TABLE 1.
Metagenomics pipelines.
| References | Country | Category | Sample type | Total patient | Sample preparation | DNA/RNA extraction | Microbial genome enrichment | Library preparation | Instrument | Software | Database |
| (Greninger et al., 2015) | California, United States | Case report | Fresh CSF | 1 | No | EZ1 Viral kit (Qiagen) | Turbo DNase (Ambion) | Nextera XT protocol (Illumina) | Illumina MiSeq | SURPI pipeline | NCBI GeneBank database |
| (Guan et al., 2015) | Tianjin, China | Prospective study | Frozen CSF | 4 | No | TIANamp Micro DNA Kit (TIANGEN BIOTECH) | Sigma-Aldrich WGA4 Kit (WGA) | Not available | BGISEQ-100 platform | Burrows-Wheeler Alignment, SoapCoverage software | Microbial Genome Databases |
| (Yao et al., 2016) | Beijing, China | retrospective study | Frozen CSF | 3 | No | TIANamp Micro DNA Kit (Tiangen Biotech) | No | Not available | BGISEQ-100 | Burrows-Wheeler Alignment | Microbial Genome Database |
| (Joanna María et al., 2016) | Mexico | Case report | Frozen CSF | 1 | No | MagNA Pure LC 2.0 instrument, Total Nucleic Acid isolation kit (Roche) | TransPlex Whole Transcriptome Amplification kit WTA, (Sigma-Aldrich) and GenomiPhi V2 (Healthcare Life Sciences) | Roche 454 GS FLX single-end library | 454 GS FLX Titanium system (Roche) | GS de novo Assembler version 2.6, | NCBI GenBank |
| (Kawada et al., 2016) | Nagoya, Japan | Prospective study | Fresh CSF | 18 | 0.45-μm filter (Merck-Millipore, Temecula, CA) | QIAamp Viral RNA Mini kit (Qiagen) | Turbo DNase (Ambion, Darmstadt, Germany) | Nextera XT DNA Sample preparation kit and ScriptSeq v2 (Illumina) | Illumina MiSeq, Illumina HiSeq 2500 | MEGAN5, CLC workbench | MEGABLAST |
| (Chiu et al., 2017) | California, United States | Case report | Fresh CSF | 1 | Not available | Not available | Not available | Not available | Illumina Miseq | SURPI+ computational pipeline | Microbial genome database |
| (Piantadosi et al., 2017) | Boston, United States | Case report | Fresh CSF | 1 | centrifugation 90 min/18,000 xg/4°C | QIAamp Viral Mini Kit (Qiagen) | TURBO DNase (Thermo Fisher) | Nextera XT | Illumina MiSeq | Kraken, de novo assembly | published computational pipeline viral-NGS |
| (Hu et al., 2018) | Nanjing, China | Case report | Fresh CSF | 1 | No | TIANamp Micro DNA Kit (TIANGEN BIO- TECH) | Sonication (Bioruptor Pico protocols) | end-repaired adaptation and PCR amplification (BGI, Tianjin, China) | BGISEQ-50 platform | Burrows-Wheeler Alignment | Microbial genome database |
| (Piantadosi et al., 2018) | Boston, United States | Case report | Fresh CSF | 1 | TURBO DNase (Thermo Fisher) | QIAamp Viral Mini Kit (Qiagen) | TURBO DNase (Thermo Fisher) | Nextera XT (Illumina) | Illumina MiSeq, HiSeq 2500 | Kraken, Geneious version 8.1.7 | NCBI GenBank Database |
| (Xing et al., 2019) | Beijing, China | Prospective study | Frozen CSF | 12 | Not available | Not available | Not available | Not available | BGISEQ-500/50 platform | Burrows-Wheeler Alignment | Microbial genome Database |
| (Tschumi et al., 2019) | Zurich, Switzerland | Case report | Fresh CSF | 1 | centrifugation and filtration | Not available | DNase treatment | Nextera XT (Illumina) | MiSeq | VirMet pipeline | NCBI GenBank database |
| (Saha et al., 2019) | Bangladesh | Retrospective study | Frozen CSF | 91 | Not available | Not available | Not available | Nextera XT (Illumina) | Illumina NovaSeq | IDseq bioinformatics pipeline | NCBI GenBank database |
| (Wang et al., 2019) | Beijing, China | Retrospective study | Frozen CSF | 23 | glass beads, vortexed 20 min, centrifuged at 8000 rcf | TIANamp Micro DNA Kit (TIANGEN BIOTECH) | No | end-repaired adaptation and PCR amplification (BGI, Tianjin, China) | BGISEQ-100 | Mapping with WBA, BLAST | Microbial genome database |
| (Wilson et al., 2019) | California, United States | Retrospective study | Fresh CSF | 204 | Not available | Not available | Not available | Nextera XT (Illumina) | Illumina HiSeq | SURPI+ pipeline | NCBI GenBank database |
| (Zhang Y. et al., 2019) | Hebei, China | Case report | Fresh CSF | 1 | No | TIANamp Micro DNA Kit (Tiangen Biotech) | No | end-repaired adaptation and PCR amplification (BGI, Tianjin, China) | BGISEQ-100 | Burrows-Wheeler Alignment | Microbial genome database |
| (Edridge et al., 2019) | Amsterdam, Netherlands | Retrospective study | Frozen CSF | 45 | Centrifugation TURBO DNase (Thermo Fisher) | Manually extracted Boom method | MseI (T?TAA; New England Biolabs) | VIDISCA library preparation | Ion PGM System | Taxonomer, CodonCode Aligner (version 6.0.2) | UBLAST |
| (Zhang X. X. et al., 2019) | Beijing, China | Retrospective study | Fresh CSF | 135 | No | TIANamp Micro DNA Kit (DP316, Tiangen Biotech, Beijing, China). | No | BGISEQ-500 standard protocol | BGISEQ-500 sequencing | Burrows-Wheeler Alignment | Microbial genome database |
| (Miller et al., 2019) | California, United States | Retrospective study | Fresh CSF | 95 | FastPrep-24 bead beater (MP Biomedicals) | EZ1 Virus Mini Kit v2.0 (Qiagen) | NEB Microbiome Enrichment Kit (New England Biolabs) Turbo DNAse (Thermo-fisher) | Nextera XT DNA Library Prep Kit (Illumina) | Illumina HiSeq | SURPI+ pipeline | GenBank reference database |
| (Eibach et al., 2019) | Agogo, Ghana | Retrospective study | Frozen CSF | 70 | No | MagMAX Viral RNA Isolation Kit (Life Technologies) | No | BGISEQ-500 standard protocol | Illumina MiSeq | CLC workbench, Trinity v2.6.6, Geneious v11, DIAMOND v0.9.6 | NCBI GenBank database |
| (Chen et al., 2020) | Yangzhou, China | Case report | Fresh CSF | 4 | Centrifugation | TIANamp Micro DNA Kit (TianGen Biotech) | Ultrasonicator (Covaris) | VAHTS Universal DNA Library Prep Kit for Illumina V3 kit | Illumina NextSeq500 | Burrows-Wheeler Alignment | Microbial genome database |
| (Lan et al., 2020) | Hunan, China | Case report | Fresh CSF | 1 | No | TIANGEN DNA Mini kit DP316 (Tiangen Biotech, Beijing, China) | No | Not available | Illumina NextSeq | Burrows-Wheeler Alignment | Microbial genome database |
| (Zhang et al., 2020) | Hunan, China | Case report | Fresh CSF | 1 | Not available | Not available | Not available | Not available | Not available | Not available | Not available |
| (Xing X. W. et al., 2020) | China | Prospective study | Frozen CSF | 213 | Glass beads, vortex | Not available | Not available | Not available | BGISEQ-500 | Burrows-Wheeler Alignment | Microbial genome database |
| (Yan et al., 2020) | Shanghai, China | Prospective study | Frozen CSF | 51 | Glass beads, vortex 2800-3200RPM for 30 min | TIANamp Micro DNA Kit (TIANGEN BIOTECH) | No | end-repaired adaptation and PCR amplification (BGI) | BGISEQ-50 platform | Burrows–Wheeler Alignmen | Microbial Genome Databases |
| (Wang et al., 2020) | Wenzhou, China | Case report | Fresh CSF | 1 | Not available | Not available | Not available | Not available | BGISEQ platform | Burrows-Wheeler Alignment | Microbial Genome Databases |
| (Wu et al., 2020) | Shanghai, China | Case report | Fresh CSF | 1 | Not available | Not available | Not available | Not available | BGISEQ platform | Burrows-Wheeler Alignment | Microbial Genome Databases |
| (Manso et al., 2020) | London, United Kingdom | Prospective study | Fresh CSF | 12 | Filtration and Turbo DNAse treatment | PureLink Viral RNA/DNA Mini Kit (Invitrogen) | No | Nextera XT DNA library prep kit (Illumina) | Illumina MiSeq | Trimmomatic v0.39, PRINSEQ, mapping with PALADIN, BWA MEM | In-house database comprising the RefSeq viral protein sequences from NCBI |
| (Carbo et al., 2020) | Leiden, Netherlands | Prospective study | Frozen CSF | 41 | No | MagNApure 96 DNA and Viral NA Small volume extraction kit (ROCHE) | SpeedVac vacuum con- centrator (Eppendorf), SeqCap EZ Hypercap probes (Roche) | NEBNext Ultra II Directional RNA Library prep kit (New England Biolabs) | Illumina NovaSeq6000 | Illumina data analysis pipeline RTA3.4.4 and bcl2fastq v2.20, Genome Detective version 1.111 | An index database constructed from NCBI |
| (Leon et al., 2020) | Barcelona, Spain | Retrospective study | Frozen CSF | 20 | No | Direct-zol RNA MicroPrep with TRI reagent (Zymo Research) | Depletion of Abundant Sequences by Hybridization (DASH) | NEBNext Ultra II Directional RNA Library prep kit (New England Biolabs) | Illumina HiSeq 4000 instrument | Geneious version 10.2.3, SPAdes version 3.10.0, MUSCLE, MAFFT. | Local database |
| (Solomon et al., 2021) | Boston, United States | Case report | Frozen CSF | 1 | Not available | Not available | Not available | Not available | Illumina HiSeq 2500 | SURPI+ pipeline | NCBI GenBank database |
| (Li et al., 2021) | Sydney, Australia | Prospective study | Frozen CSF | 18 | No | RNeasy plus universal kit (QIAGEN) | No | Trio RNA-Seq kit (NuGEN Technologies, United States) was | Illumina NovaSeq platform | Blastn, Blastx, Diamond, Megahit | NCBI GenBank databases, |
| (Zhan et al., 2021) | Hangzhou, China | Case report | Fresh CSF | 1 | Not available | Not available | Not available | Not available | BGISEQ-500 sequencing | Not available | Not available |
| (Zhou et al., 2021) | Hunan, China | Case report | Fresh CSF | 1 | No | Not available | No | Nexter XT | NextSeq 550 | Kraken | In-house database |
| (Mao et al., 2021) | Guangzhou, China | Case report | Frozen CSF | 1 | Not available | TIANamp Magnetic DNA Kit (Tiangen) | Not available | PACEseq mNGS (Hugobiotech) | NextSeq 550 | Burrows-Wheeler Alignment | Microbial genome database |
| (Zhang et al., 2021a) | Hunan, China | Case report | Fresh CSF | 1 | Not available | Not available | Not available | Not available | Not available | Not available | Not available |
| (Huang et al., 2021) | Guangzhou, China | Case report | Fresh CSF | 1 | centrifugation 5 min at 15,000 rpm | magnetic beads [Sagene, Guangzhou, CHINA] | No | Nexter XT | Illumina NextSeq 550 DX | Not available | Not available |
| (Xing N. et al., 2021) | Hebei, China | Retrospective study | Fresh CSF | 7 | Not available | Not available | Not available | Not available | BGISEQ-500 sequencing | Burrows-Wheeler Alignment | Microbial genome database |
| (Erdem et al., 2021) | Ohio, United States | Prospective study | Frozen CSF | 37 | No | QIAamp Viral RNA Mini Kit (Qiagen) | No | TruSeq Universal kit (Illumina) | Illumina HiSeq4000 | FastQC, Cutadpat and PRINSEQ tools, Bowtie2 mapper 2.0.6, CDHIT tool. de novo assembled using MIRA (v 4.0), MegaBLAST | NCBI GeneBank database |
| (Xing X.-W. et al., 2021) | China | Case report | Frozen CSF | 1 | Not available | Not available | Not available | BGISEQ-500 standard protocol | BGISEQ 50 MGI DNBSEQ | Burrows-Wheeler Alignment | Microbial genome database |
| (Yin et al., 2021) | Jiangsu, China | Retrospective study | Frozen CSF | 1 | No | TIANamp Magnetic DNA Kit (Tiangen) | No | KAPA Hyper Prep Kit (KAPA Biosystems) according | Illumina NextSeq 550Dx | Trimmomatic v.0.36 software, Bowtie2 software. Kraken 2 software | Microbial genome database |
| (Zeng et al., 2021) | Changsha, China | Case report | Fresh CSF | 1 | Not available | Not available | Not available | PACEseq mNGS test (Hugobiotech) | Illumina NextSeq 550 | Not available | Not available |
| (Guan et al., 2021) | Riyadh, Saudi Arabia | Case report | Frozen CSF | 1 | No | DNeasy Blood and Tissue Kits (QIAGEN) | No | NuGEN Ovation Ultralow Library System V2 (NuGEN) | Illumina HiSeq 4000, Illumina iSeq 100 | MEGAHIT assembler v1⋅1 ⋅4, BBmap with 0 ⋅98, Metabat v2 ⋅12 ⋅1, Spades | NCBI GenBank database |
| (Zhang et al., 2021b) | Zhejiang, China | Case report | Fresh CSF | 1 | Not available | Not available | Not available | Nexter XT | Illumina NextSeq | Kraken | Kraken microbial database |
| (Piantadosi et al., 2021) | Boston, United States | Prospective study | Fresh CSF | 68 | No | QIAamp viral RNA minikit (Qiagen) | NEBNext microbiome DNA enrichment kit (New England BioLabs) | Nextera XT DNA library prep kit (Illumina) | Illumina MiSeq | KrakenUniq, BLAST | NCBI GenBank database |
| (Morsli et al., 2021d) | Marseille, France | Case report | Fresh CSF | 1 | Proteinase K 20 min | QIAamp Viral RNA Mini Kit solutions (Qiagen) | Turbo DNase (Thermo Fisher) and | Nextera XT V2 | Illumina iSeq 100 | Spade, BLAST, CLC workbench | NCBI GenBank database |
| (Fan et al., 2021) | Guangzhou, China | Retrospective study | Frozen CSF | 11 | Not available | Not available | Not available | Not available | BGISEQ platform | Burrows-Wheeler Alignment | Microbial Genome Databases |
| (Morsli et al., 2021c) | Marseille, France | Case report | Fresh CSF | 1 | Proteinase K 20 min | Virus Mini Kit v2.0 (Qiagen) | Spiked primer enrichment | Nextera XT V2 | Illumina Miseq, iSeq 100 | Spade, BLAST, CLC workbench | NCBI GenBank database |
| (Morsli et al., 2021b) | Marseille, France | Case report | Fresh CSF | 1 | Proteinase K 20 min | EZ1 DNA Kit (Qiagen) | No | Oxford Nanopore MinION library preparation | Oxford Nanopore MinION | EPI2ME, Kraken-2, Pavian | NCBI GenBank database |
| (Morsli et al., 2021a) | Marseille, France | Case report | Fresh CSF | 1 | Proteinase K 20 min | EZ1 DNA Kit (Qiagen) | No | Oxford Nanopore MinION library preparation | Oxford nanopore MinION, Illumina iSeq | EPI2M2, Spades, CLC genomic workbench | NCBI GenBank database |
| (Gao et al., 2021) | Beijing, China | Prospective study | Fresh CSF | 38 | centrifugation 10 min at 13,000 rpm | QIAamp DNA Microbiome Kit (Qiagen) | NEBNext microbiome DNA enrichment kit (New England BioLabs) | Nextera XT kit v2 Ion Torrent end-repair library | Illumina MiSeq, Ion Torrent Proton | Burrows-Wheeler alignment was | Microbial genome databases |
| (Morsli et al., 2022) | Marseille, France | Case report | Fresh CSF | 1 | Proteinase K 20 min | EZ1 DNA Kit (Qiagen) | No | Oxford Nanopore MinION library preparation | Oxford Nanopore MinION | EPI2ME and CLC Genomics Workbench, software | NCBI GenBank database |