola sp. nov.

Candidatus Anaerobutyricum avicola (a.vi’co.la. L. fem. n. avis bird; L. suff. -cola inhabitant of; N.L. n. avicola inhabitant of birds)

Description of Candidatus Anaerobutyricum faecale sp. nov.

Candidatus Anaerobutyricum faecale (fae.ca’le. L. neut. adj. faecale of faeces)

Description of Candidatus Anaerobutyricum stercoripullorum sp. nov.

Candidatus Anaerobutyricum stercoripullorum (ster.co.ri.pul.lo’rum. L. neut. n. stercus dung; L. masc. n. pullus a young chicken; N.L. gen. n. stercoripullorum of the faceces of young chickens)

Description of Candidatus Anaerobutyricum stercoris sp. nov.

Candidatus Anaerobutyricum stercoris (ster’co.ris. L. gen. n. stercoris of dung, excrement)

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Description of Candidatus Anaerofilum excrementigallinarum sp. nov.

Candidatus Anaerofilum excrementigallinarum (ex.cre.men.ti.gal.li.na’rum. L. neut. n. excrementum excrement; L. fem. n. gallina hen; N.L. gen. n. excrementigallinarum of hen excrement)

Description of Candidatus Anaerofilum faecale sp. nov.

Candidatus Anaerofilum faecale (fae.ca’le. L. neut. adj. faecale of faeces)

Description of Candidatus Anaeromassilibacillus stercoravium sp. nov.

Candidatus Anaeromassilibacillus stercoravium (ster.cor.a’vi.um. L. neut. n. stercus dung; L. fem. n. avis bird; N.L. gen. n. stercoravium of bird faeces)

Description of Candidatus Anaerostipes avicola sp. nov.

Candidatus Anaerostipes avicola (a.vi’co.la. L. fem. n. avis bird; L. suff. -cola inhabitant of; N.L. n. avicola inhabitant of birds)

Description of Candidatus Anaerostipes avistercoris sp. nov.

Candidatus Anaerostipes avistercoris (a.vi.ster’co.ris. L. fem. n. avis bird; L. neut. n. stercus dung; N.L. gen. n. avistercoris of bird faeces)

Description of Candidatus Anaerostipes excrementavium sp. nov.

Candidatus Anaerostipes excrementavium (ex.cre.ment.a’vi.um. L. neut. n. excrementum excrement; L. fem. n. avis bird; N.L. gen. n. excrementavium of bird excrement)

Description of Candidatus Anaerotignum merdipullorum sp. nov.

Candidatus Anaerotignum merdipullorum (mer.di.pul.lo’rum. L. fem. n. merda faeces; L. masc. n. pullus a young chicken; N.L. gen. n. merdipullorum of the faeces of young chickens)

Description of Candidatus Anaerotruncus excrementipullorum sp. nov.

Candidatus Anaerotruncus excrementipullorum (ex.cre.men.ti.pul.lo’rum. L. neut. n. excrementum excrement; L. masc. n. pullus a young chicken; N.L. gen. n. excrementipullorum of young chicken excrement)

Description of Candidatus Aphodenecus gen. nov.

Candidatus Aphodenecus (Aph.od.en.e’cus. Gr. fem. n. aphodos dung; Gr. masc. enoikos inhabitant; N.L. masc. n. Aphodenecus a microbe associated with faeces)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Aphodenecus pullistercoris. This is a name for the alphanumeric GTDB genus Spiro-01. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Sphaerochaetales and to the family Sphaerochaetaceae.

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Description of Candidatus Aphodenecus pullistercoris sp. nov.

Candidatus Aphodenecus pullistercoris (pul.li.ster’co.ris. L. masc. n. pullus a young chicken; L. neut. n. stercus dung; N.L. gen. n. pullistercoris of young chicken faeces)

Description of Candidatus Aphodocola gen. nov.

Candidatus Aphodocola (Aph.o.do’co.la. Gr. fem. n. aphodos dung; L. suff. -cola inhabitant of; N.L. fem. n. Aphodocola a microbe associated with faeces)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Aphodocola excrementigallinarum. This is a name for the alphanumeric GTDB genus CAG-594. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order RF39 and to the family CAG-433.

Description of Candidatus Aphodocola excrementigallinarum sp. nov.

Candidatus Aphodocola excrementigallinarum (ex.cre.men.ti.gal.li.na’rum. L. neut. n. excrementum excrement; L. fem. n. gallina hen; N.L. gen. n. excrementigallinarum of hen excrement)

Description of Candidatus Aphodomonas gen. nov.

Candidatus Aphodomonas (Aph.o.do.mo’nas. Gr. fem. n. aphodos dung; L. fem. n. monas a monad; N.L. fem. n. Aphodomonas a microbe associated with faeces)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Aphodomonas merdavium. This is a name for the alphanumeric GTDB genus SFFS01. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Christensenellales and to the family CAG-74.

Description of Candidatus Aphodomonas merdavium sp. nov.

Candidatus Aphodomonas merdavium (merd.a’vi.um. L. fem. n. merda faeces; L. fem. n. avis bird; N.L. gen. n. merdavium of bird faeces)

Description of Candidatus Aphodomorpha gen. nov.

Candidatus Aphodomorpha (Aph.o.do.mor’pha. Gr. fem. n. aphodos dung; Gr. fem. n. morphe a form, shape; N.L. fem. n. Aphodomorpha a microbe associated with faeces)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Aphodomorpha intestinavium. This is a name for the alphanumeric GTDB genus UMGS1241. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Christensenellales and to the family CAG-138.

Description of Candidatus Aphodomorpha intestinavium sp. nov.

Candidatus Aphodomorpha intestinavium (in.tes.tin.a’vi.um. L. neut. n. intestinum gut; L. fem. n. avis bird; N.L. gen. n. intestinavium of the gut of birds)

Description of Candidatus Aphodoplasma gen. nov.

Candidatus Aphodoplasma (Aph.o.do.plas’ma. Gr. fem. n. aphodos dung; Gr. neut. n. plasma a form; N.L. neut. n. Aphodoplasma a microbe associated with faeces)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Aphodoplasma excrementigallinarum. This is a name for the alphanumeric GTDB genus UMGS1253. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Monoglobales_A and to the family UMGS1253.

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Description of Candidatus Aphodoplasma excrementigallinarum sp. nov.

Candidatus Aphodoplasma excrementigallinarum (ex.cre.men.ti.gal.li.na’rum. L. neut. n. excrementum excrement; L. fem. n. gallina hen; N.L. gen. n. excrementigallinarum of hen excrement)

Description of Candidatus Aphodosoma gen. nov.

Candidatus Aphodosoma (Aph.o.do.so’ma. Gr. fem. n. aphodos dung; Gr. neut. n. soma a body; N.L. neut. n. Aphodosoma a microbe associated with faeces)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Aphodosoma intestinipullorum. This is a name for the alphanumeric GTDB genus SFVR01. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Bacteroidales and to the family Paludibacteraceae.

Description of Candidatus Aphodosoma intestinipullorum sp. nov.

Candidatus Aphodosoma intestinipullorum (in.tes.ti.ni.pul.lo’rum. L. neut. n. intestinum gut; L. masc. n. pullus a young chicken; N.L. gen. n. intestinipullorum of the gut of young chickens)

Description of Candidatus Aphodousia gen. nov.

Candidatus Aphodousia (Aph.od.ou’si.a. Gr. fem. n. aphodos dung; Gr. fem. n. ousia an essence; N.L. fem. n. Aphodousia a microbe associated with faeces)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Aphodousia faecavium. This is a name for the alphanumeric GTDB genus CAG-521. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Burkholderiales and to the family Burkholderiaceae.

Description of Candidatus Aphodousia faecalis sp. nov.

Candidatus Aphodousia faecalis (fae.ca’lis. L. fem. adj. faecalis of faeces)

Description of Candidatus Aphodousia faecavium sp. nov.

Candidatus Aphodousia faecavium (faec.a’vi.um. L. fem. n. faex, faecis excrement; L. fem. n. avis bird; N.L. gen. n. faecavium of bird faeces)

Description of Candidatus Aphodousia faecigallinarum sp. nov.

Candidatus Aphodousia faecigallinarum (fae.ci.gal.li.na’rum. L. fem. n. faex, faecis excrement; L. fem. n. gallina hen; N.L. gen. n. faecigallinarum of hen faeces)

Description of Candidatus Aphodousia faecipullorum sp. nov.

Candidatus Aphodousia faecipullorum (fae.ci.pul.lo’rum. L. fem. n. faex, faecis excrement; L. masc. n. pullus a young chicken; N.L. gen. n. faecipullorum of young chicken faeces)

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Description of Candidatus Aphodousia gallistercoris sp. nov.

Candidatus Aphodousia gallistercoris (gal.li.ster’co.ris. L. masc. n gallus chicken; L. neut. n. stercus dung; N.L. gen. n. gallistercoris of chicken faeces)

Description of Candidatus Aphodovivens gen. nov.

Candidatus Aphodovivens (Aph.o.do.vi’vens. Gr. fem. n. aphodos dung; N.L. pres. part. vivens living; N.L. fem. n. Aphodovivens a microbe associated with faeces)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Aphodovivens avicola. This is a name for the alphanumeric GTDB genus UMGS1293. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Coriobacteriales and to the family Eggerthellaceae.

Description of Candidatus Aphodovivens avicola sp. nov.

Candidatus Aphodovivens avicola (a.vi’co.la. L. fem. n. avis bird; L. suff. -cola inhabitant of; N.L. n. avicola inhabitant of birds)

Description of Candidatus Aphodovivens avistercoris sp. nov.

Candidatus Aphodovivens avistercoris (a.vi.ster’co.ris. L. fem. n. avis bird; L. neut. n. stercus dung; N.L. gen. n. avistercoris of bird faeces)

Description of Candidatus Aphodovivens excrementavium sp. nov.

Candidatus Aphodovivens excrementavium (ex.cre.ment.a’vi.um. L. neut. n. excrementum excrement; L. fem. n. avis bird; N.L. gen. n. excrementavium of bird excrement)

Description of Candidatus Aquabacterium excrementipullorum sp. nov.

Candidatus Aquabacterium excrementipullorum (ex.cre.men.ti.pul.lo’rum. L. neut. n. excrementum excrement; L. masc. n. pullus a young chicken; N.L. gen. n. excrementipullorum of young chicken excrement)

Description of Candidatus Atopostipes pullistercoris sp. nov.

Candidatus Atopostipes pullistercoris (pul.li.ster’co.ris. L. masc. n. pullus a young chicken; L. neut. n. stercus dung; N.L. gen. n. pullistercoris of young chicken faeces)

Description of Candidatus Avacholeplasma gen. nov.

Candidatus Avacholeplasma (Av.a.cho.le.plas’ma. L. fem. n. avis bird; N.L. neut. n. Acholeplasma a genus name; N.L. neut n. Avacholeplasma a genus related to the genus Acholeplasma but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avacholeplasma faecigallinarum. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Acholeplasmatales and to the family Anaeroplasmataceae.

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Description of Candidatus Avacholeplasma faecigallinarum sp. nov.

Candidatus Avacholeplasma faecigallinarum (fae.ci.gal.li.na’rum. L. fem. n. faex, faecis excrement; L. fem. n. gallina hen; N.L. gen. n. faecigallinarum of hen faeces)

Description of Candidatus Avacidaminococcus gen. nov.

Candidatus Avacidaminococcus (Av.a.cid.a.mi.no.coc’cus. L. fem. n. avis bird; N.L. masc. n. Acidaminococcus a genus name; N.L. masc. n. Avacidaminococcus a genus related to the genus Acidaminococcus but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avacidaminococcus intestinavium. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Acidaminococcales and to the family Acidaminococcaceae.

Description of Candidatus Avacidaminococcus intestinavium sp. nov.

Candidatus Avacidaminococcus intestinavium (in.tes.tin.a’vi.um. L. neut. n. intestinum gut; L. fem. n. avis bird; N.L. gen. n. intestinavium of the gut of birds)

Description of Candidatus Avamphibacillus gen. nov.

Candidatus Avamphibacillus (Av.am.phi.ba.cil’lus. L. fem. n. avis bird; N.L. masc. n. Amphibacillus a genus name; N.L. masc. n. Avamphibacillus a genus related to the genus Amphibacillus but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avamphibacillus intestinigallinarum. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Bacillales and to the family Amphibacillaceae.

Description of Candidatus Avamphibacillus intestinigallinarum sp. nov.

Candidatus Avamphibacillus intestinigallinarum (in.tes.ti.ni.gal.li.na’rum. L. neut. n. intestinum gut; L. fem. n. gallina hen; N.L. gen. n. intestinigallinarum of the gut of the hens)

Description of Candidatus Avanaerovorax gen. nov.

Candidatus Avanaerovorax (Av.an.a.e.ro.vo’rax. L. fem. n. avis bird; N.L. masc. n. Anaerovorax a genus name; N.L. masc. n. Avanaerovorax a genus related to the genus Anaerovorax but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avanaerovorax faecigallinarum. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Peptostreptococcales and to the family Anaerovoracaceae.

Description of Candidatus Avanaerovorax faecigallinarum sp. nov.

Candidatus Avanaerovorax faecigallinarum (fae.ci.gal.li.na’rum. L. fem. n. faex, faecis excrement; L. fem. n. gallina hen; N.L. gen. n. faecigallinarum of hen faeces)

Description of Candidatus Aveggerthella gen. nov.

Candidatus Aveggerthella (Av.eg.ger.thel’la. L. fem. n. avis bird; N.L. fem. n. Eggerthella a genus name; N.L. fem. n. Aveggerthella a genus related to the genus Eggerthella but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avieggerthella excrementigallinarum. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Coriobacteriales and to the family Eggerthellaceae.

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Description of Candidatus Aveggerthella excrementigallinarum sp. nov.

Candidatus Aveggerthella excrementigallinarum (ex.cre.men.ti.gal.li.na’rum. L. neut. n. excrementum excrement; L. fem. n. gallina hen; N.L. gen. n. excrementigallinarum of hen excrement)

Description of Candidatus Aveggerthella stercoripullorum sp. nov.

Candidatus Aveggerthella stercoripullorum (ster.co.ri.pul.lo’rum. L. neut. n. stercus dung; L. masc. n. pullus a young chicken; N.L. gen. n. stercoripullorum of the faceces of young chickens)

Description of Candidatus Avelusimicrobium gen. nov.

Candidatus Avelusimicrobium (Av.e.lu.si.mi.cro’bi.um. L. fem. n. avis bird; N.L. neut. n. Elusimicrobium a genus name; N.L. neut. n. Avelusimicrobium a genus related to the genus Elusimicrobium but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avielusimicrobium excrementipullorum. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Elusimicrobiales and to the family Elusimicrobiaceae.

Description of Candidatus Avelusimicrobium excrementipullorum sp. nov.

Candidatus Avelusimicrobium excrementipullorum (ex.cre.men.ti.pul.lo’rum. L. neut. n. excrementum excrement; L. masc. n. pullus a young chicken; N.L. gen. n. excrementipullorum of young chicken excrement)

Description of Candidatus Avibacteroides gen. nov.

Candidatus Avibacteroides (A.vi.bac.te.ro’i.des. L. fem. n. avis bird; N.L. masc. n. Bacteroides a genus name; N.L. masc. n. Avibacteroides a genus related to the genus Bacteroides but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avibacteroides excrementipullorum. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Bacteroidales and to the family Bacteroidaceae.

Description of Candidatus Avibacteroides avistercoris sp. nov.

Candidatus Avibacteroides avistercoris (a.vi.ster’co.ris. L. fem. n. avis bird; L. neut. n. stercus dung; N.L. gen. n. avistercoris of bird faeces)

Description of Candidatus Avibacteroides excrementipullorum sp. nov.

Candidatus Avibacteroides excrementipullorum (ex.cre.men.ti.pul.lo’rum. L. neut. n. excrementum excrement; L. masc. n. pullus a young chicken; N.L. gen. n. excrementipullorum of young chicken excrement)

Description of Candidatus Avibacteroides faecavium sp. nov.

Candidatus Avibacteroides faecavium (faec.a’vi.um. L. fem. n. faex, faecis excrement; L. fem. n. avis bird; N.L. gen. n. faecavium of bird faeces)

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Description of Candidatus Avichristensenella gen. nov.

Candidatus Avichristensenella (A.vi.chris.ten.sen.el’la. L. fem. n. avis bird; N.L. fem. n. Christensenella a genus name; N.L. fem. n. Avichristensenella a genus related to the genus Christensenella but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avichristensenella intestinipullorum. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Christensenellales and to the family CAG-74.

Description of Candidatus Avichristensenella intestinipullorum sp. nov.

Candidatus Avichristensenella intestinipullorum (in.tes.ti.ni.pul.lo’rum. L. neut. n. intestinum gut; L. masc. n. pullus a young chicken; N.L. gen. n. intestinipullorum of the gut of young chickens)

Description of Candidatus Avidehalobacter gen. nov.

Candidatus Avidehalobacter (A.vi.de.ha.lo.bac’ter. L. fem. n. avis bird; N.L. masc. n. Dehalobacter a genus name; N.L. masc. n. Avidehalobacter a genus related to the genus Dehalobacter but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avidehalobacter gallistercoris. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order UBA4068 and to the family UBA5755.

Description of Candidatus Avidehalobacter gallistercoris sp. nov.

Candidatus Avidehalobacter gallistercoris (gal.li.ster’co.ris. L. masc. n gallus chicken; L. neut. n. stercus dung; N.L. gen. n. gallistercoris of chicken faeces)

Description of Candidatus Avidesulfovibrio gen. nov.

Candidatus Avidesulfovibrio (A.vi.de.sul.fo.vi’bri.o. L. fem. n. avis bird; N.L. masc. n. Desulfovibrio a genus name; N.L. masc. n. Avidesulfovibrio a genus related to the genus Desulfovibrio but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avidesulfovibrio excrementigallinarum. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Desulfovibrionales and to the family Desulfovibrionaceae.

Description of Candidatus Avidesulfovibrio excrementigallinarum sp. nov.

Candidatus Avidesulfovibrio excrementigallinarum (ex.cre.men.ti.gal.li.na’rum. L. neut. n. excrementum excrement; L. fem. n. gallina hen; N.L. gen. n. excrementigallinarum of hen excrement)

Description of Candidatus Avigastranaerophilus gen. nov.

Candidatus Avigastranaerophilus (A.vi.gastr.an.a.e.ro’phi.lus. L. fem. n. avis bird; N.L. masc. n. Gastranaerophilus a genus name; N.L. masc. n. Avigastranaerophilus a genus related to the genus Gastranaerophilus but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avigastranaerophilus faecigallinarum. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Gastranaerophilales and to the family Gastranaerophilaceae.

Description of Candidatus Avigastranaerophilus faecigallinarum sp. nov.

Candidatus Avigastranaerophilus faecigallinarum (fae.ci.gal.li.na’rum. L. fem. n. faex, faecis excrement; L. fem. n. gallina hen; N.L. gen. n. faecigallinarum of hen faeces)

Description of Candidatus Avilachnospira gen. nov.

Candidatus Avilachnospira (A.vi.lach.no.spi’ra. L. fem. n. avis bird; N.L. fem. n. Lachnospira a genus name; N.L. fem. n. Avilachnospira a genus related to the genus Lachnospira but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avilachnospira avistercoris. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Lachnospirales and to the family Lachnospiraceae.

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Description of Candidatus Avilachnospira avicola sp. nov.

Candidatus Avilachnospira avicola (a.vi’co.la. L. fem. n. avis bird; L. suff. -cola inhabitant of; N.L. n. avicola inhabitant of birds)

Description of Candidatus Avilachnospira avistercoris sp. nov.

Candidatus Avilachnospira avistercoris (a.vi.ster’co.ris. L. fem. n. avis bird; L. neut. n. stercus dung; N.L. gen. n. avistercoris of bird faeces)

Description of Candidatus Avimonoglobus gen. nov.

Candidatus Avimonoglobus (A.vi.mo.no.glo’bus. L. fem. n. avis bird; N.L. masc. n. Monoglobus a genus name; N.L. masc. n. Avimonoglobus a genus related to the genus Monoglobus but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avimonoglobus intestinipullorum. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Monoglobales_A and to the family UBA1381.

Description of Candidatus Avimonoglobus intestinipullorum sp. nov.

Candidatus Avimonoglobus intestinipullorum (in.tes.ti.ni.pul.lo’rum. L. neut. n. intestinum gut; L. masc. n. pullus a young chicken; N.L. gen. n. intestinipullorum of the gut of young chickens)

Description of Candidatus Avimuribaculum gen. nov.

Candidatus Avimuribaculum (A.vi.mu.ri.ba’cu.lum. L. fem. n. avis bird; N.L. neut. n. Muribaculum a genus name; N.L. neut. n. Avimuribaculum a genus related to the genus Muribaculum but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avimuribaculum pullicola. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Bacteroidales and to the family Muribaculaceae.

Description of Candidatus Avimuribaculum pullicola sp. nov.

Candidatus Avimuribaculum pullicola (pul.li’co.la. L. masc. n. pullus a young chicken; L. suff. -cola inhabitant of; N.L. n. pullicola an inhabitant of young chickens)

Description of Candidatus Avipropionibacterium gen. nov.

Candidatus Avipropionibacterium (A.vi.pro.pi.o.ni.bac.te’ri.um. L. fem. n. avis bird; N.L. neut. n. Propionibacterium a genus name; N.L. neut. n. Avipropionibacterium a genus related to the genus Propionibacterium but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avipropionibacterium avicola. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Propionibacteriales and to the family Propionibacteriaceae.

Description of Candidatus Avipropionibacterium avicola sp. nov.

Candidatus Avipropionibacterium avicola (a.vi’co.la. L. fem. n. avis bird; L. suff. -cola inhabitant of; N.L. n. avicola inhabitant of birds)

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Description of Candidatus Avirikenella gen. nov.

Candidatus Avirikenella (A.vi.ri.ke.nel’la. L. fem. n. avis bird; N.L. fem. n. Rikenella a genus name; N.L. fem. n. Avirikenella a genus related to the genus Rikenella but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avirikenella pullistercoris. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Bacteroidales and to the family Rikenellaceae.

Description of Candidatus Avirikenella pullistercoris sp. nov.

Candidatus Avirikenella pullistercoris (pul.li.ster’co.ris. L. masc. n. pullus a young chicken; L. neut. n. stercus dung; N.L. gen. n. pullistercoris of young chicken faeces)

Description of Candidatus Avisuccinivibrio gen. nov.

Candidatus Avisuccinivibrio (A.vi.suc.ci.ni.vi’bri.o. L. fem. n. avis bird; N.L. masc. n. Succinivibrio a genus name; N.L. masc. n. Avisuccinivibrio a genus related to the genus Succinivibrio but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avisuccinivibrio stercorigallinarum. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Enterobacterales and to the family Succinivibrionaceae.

Description of Candidatus Avisuccinivibrio pullicola sp. nov.

Candidatus Avisuccinivibrio pullicola (pul.li’co.la. L. masc. n. pullus a young chicken; L. suff. -cola inhabitant of; N.L. n. pullicola an inhabitant of young chickens)

Description of Candidatus Avisuccinivibrio stercorigallinarum sp. nov.

Candidatus Avisuccinivibrio stercorigallinarum (ster.co.ri.gal.li.na’rum. L. neut. n. stercus dung; L. fem. n. gallina hen; N.L. gen. n. stercorigallinarum of hen faeces)

Description of Candidatus Avitreponema gen. nov.

Candidatus Avitreponema (A.vi.tre.po.ne’ma. L. fem. n. avis bird; N.L. neut. n. Treponema a genus name; N.L. neut. n. Avitreponema a genus related to the genus Treponema but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avitreponema avistercoris. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Treponematales and to the family Treponemataceae.

Description of Candidatus Avitreponema avistercoris sp. nov.

Candidatus Avitreponema avistercoris (a.vi.ster’co.ris. L. fem. n. avis bird; L. neut. n. stercus dung; N.L. gen. n. avistercoris of bird faeces)

Description of Candidatus Avoscillospira gen. nov.

Candidatus Avoscillospira (Av.os.cil.lo.spi’ra. L. fem. n. avis bird; N.L. fem. n. Oscillospira a genus name; N.L. fem. n. Avoscillospira a genus related to the genus Oscillospira but distinct from it and found in poultry)

A bacterial genus identified by metagenomic analyses. The genus includes all bacteria with genomes that show ≥60% average amino acid identity (AAI) to the type genome from the type species Candidatus Avioscillospira stercorigallinarum. This genus has been assigned by GTDB-Tk v1.3.0 working on GTDB Release 05-RS95 (Chaumeil et al., 2019; Parks et al., 2020) to the order Oscillospirales and to the family Oscillospiraceae.

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Description of Candidatus Avoscillospira avicola sp. nov.

Candidatus Avoscillospira avicola (a.vi’co.la. L. fem. n. avis bird; L. suff. -cola inhabitant of; N.L. n. avicola inhabitant of birds)

Description of Candidatus Avoscillospira avistercoris sp. nov.

Candidatus Avoscillospira avistercoris (a.vi.ster’co.ris. L. fem. n. avis bird; L. neut. n. stercus dung; N.L. gen. n. avistercoris of bird faeces)

Description of Candidatus Avoscillospira stercorigallinarum sp. nov.

Candidatus Avoscillospira stercorigallinarum (ster.co.ri.gal.li.na’rum. L. neut. n. stercus dung; L. fem. n. gallina hen; N.L. gen. n. stercorigallinarum of hen faeces)

Description of Candidatus Avoscillospira stercoripullorum sp. nov.

Candidatus Avoscillospira stercoripullorum (ster.co.ri.pul.lo’rum. L. neut. n. stercus dung; L. masc. n. pullus a young chicken; N.L. gen. n. stercoripullorum of the faceces of young chickens)

Description of Candidatus Bacteroides avicola sp. nov.

Candidatus Bacteroides avicola (a.vi’co.la. L. fem. n. avis bird; L. suff. -cola inhabitant of; N.L. n. avicola inhabitant of birds)

Description of Candidatus Bacteroides intestinavium sp. nov.

Candidatus Bacteroides intestinavium (in.tes.tin.a’vi.um. L. neut. n. intestinum gut; L. fem. n. avis bird; N.L. gen. n. intestinavium of the gut of birds)

Description of Candidatus Bacteroides intestinigallinarum sp. nov.

Candidatus Bacteroides intestinigallinarum (in.tes.ti.ni.gal.li.na’rum. L. neut. n. intestinum gut; L. fem. n. gallina hen; N.L. gen. n. intestinigallinarum of the gut of the hens)

Description of Candidatus Bacteroides intestinipullorum sp. nov.

Candidatus Bacteroides intestinipullorum (in.tes.ti.ni.pul.lo’rum. L. neut. n. intestinum gut; L. masc. n. pullus a young chicken; N.L. gen. n. intestinipullorum of the gut of young chickens)

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Description of Candidatus Bacteroides merdavium sp. nov.

Candidatus Bacteroides merdavium (merd.a’vi.um. L. fem. n. merda faeces; L. fem. n. avis bird; N.L. gen. n. merdavium of bird faeces)

Description of Candidatus Bacteroides merdigallinarum sp. nov.

Candidatus Bacteroides merdigallinarum (mer.di.gal.li.na’rum. L. fem. n. merda faeces; L. fem. n. gallina hen; N.L. gen. n. merdigallinarum of hen faeces)

Description of Candidatus Bacteroides merdipullorum sp. nov.

Candidatus Bacteroides merdipullorum (mer.di.pul.lo’rum. L. fem. n. merda faeces; L. masc. n. pullus a young chicken; N.L. gen. n. merdipullorum of the faeces of young chickens)

Description of Candidatus Bacteroides pullicola sp. nov.

Candidatus Bacteroides pullicola (pul.li’co.la. L. masc. n. pullus a young chicken; L. suff. -cola inhabitant of; N.L. n. pullicola an inhabitant of young chickens)

Description of Candidatus Bariatricus faecipullorum sp. nov.

Candidatus Bariatricus faecipullorum (fae.ci.pul.lo’rum. L. fem. n. faex, faecis excrement; L. masc. n. pullus a young chicken; N.L. gen. n. faecipullorum of young chicken faeces)

Description of Candidatus Barnesiella excrementavium sp. nov.

Candidatus Barnesiella excrementavium (ex.cre.ment.a’vi.um. L. neut. n. excrementum excrement; L. fem. n. avis bird; N.L. gen. n. excrementavium of bird excrement)

Description of Candidatus Barnesiella excrementigallinarum sp. nov.

Candidatus Barnesiella excrementigallinarum (ex.cre.men.ti.gal.li.na’rum. L. neut. n. excrementum excrement; L. fem. n. gallina hen; N.L. gen. n. excrementigallinarum of hen excrement)

Description of Candidatus Barnesiella excrementipullorum sp. nov.

Candidatus Barnesiella excrementipullorum (ex.cre.men.ti.pul.lo’rum. L. neut. n. excrementum excrement; L. masc. n. pullus a young chicken; N.L. gen. n. excrementipullorum of young chicken excrement)

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Description of Candidatus Barnesiella merdigallinarum sp. nov.

Candidatus Barnesiella merdigallinarum (mer.di.gal.li.na’rum. L. fem. n. merda faeces; L. fem. n. gallina hen; N.L. gen. n. merdigallinarum of hen faeces)

Description of Candidatus Barnesiella merdipullorum sp. nov.

Candidatus Barnesiella merdipullorum (mer.di.pul.lo’rum. L. fem. n. merda faeces; L. masc. n. pullus a young chicken; N.L. gen. n. merdipullorum of the faeces of young chickens)

Description of Candidatus Bilophila faecipullorum sp. nov.

Candidatus Bilophila faecipullorum (fae.ci.pul.lo’rum. L. fem. n. faex, faecis excrement; L. masc. n. pullus a young chicken; N.L. gen. n. faecipullorum of young chicken faeces)

Description of Candidatus Blautia avicola sp. nov.

Candidatus Blautia avicola (a.vi’co.la. L. fem. n. avis bird; L. suff. -cola inhabitant of; N.L. n. avicola inhabitant of birds)

Description of Candidatus Blautia avistercoris sp. nov.

Candidatus Blautia avistercoris (a.vi.ster’co.ris. L. fem. n. avis bird; L. neut. n. stercus dung; N.L. gen. n. avistercoris of bird faeces)

A bacterial species identified by metagenomic analyses. This species includes all bacteria with genomes that show ≥95% average nucleotide identity (ANI) to the type genome, which has been assigned the MAG ID 5548 and which is available via NCBI BioSample SAMN15816924. This is a new name for the alphanumeric GTDB species sp002159835. Although GTDB has assigned this species to the genus it calls Blautia_A, this genus designation cannot be incorporated into a well-formed binomial, so in naming this species, we have used the current validly published name for the genus. The GC content of the type genome is 45.38% and the genome length is 2.5 Mbp.

Description of Candidatus Blautia excrementigallinarum sp. nov.

Candidatus Blautia excrementigallinarum (ex.cre.men.ti.gal.li.na’rum. L. neut. n. excrementum excrement; L. fem. n. gallina hen; N.L. gen. n. excrementigallinarum of hen excrement)

A bacterial species identified by metagenomic analyses. This species includes all bacteria with genomes that show ≥95% average nucleotide identity (ANI) to the type genome, which has been assigned the MAG ID ChiSjej6B24-370 and which is available via NCBI BioSample SAMN15816894. Although GTDB has assigned this species to the genus it calls Blautia_A, this genus designation cannot be incorporated into a well-formed binomial, so in naming this species, we have used the current validly published name for the genus. The GC content of the type genome is 49.44% and the genome length is 2.3 Mbp.

Description of Candidatus Blautia excrementipullorum sp. nov.

Candidatus Blautia excrementipullorum (ex.cre.men.ti.pul.lo’rum. L. neut. n. excrementum excrement; L. masc. n. pullus a young chicken; N.L. gen. n. excrementipullorum of young chicken excrement)

A bacterial species identified by metagenomic analyses. This species includes all bacteria with genomes that show ≥95% average nucleotide identity (ANI) to the type genome, which has been assigned the MAG ID CHK197-7439 and which is available via NCBI BioSample SAMN15816885. Although GTDB has assigned this species to the genus it calls Blautia_A, this genus designation cannot be incorporated into a well-formed binomial, so in naming this species, we have used the current validly published name for the genus. The GC content of the type genome is 46.79% and the genome length is 3.3 Mbp.

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Description of Candidatus Blautia faecavium sp. nov.

Candidatus Blautia faecavium (faec.a’vi.um. L. fem. n. faex, faecis excrement; L. fem. n. avis bird; N.L. gen. n. faecavium of bird faeces)

A bacterial species identified by metagenomic analyses. This species includes all bacteria with genomes that show ≥95% average nucleotide identity (ANI) to the type genome, which has been assigned the MAG ID ChiSjej1B19-5720 and which is available via NCBI BioSample SAMN15816886. Although GTDB has assigned this species to the genus it calls Blautia_A, this genus designation cannot be incorporated into a well-formed binomial, so in naming this species, we have used the current validly published name for the genus. The GC content of the type genome is 45.35% and the genome length is 3.5 Mbp.

Description of Candidatus Blautia faecigallinarum sp. nov.

Candidatus Blautia faecigallinarum (fae.ci.gal.li.na’rum. L. fem. n. faex, faecis excrement; L. fem. n. gallina hen; N.L. gen. n. faecigallinarum of hen faeces)

A bacterial species identified by metagenomic analyses. This species includes all bacteria with genomes that show ≥95% average nucleotide identity (ANI) to the type genome, which has been assigned the MAG ID 14324 and which is available via NCBI BioSample SAMN15816901. Although GTDB has assigned this species to the genus it calls Blautia_A, this genus designation cannot be incorporated into a well-formed binomial, so in naming this species, we have used the current validly published name for the genus. The GC content of the type genome is 48.52% and the genome length is 2.9 Mbp.

Description of Candidatus Blautia faecipullorum sp. nov.

Candidatus Blautia faecipullorum (fae.ci.pul.lo’rum. L. fem. n. faex, faecis excrement; L. masc. n. pullus a young chicken; N.L. gen. n. faecipullorum of young chicken faeces)

A bacterial species identified by metagenomic analyses. This species includes all bacteria with genomes that show ≥95% average nucleotide identity (ANI) to the type genome, which has been assigned the MAG ID ChiSxjej6B18-2004 and which is available via NCBI BioSample SAMN15816906. Although GTDB has assigned this species to the genus it calls Blautia_A, this genus designation cannot be incorporated into a well-formed binomial, so in naming this species, we have used the current validly published name for the genus. The GC content of the type genome is 48.18% and the genome length is 3.5 Mbp.

Description of Candidatus Blautia gallistercoris sp. nov.

Candidatus Blautia gallistercoris (gal.li.ster’co.ris. L. masc. n gallus chicken; L. neut. n. stercus dung; N.L. gen. n. gallistercoris of chicken faeces)

A bacterial species identified by metagenomic analyses. This species includes all bacteria with genomes that show ≥95% average nucleotide identity (ANI) to the type genome, which has been assigned the MAG ID ChiSjej1B19-8411 and which is available via NCBI BioSample SAMN15816925. This is a new name for the alphanumeric GTDB species sp900542045. Although GTDB has assigned this species to the genus it calls Blautia_A, this genus designation cannot be incorporated into a well-formed binomial, so in naming this species, we have used the current validly published name for the genus. The GC content of the type genome is 48.96% and the genome length is 2.8 Mbp.

Description of Candidatus Blautia intestinavium sp. nov.

Candidatus Blautia intestinavium (in.tes.tin.a’vi.um. L. neut. n. intestinum gut; L. fem. n. avis bird; N.L. gen. n. intestinavium of the gut of birds)

A bacterial species identified by metagenomic analyses. This species includes all bacteria with genomes that show ≥95% average nucleotide identity (ANI) to the type genome, which has been assigned the MAG ID CHK186-553 and which is available via NCBI BioSample SAMN15816890. Although GTDB has assigned this species to the genus it calls Blautia_A, this genus designation cannot be incorporated into a well-formed binomial, so in naming this species, we have used the current validly published name for the genus. The GC content of the type genome is 47.27% and the genome length is 2.8 Mbp.

Description of Candidatus Blautia intestinigallinarum sp. nov.

Candidatus Blautia intestinigallinarum (in.tes.ti.ni.gal.li.na’rum. L. neut. n. intestinum gut; L. fem. n. gallina hen; N.L. gen. n. intestinigallinarum of the gut of the hens)

A bacterial species identified by metagenomic analyses. This species includes all bacteria with genomes that show ≥95% average nucleotide identity (ANI) to the type genome, which has been assigned the MAG ID CHK186-9876 and which is available via NCBI BioSample SAMN15816891. Although GTDB has assigned this species to the genus it calls Blautia_A, this genus designation cannot be incorporated into a well-formed binomial, so in naming this species, we have used the current validly published name for the genus. The GC content of the type genome is 46.77% and the genome length is 2.7 Mbp.

Description of Candidatus Blautia intestinipullorum sp. nov.

Candidatus Blautia intestinipullorum (in.tes.ti.ni.pul.lo’rum. L. neut. n. intestinum gut; L. masc. n. pullus a young chicken; N.L. gen. n. intestinipullorum of the gut of young chickens)

A bacterial species identified by metagenomic analyses. This species includes all bacteria with genomes that show ≥95% average nucleotide identity (ANI) to the type genome, which has been assigned the MAG ID ChiW16-4312 and which is available via NCBI BioSample SAMN15816892. Although GTDB has assigned this species to the genus it calls Blautia_A, this genus designation cannot be incorporated into a well-formed binomial, so in naming this species, we have used the current validly published name for the genus. The GC content of the type genome is 47.05% and the genome length is 2.4 Mbp.

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Description of Candidatus Blautia merdavium sp. nov.

Candidatus Blautia merdavium (merd.a’vi.um. L. fem. n. merda faeces; L. fem. n. avis bird; N.L. gen. n. merdavium of bird faeces)

Description of Candidatus Blautia merdigallinarum sp. nov.

Candidatus Blautia merdigallinarum (mer.di.gal.li.na’rum. L. fem. n. merda faeces; L. fem. n. gallina hen; N.L. gen. n. merdigallinarum of hen faeces)

Description of Candidatus Blautia merdipullorum sp. nov.

Candidatus Blautia merdipullorum (mer.di.pul.lo’rum. L. fem. n. merda faeces; L. masc. n. pullus a young chicken; N.L. gen. n. merdipullorum of the faeces of young chickens)

Description of Candidatus Blautia ornithocaccae sp. nov.

Candidatus Blautia ornithocaccae (or.ni.tho.cac’cae. Gr. masc. or fem. n. ornis, ornithos bird Gr. fem. n. kakke faeces; N.L. gen. n. ornithocaccae of bird faeces)

Description of Candidatus Blautia pullicola sp. nov.

Candidatus Blautia pullicola (pul.li’co.la. L. masc. n. pullus a young chicken; L. suff. -cola inhabitant of; N.L. n. pullicola an inhabitant of young chickens)

Description of Candidatus Blautia pullistercoris sp. nov.

Candidatus Blautia pullistercoris (pul.li.ster’co.ris. L. masc. n. pullus a young chicken; L. neut. n. stercus dung; N.L. gen. n. pullistercoris of young chicken faeces)

Description of Candidatus Blautia stercoravium sp. nov.

Candidatus Blautia stercoravium (ster.cor.a’vi.um. L. neut. n. stercus dung; L. fem. n. avis bird; N.L. gen. n. stercoravium of bird faeces)

Description of Candidatus Blautia stercorigallinarum sp. nov.

Candidatus Blautia stercorigallinarum (ster.co.ri.gal.li.na’rum. L. neut. n. stercus dung; L. fem. n. gallina hen; N.L. gen. n. stercorigallinarum of hen faeces)

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Description of Candidatus Blautia stercoripullorum sp. nov.

Candidatus Blautia stercoripullorum (ster.co.ri.pul.lo’rum. L. neut. n. stercus dung; L. masc. n. pullus a young chicken; N.L. gen. n. stercoripullorum of the faceces of young chickens)

Description of Candidatus Borkfalkia avicola sp. nov.

Candidatus Borkfalkia avicola (a.vi’co.la. L. fem. n. avis bird; L. suff. -cola inhabitant of; N.L. n. avicola inhabitant of birds)

Description of Candidatus Borkfalkia avistercoris sp. nov.

Candidatus Borkfalkia avistercoris (a.vi.ster’co.ris. L. fem. n. avis bird; L. neut. n. stercus dung; N.L. gen. n. avistercoris of bird faeces)

Description of Candidatus Borkfalkia excrementavium sp. nov.

Candidatus Borkfalkia excrementavium (ex.cre.ment.a’vi.um. L. neut. n. excrementum excrement; L. fem. n. avis bird; N.L. gen. n. excrementavium of bird excrement)

Description of Candidatus Borkfalkia excrementigallinarum sp. nov.

Candidatus Borkfalkia excrementigallinarum (ex.cre.men.ti.gal.li.na’rum. L. neut. n. excrementum excrement; L. fem. n. gallina hen; N.L. gen. n. excrementigallinarum of hen excrement)

Description of Candidatus Borkfalkia excrementipullorum sp. nov.

Candidatus Borkfalkia excrementipullorum (ex.cre.men.ti.pul.lo’rum. L. neut. n. excrementum excrement; L. masc. n. pullus a young chicken; N.L. gen. n. excrementipullorum of young chicken excrement)

Description of Candidatus Borkfalkia faecavium sp. nov.

Candidatus Borkfalkia faecavium (faec.a’vi.um. L. fem. n. faex, faecis excrement; L. fem. n. avis bird; N.L. gen. n. faecavium of bird faeces)

Description of Candidatus Borkfalkia faecigallinarum sp. nov.

Candidatus Borkfalkia faecigallinarum (fae.ci.gal.li.na’rum. L. fem. n. faex, faecis excrement; L. fem. n. gallina hen; N.L. gen. n. faecigallinarum of hen faeces)

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Description of Candidatus Borkfalkia faecipullorum sp. nov.

Candidatus Borkfalkia faecipullorum (fae.ci.pul.lo’rum. L. fem. n. faex, faecis excrement; L. masc. n. pullus a young chicken; N.L. gen. n. faecipullorum of young chicken faeces)

Description of Candidatus Borkfalkia stercoripullorum sp. nov.

Candidatus Borkfalkia stercoripullorum (ster.co.ri.pul.lo’rum. L. neut. n. stercus dung; L. masc. n. pullus a young chicken; N.L. gen. n. stercoripullorum of the faceces of young chickens)

Description of Candidatus Brachybacterium intestinipullorum sp. nov.

Candidatus Brachybacterium intestinipullorum (in.tes.ti.ni.pul.lo’rum. L. neut. n. intestinum gut; L. masc. n. pullus a young chicken; N.L. gen. n. intestinipullorum of the gut of young chickens)

Description of Candidatus Brachybacterium merdavium sp. nov.

Candidatus Brachybacterium merdavium (merd.a’vi.um. L. fem. n. merda faeces; L. fem. n. avis bird; N.L. gen. n. merdavium of bird faeces)

Description of Candidatus Brachybacterium merdigallinarum sp. nov.

Candidatus Brachybacterium merdigallinarum (mer.di.gal.li.na’rum. L. fem. n. merda faeces; L. fem. n. gallina hen; N.L. gen. n. merdigallinarum of hen faeces)

Description of Candidatus Brevibacterium intestinavium sp. nov.

Candidatus Brevibacterium intestinavium (in.tes.tin.a’vi.um. L. neut. n. intestinum gut; L. fem. n. avis bird; N.L. gen. n. intestinavium of the gut of birds)

Description of Candidatus Brevibacterium intestinigallinarum sp. nov.

Candidatus Brevibacterium intestinigallinarum (in.tes.ti.ni.gal.li.na’rum. L. neut. n. intestinum gut; L. fem. n. gallina hen; N.L. gen. n. intestinigallinarum of the gut of the hens)

Description of Candidatus Butyricicoccus avicola sp. nov.

Candidatus Butyricicoccus avicola (a.vi’co.la. L. fem. n. avis bird; L. suff. -cola inhabitant of; N.L. n. avicola inhabitant of birds)