Table - PMC

. 2023 Jan 25;26(2):106044. doi: 10.1016/j.isci.2023.106044

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples

Blood and fecal samples used for transcriptome, microbiome and nemabiome analysis	Author’s collection (INRAE, National Research Institute for Agriculture, Food and Environment	https://www.inrae.fr/en

Chemicals, peptides, and recombinant proteins

Strongid® oral paste	Zoetis	REF#: 5414736010373
Dipyralgine®	Med’Vet	REF#: 08713184045331

Critical commercial assays

Stool DNA Kit	Omega Bio-Tek	REF#: M6399-01
Preserved Blood RNA Purification Kit I	Norgen Biotek Corp.	Cat. #: 43400
Illumina Truseq Stranded mRNA	Illumina	20020595
MiSeq 500 cycle reagent kit v3	Illumina	N/A

Deposited data

16S rRNA amplicon sequences from 520 fecal samples	This manuscript	Data available in the DDBJ/EMBL/GenBank under the BioProject PRJNA819964 and accessions from SRR18489300 to SRR18489819. The accession numbers of the BioSamples included here are SAMN26941952 to SAMN26942471
ITS-2 amplicon sequences from 66 fecal samples	This manuscript	Data available in the DDBJ/EMBL/GenBank under the BioProject PRJNA849212, and the accession codes from SRR19660475 to SRR19660667, and BioSamples codes from SAMN29052165 to SAMN29052167
Illumina RNAseq sequences from 72 blood samples	This manuscript	Data available in the DDBJ/EMBL/GenBank under the BioProject PRJNA849212, and the accession codes from SRR20644566 to SRR20644637, and Biosamples codes from SAMN29961920 to SAMN29961866
Nematode ITS-2 database	https://www.nemabiome.ca/its2-database.html	v1.3
SILVA 16S rRNA full-length database	https://www.arb-silva.de/documentation/release-138/	release 138
SILVA 16S rRNA region-specific (515F/806R)	Silva 138 99% OTUs from 515F/806R region of sequences	release 138
NCBI 16S ribosomal RNA reference database	https://www.ncbi.nlm.nih.gov/refseq/targetedloci/16S_process/	released on May 25^th, 2020
Equus caballus reference transcriptome	Ensembl v. 103	v3

Experimental models: Organisms/strains

40 adult pony females (Equus caballus)	Bred in-house at Animal Physiology Facility	https://doi.org/10.15454/1.5573896321728955E12

Oligonucleotides

16S rRNA forward: GTGCCAGCMGCCGCGGTAA	This paper	N/A
16S rRNA reverse: GGACTACHVGGGTWTCTAAT	This paper	N/A
ITS-2 Forward:5′- ACGTCTGGTTCAGGGTTGTT-3′	This paper	N/A
ITS-2 Reverse: 5′- GTTTCTTTTCCTCCGCT-3′	This paper	N/A

Software and algorithms

R	R Core Team, 2013	v. 4.0.2
DADA2	Callahan et al. (2016)¹⁰⁷	https://benjjneb.github.io/dada2/
DeSeq2	Love et al. (2014)¹⁰⁸	v. 1.30.1
QIIME2	https://qiime2.org/	v. 2021.2
Cutadapt	Martin et al. (2011)⁹⁵	(v. 3.4)
DECIPHER	Murali et al. (2018)¹⁰⁹	v. 2.18.1
Phyloseq R package	McMurdie and Holmes (2013)¹¹⁰	v. 1.34.0
BLAST-ed	https://blast.ncbi.nlm.nih.gov/Blast.cgi	nt
Trimmomatic	Bolger et al. (2014)¹¹¹	v. 0.36
Salmon	Patro et al. (2017)¹¹²	v. 1.4
variancePartition R package	Bates et al. (2015)¹¹³	v. 1.20
g:profiler2 R package	Bolger et al. (2014)¹¹¹	v.0.2.1
Microbiome R package	http://microbiome.github.io	v. 1.15.3
lme4 R package	Bates et al. (2015)¹¹³	v. 1.1-27.1
vegan R package	Dixon et al. (2013)¹¹⁴	v. 2.5.7
betapart R package	Baselga et al. (2013)¹¹⁵	v. 1.5.6
MaAsLin 2 R package	Mallick et al. (2021)¹¹⁶	v. 1.8.0
Sjmisc R package	https://strengejacke.github.io/sjmisc/	v. 2.8.9
pROC R package	Robin et al. (2011)¹¹⁷	v. 1.18.0
ROCit R package	https://github.com/cran/ROCit	v. 2.1.1
eggCounts R package	Wang et al. (2018)¹¹⁸	v. 2.3.2
multispatialCCM R package	Clark et al. (2015)⁶⁸	v. 1.2
rEDM R package	Ye et al. (2018)¹¹⁹	v. 0.7.5

Other

NanoDrop 8000 spectrophotometer	Thermo Fisher Scientific	https://www.thermofisher.com/order/catalog/product/ND-8000-GL
Bioanalyzer 2100	Agilent Technologies	https://www.agilent.com/en/product/automated-electrophoresis/bioanalyzer-systems/bioanalyzer-instrument
NovaSeq 6000 system	Illumina	https://www.illumina.com/systems/sequencing-platforms/novaseq.html
MiSeq system	Illumina	https://www.illumina.com/systems/sequencing-platforms/miseq.html