Verified Rigor RecordRigor Reviewed

Rigor-Reviewed Manuscript

Culture of previously uncultured members of the human gut microbiota by culturomics · 10.1038/nmicrobiol.2016.203

Name: Verified Rigor Record — Culture of previously uncultured members of the human gut microbiota by culturomics · 10.1038/nmicrobiol.2016.203
Item: Culture of previously uncultured members of the human gut microbiota by culturomics · 10.1038/nmicrobiol.2016.203
Rating: 79
Author: Αlpha¹

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Αlpha¹ Editorial

This rigor review was examined and confirmed by Αlpha¹ Editorial · July 6, 2026

Αlpha¹ Rigor Review

Rigor Reviewed

WARN

Warnings to address · Observational Study

Eight dimensions — click a segment for details

Critical

High-priority

Model-reported confidence: moderateReviewer agreement: moderateEngine: 7.6.0Source: full text

Not verified in this report

No reported statistical tests were found to recompute.

This Αlpha¹ Rigor Review uses AI Rigor Reviewers trained on a curated corpus of high-fidelity and retracted papers, with expert supervision and curation. It can still make mistakes; verify each finding against the source before relying on it.

The paper presents a large-scale culturomics study that successfully expands the known human gut prokaryotic repertoire. It has strong scientific premise and data availability, with detailed methods and ethics approval. However, it has notable reporting gaps: demographics are not systematically reported, inclusion/exclusion criteria are missing for the main sample set, no power analysis or outlier handling is provided, reagent catalog numbers and software versions are incomplete, a reporting guideline is not referenced, and a headline conclusion ('doubles' the species count) is slightly overstated.

The evaluation was performed on the published paper text, with three independent rigor reviewers and a separate copyedit pass. The statistical analysis dimension was scored as not applicable because no inferential statistics were used. The reviewers showed good agreement on most dimensions, diverging mainly on biological variables (warn vs. fail) and ethical approvals (pass vs. warn); I weighed the evidence and resolved these to warn. The verification components flagged one retracted citation, an arithmetic discrepancy in phyla counts, and one overstated claim.

12 major claims checked against the paper's own evidence: 1 not fully backed by the presented evidence (unsupported or overstated).

3 integrity concerns flagged (0 high).

Rigor

Eight Dimensions3 pass · 5 warn

12 major claims1 overstated3 partial8 supported

The introduction cites prior metagenomic studies and previous culturomics work, noting that many sequences remain unassigned and that culture techniques have been neglected. It provides a logical rationale: culturomics can fill gaps left by metagenomics and is essential for understanding the microbiome's role in health and disease. The paper explicitly addresses limitations of prior culturomics studies (e.g., low sample numbers, missed taxa) and describes new protocols to overcome them.

Sub-criteria

prior work citedADEQUATE

premise rationaleADEQUATE

limitations addressedADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 95% conf

The paper clearly establishes the scientific premise by citing prior work on metagenomics and culturomics, providing a logical rationale for the study, and addressing limitations of previous culturomics studies.

Evidence

direct quote[Introduction, paragraph 1]

“Metagenomics revolutionized the understanding of the relations among the human microbiome, health and diseases, but generated a countless number of sequences that have not been assigned to a known microorganism.”

direct quote[Introduction, paragraph 2]

“We recently introduced microbial culturomics, a culturing approach that uses multiple culture conditions and matrix-assisted laser desorption/ionization–time of flight and 16S rRNA for identification.”

direct quote[Introduction, paragraph 2]

“Here, we have selected the best culture conditions to increase the number of studied samples and have applied new protocols (fresh-sample inoculation; detection of microcolonies and specific cultures of Proteobacteria and microaerophilic and halophilic prokaryotes) to address the weaknesses of the previous studies.”

PASSReviewer 2· 95% conf

The paper clearly establishes the scientific foundation by citing prior work on metagenomics and culturomics, providing a logical rationale for the study, and addressing limitations of previous approaches.

Evidence

direct quote[Introduction, paragraph 1]

direct quote[Introduction, paragraph 3]

“We have selected the best culture conditions to increase the number of studied samples and have applied new protocols (fresh-sample inoculation; detection of microcolonies and specific cultures of Proteobacteria and microaerophilic and halophilic prokaryotes) to address the weaknesses of the previous studies.”

PASSReviewer 3· 95% conf

The scientific premise is clearly established, with prior work cited and a logical rationale linking the limitations of metagenomics and neglected culture techniques to the study's objectives.

Evidence

direct quote[Introduction, paragraphs 1-2]

“The study of the human gut microbiota has been revived by metagenomic studies... However, a growing problem is the gaps that remain in metagenomics, which correspond to unidentified sequences that may be correlated with an identified organism.”

direct quote[Introduction, paragraph 2]

paraphrase[Abstract and Introduction]

“The authors state that culturomics aims to resolve gaps in metagenomics by doubling the number of species isolated from the human gut.”

The study is a large-scale culturomics effort with multiple sub-studies (standardization, cohorts, fresh samples, Proteobacteria, microaerophilic, halophilic, microcolonies, duodenal samples). No randomization or blinding is reported, which is expected for this type of observational work. Inclusion/exclusion criteria are provided for some cohorts (e.g., preterm neonates with necrotizing enterocolitis, pilgrims) but not for all samples. Outlier handling is not mentioned. Negative controls are reported for halophilic cultures and acidophilic bacteria, but not for all culture conditions. Independent replication is not applicable as this is a single large study.

Sub-criteria

controlsINADEQUATE

power analysisNOT REPORTED

blinding levelsNOT REPORTED

outlier handlingNOT REPORTED

randomization unitNOT REPORTED

inclusion exclusionINADEQUATE

randomization methodNOT REPORTED

replicate distinctionNOT REPORTED

independent replicationN/A

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 85% conf

The study design is largely descriptive and observational, with no randomization, blinding, or power analysis. Inclusion/exclusion criteria are described for some cohorts but not all, and outlier handling is not reported. Controls are used in some experiments (e.g., negative controls for halophilic cultures), but not consistently across all sub-studies.

Evidence

direct quote[Methods, Cohorts section]

“Only patients with definite or advanced necrotizing enterocolitis corresponding to Bell stages II and III were included.”

direct quote[Methods, Halophilic bacteria section]

“Negative controls (no inoculation of the culture medium) were included for each culture condition.”

absence[Methods]

No randomization, blinding, power analysis, or outlier handling is reported.

WARNReviewer 2· 75% conf

The study design is descriptive and exploratory; formal experimental design elements like randomization, blinding, and power analysis are absent, but inclusion/exclusion criteria and controls are partially reported.

Evidence

direct quote[Methods, Preterm neonates]

“Only patients with definite or advanced necrotizing enterocolitis corresponding to Bell stages II and III were included.”

direct quote[Methods, Halophilic bacteria]

“Negative controls (no inoculation of the culture medium) were included for each culture condition.”

absence[Methods]

Power analysis is not reported

WARNReviewer 3· 85% conf

Study design is well-described but lacks several methodological rigor elements: no randomization, blinding, power analysis, or pre-specified inclusion/exclusion criteria for the main analysis.

Evidence

absence[Methods]

The study does not report an a priori power analysis.

direct quote[Methods, 'Preterm neonates' section]

“Only patients with definite or advanced necrotizing enterocolitis corresponding to Bell stages II and III were included.”

direct quote[Methods, 'Halophilic bacteria' and 'Acidophilic bacteria' sections]

“Negative controls (no inoculation of the culture medium) were included for each condition.”

The paper describes samples from healthy individuals and patients with various diseases (e.g., anorexia nervosa, obesity, malnutrition, HIV) and from different geographic regions. However, age, sex, and other demographics are not reported for the human subjects. For the isolated prokaryotes, species, strain, and source are reported (e.g., CSUR and DSMZ deposit numbers). Housing conditions are not applicable as this is a human study.

Sub-criteria

demographicsINADEQUATE

sex reportedNOT REPORTED

sex justifiedN/A

age weight healthINADEQUATE

housing conditionsN/A

species strain sourceN/A

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 80% conf

The paper reports the source and health status of human samples (healthy individuals and patients with various diseases) and provides some demographic information (geographic origin, disease conditions). However, age, sex, and other demographics are not systematically reported for all samples, and species/strain/source information is provided for isolated prokaryotes but not for the human subjects.

Evidence

direct quote[Methods, Samples section]

“To obtain a larger diversity of gut microbiota, we analysed 943 different stool samples and 30 small intestine and colonic samples from healthy individuals living or travelling in different geographical regions (Europe, rural and urban Africa, Polynesia, India and so on) and from patients with diverse diseases (for example, anorexia nervosa, obesity, malnutrition and HIV).”

direct quote[Methods, International deposition section]

“Most of the strains isolated in this study were deposited in CSUR (WDCM 875) and are easily available at http://www.mediterranee-infection.com/article.php?laref=14&titre=collection-de-souches&PHPSESSID=cncregk417fl97gheb8k7u7t07”

FAILReviewer 2· 85% conf

Key biological variables such as sex, age, and demographics of human participants are not reported, failing to meet basic reporting standards for human studies.

Evidence

direct quote[Methods, Samples]

“we analysed 943 different stool samples and 30 small intestine and colonic samples from healthy individuals living or travelling in different geographical regions (Europe, rural and urban Africa, Polynesia, India and so on) and from patients with diverse diseases (for example, anorexia nervosa, obesity, malnutrition and HIV).”

absence[Results, Table 1]

No demographic table is provided.

WARNReviewer 3· 80% conf

Biological variables are partially reported: species/strain/source is well-described, but sex, age, weight, and health status are not systematically reported for the majority of samples.

Evidence

direct quote[Results and Methods, 'International deposition of the strains']

“The new prokaryote species are available in the Collection de Souches de l'Unité des Rickettsies (CSUR) and Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ).”

direct quote[Methods, 'Samples']

“The main characteristics are summarized in Supplementary Table 4a.”

direct quote[Methods, 'Preterm neonates']

“Fifteen controls were matched to 15 patients with necrotizing enterocolitis by sex, gestational age, birth weight...”

The paper includes a clear ethics statement: the study was approved by the local Ethics Committee of the IFR48 in Marseille, France (agreement no. 09–022). Consent was obtained from each patient. The study involves human stool samples and is observational, so these approvals cover the human research requirements. Regulatory compliance (Declaration of Helsinki) is implied by the ethics committee approval, but not explicitly stated; this is standard and adequate.

Sub-criteria

iacuc statementN/A

informed consentADEQUATE

irb ethics statementADEQUATE

regulatory complianceINADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 90% conf

The paper reports ethics approval from a named committee and informed consent, meeting the requirements for human observational research.

Evidence

direct quote[Methods, Samples section]

“Consent was obtained from each patient, and the study was approved by the local Ethics Committee of the IFR48 (Marseille, France; agreement no. 09–022).”

direct quote[Methods, Samples section]

“Consent was obtained from each patient”

WARNReviewer 2· 90% conf

Ethics approval and informed consent are stated, but regulatory compliance with a recognized framework is not explicitly mentioned.

Evidence

direct quote[Methods, Samples]

“Consent was obtained from each patient, and the study was approved by the local Ethics Committee of the IFR48 (Marseille, France; agreement no. 09–022).”

absence[Methods, Samples]

Regulatory compliance is not stated.

PASSReviewer 3· 95% conf

Ethical approvals and consent are adequately reported for the human subjects involved.

Evidence

direct quote[Methods, 'Samples']

“Consent was obtained from each patient, and the study was approved by the local Ethics Committee of the IFR48 (Marseille, France; agreement no. 09-022).”

direct quote[Methods, 'Samples']

“Consent was obtained from each patient...”

The paper identifies many reagents (e.g., blood culture bottles, agar types, antibiotics) with vendor names, but catalog numbers are often missing. Software tools (e.g., MALDI-TOF Microflex LT, QIIME, USEARCH) are named but versions are not always provided. Custom code is not mentioned. The study does not use antibodies, cell lines, or model organisms, so those criteria are not applicable.

Sub-criteria

mycoplasma testingN/A

reagents identifiedINADEQUATE

organisms identifiedN/A

antibodies identifiedN/A

cell line authenticationN/A

software tools identifiedINADEQUATE

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 85% conf

Key resources such as culture media, reagents, and software are identified, but some are not fully specified (e.g., vendor/catalog numbers for some reagents, software versions). The paper does not use antibodies, cell lines, or organisms in the traditional sense, so those criteria are not applicable.

Evidence

direct quote[Methods, Culturomics section]

“We inoculated 100 µl of liquid sample in an 8 ml bottle containing Trypticase Soy Broth (BD Diagnostics)”

direct quote[Methods, Metagenomic 16S sequences section]

“We used the PEAR software (PMID 24142950) for merging raw Illumina paired-end reads using default parameters.”

WARNReviewer 2· 80% conf

Organisms are well-identified with deposition in public collections, but reagents and software lack complete catalog numbers and versions, and antibody/cell line criteria are not applicable.

Evidence

direct quote[Methods, International deposition of the strains]

direct quote[Methods, Metagenomic 16S sequences]

“We used the PEAR software (PMID 24142950) for merging raw Illumina paired-end reads using default parameters.”

absence[Methods, Culturomics]

Reagent catalog numbers are largely missing.

WARNReviewer 3· 85% conf

Key resources are partially identified: software and reagents are detailed, but antibodies and cell lines are not applicable, and organism identification is adequate. Reporting of specific culture media components and borderline culturomics reagents is adequate.

Evidence

direct quote[Methods, various sections]

“We inoculated 100 µl of liquid sample in an 8 ml bottle containing Trypticase Soy Broth (BD Diagnostics)...”

direct quote[Methods, 'Identification methods' and 'Metagenomic 16S sequences']

“This analysis was performed using a Microflex LT system (Bruker Daltonics).”

direct quote[Methods, 'International deposition of the strains']

“Most of the strains isolated in this study were deposited in CSUR (WDCM 875)...”

The study is largely descriptive, reporting counts and percentages of isolated species. No inferential statistical tests are used, so criteria like tests_named, assumptions_verified, exact_p_values, and effect_sizes_ci are not applicable. Software used for identification (MALDI-TOF) is named, but statistical software is not mentioned. Data presentation includes per-group n and error bars are not used (as no inferential statistics are reported). Mathematical plausibility is not applicable as no summary statistics requiring verification are reported.

Sub-criteria

tests namedN/A

exact p valuesN/A

effect sizes ciN/A

data presentationADEQUATE

software identifiedINADEQUATE

assumptions verifiedN/A

mathematical plausibilityN/A

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 80% conf

The paper is primarily descriptive and does not use inferential statistics for hypothesis testing. Statistical tests are not named, assumptions are not verified, and exact p-values are not reported. The paper focuses on counts and proportions of isolated species, which are presented in tables and figures. Data presentation is adequate with per-group n stated, but individual data points are not shown.

Evidence

absence[Results]

No inferential statistical tests are used; the study is descriptive.

direct quote[Figure 1 legend]

“Figure 1 Number of different bacteria and archaea isolated during the culturomics studies.”

WARNReviewer 2· 80% conf

No inferential statistical tests are used, so most sub-criteria are not applicable; software identification is adequate, but data presentation lacks individual data points and mathematical plausibility is acceptable.

Evidence

direct quote[Methods, Metagenomic 16S sequences]

“We used the PEAR software (PMID 24142950) for merging raw Illumina paired-end reads using default parameters.”

paraphrase[Results, Figure 1]

“Results are presented as bar charts and pie charts showing species counts; individual data points are not shown.”

WARNReviewer 3· 80% conf

Statistical analysis is minimal; the paper primarily reports descriptive counts and percentages. Inferential statistics are not used, so many sub-criteria are not applicable. Data presentation is adequate for a descriptive study.

Evidence

absence[Throughout Results]

No inferential statistical tests are used; only descriptive statistics.

direct quote[Methods, 'Metagenomic 16S sequences']

“The paired-end reads of the corresponding raw fastq files were assembled into contigs using Pandaseq.”

paraphrase[Results and Figures 1-3]

“The paper uses bar charts to show the number of species isolated per category and phylogenetic trees for new species.”

The paper states that 16S rRNA sequences and genome sequences have been deposited in GenBank, and metagenomic sequencing data have been deposited in NCBI under Bioproject PRJEB13171. This provides concrete access routes. No custom code was used, so code sharing is not applicable.

Sub-criteria

code sharingN/A

accession numbersADEQUATE

repository depositADEQUATE

data availability statementADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 90% conf

The paper provides a data availability statement with accession numbers for 16S rRNA sequences, genome sequences, and metagenomic data deposited in public repositories (GenBank, NCBI Bioproject). Code sharing is not applicable as no custom code is described.

Evidence

direct quote[Data availability section]

“The GenBank accession numbers for the sequences of the16SrRNA genes of the new bacterial species as well as their accession numbers in both Collection de Souches de l'Unité des Rickettsies (CSUR, WDCM 875) and the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) are listed in . Sequencing metagenomics data have been deposited in NCBI under Bioproject PRJEB13171 https://www.ncbi.nlm.nih.gov/bioproject/PRJEB13171/ .”

PASSReviewer 2· 90% conf

Data availability is clearly stated with deposition in public repositories and accession numbers provided; custom code was not shared, but this is a minor gap.

Evidence

direct quote[Data availability]

“Sequencing metagenomics data have been deposited in NCBI under Bioproject PRJEB13171”

direct quote[Data availability]

“The GenBank accession numbers for the sequences of the16SrRNA genes of the new bacterial species as well as their accession numbers in both CSUR and DSMZ are listed in .”

WARNReviewer 3· 90% conf

Data availability is partially addressed: 16S rRNA sequences and genome sequences have GenBank accession numbers, and metagenomic data are deposited in NCBI (PRJEB13171). However, no code availability statement is provided.

Evidence

direct quote[Methods, 'Data availability']

“The GenBank accession numbers for the sequences of the16SrRNA genes of the new bacterial species... Sequencing metagenomics data have been deposited in NCBI under Bioproject PRJEB13171.”

absence[Methods]

Custom code sharing is not reported.

Methods are described in detail, allowing replication. Limitations are discussed (e.g., the need for further genome sequencing, the challenge of culturing certain bacteria). Funding sources and conflicts of interest are stated. No reporting guideline (e.g., STROBE) is referenced, which is common for this type of study. The conclusions are generally proportional, but the claim that culturomics 'doubles the number of species isolated at least once from the human gut' is supported by the data.

Sub-criteria

funding coiADEQUATE

trial registrationN/A

reporting guidelineNOT REPORTED

methods completenessADEQUATE

all outcomes reportedADEQUATE

limitations discussedADEQUATE

conclusions proportionalADEQUATE

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 85% conf

The paper provides detailed methods, discusses limitations, and includes funding and conflict of interest statements. However, it does not reference a reporting guideline, and the conclusions, while largely proportional, may slightly overstate the role of culturomics in filling metagenomic gaps.

Evidence

direct quote[Methods]

“Culturomics is a high-throughput method that multiplies culture conditions in order to detect higher bacterial diversity.”

direct quote[Discussion, paragraph 2]

“As 519 of the species found by culturomics in the gut for the first time () were not included in the HMP () and because hundreds of their genomes are not yet available, the results of this study should prompt further genome sequencing to obtain a better identification in gut metagenomic studies.”

direct quote[Acknowledgements]

“This work was funded by IHU Méditerranée Infection as a part of a Foundation Louis D grant and by the Deanship of Scientific Research (DSR), King Abdulaziz University, under grant no. 1–141/1433 HiCi.”

PASSReviewer 2· 85% conf

Methods are detailed, all outcomes are reported, conclusions are proportional, and funding is disclosed; however, a dedicated limitations section and a conflict of interest statement are missing.

Evidence

direct quote[Methods, Culturomics]

“Culturomics is a high-throughput method that multiplies culture conditions in order to detect higher bacterial diversity.”

direct quote[Acknowledgements]

absence[End of manuscript]

No conflict of interest statement is provided.

WARNReviewer 3· 85% conf

Reporting transparency is moderate: methods are detailed, limitations are discussed, and conclusions are proportional. However, the study is not a clinical trial, so trial registration is not applicable, and no formal reporting guideline (e.g., STROBE) is referenced. A funding and COI statement is present.

Evidence

paraphrase[Methods section]

“The Methods describe sample collection, culture conditions, identification protocols, metagenomic analysis, and data deposition in great detail.”

direct quote[Discussion/Results, final paragraphs]

“We believe that this work is a key step in the rebirth of the use of culturing in human microbiology... and only the efforts of several teams around the world in identifying the gut microbiota repertoire will allow an understanding...”

direct quote[Acknowledgements]

10 copyedit issues flagged: mostly consistency, clarity, typo.

Checked 38 references: 37 verified — 1 retracted.

Reproducibility

7 data/code links checked; 3 live, 2 dead.

Αlpha¹ Rigor Action ItemsFinal pass before journal submission

This paper is already published. The findings are broadly robust due to the large sample size and detailed protocols, but an informed reader should weigh the following: the missing participant demographics limit the ability to assess generalizability; the baseline number of previously known species has an unexplained discrepancy (688 vs 526/531); and the headline claim of 'doubling' the species count is a 1.5-fold increase, not double. A correction or published erratum addressing the phyla count arithmetic error (1057 vs sum 1058) and tempering the 'doubles' claim would strengthen the record.

1.
HIGHreporting
Correct the phyla count arithmetic: the sum of phyla counts (600+181+173+88+9+3+2+1+1=1058) does not match the stated total of 1057 prokaryotic species. Verify the numbers and correct either the individual counts or the total.
An internal contradiction in the reported data undermines reader trust and could indicate a transcription error.
2.
HIGHreporting
Temper the claim in the Abstract that culturomics 'doubles the number of species isolated at least once from the human gut' to reflect the actual 1.5-fold increase (from ~690 to 1057).
Overstating a headline conclusion is a common cause of reader criticism and may affect interpretation of the study's impact.
3.
HIGHreporting
Resolution of the baseline discrepancy: clarify why the introduction states 688 bacteria and 2 archaea (690 total) were previously known from the human gut, while the reported numbers imply only 526 previously known species (1057 total - 531 new).
This large unexplained inconsistency in the baseline number weakens the paper's core narrative and requires a correction or explanation.
4.
HIGHreporting
Remove or replace the retracted citation (Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample, doi:10.1007/s10096-013-1900-2) with a non-retracted reference.
Citing retracted literature is a clear integrity concern and should be corrected.
5.
HIGHreporting
Add a statement of compliance with the Declaration of Helsinki or other relevant regulatory framework to the Methods/Samples ethics section.
While an ethics committee approval is reported, explicit regulatory compliance is expected for human subjects research.
6.
HIGHreporting
Add a dedicated conflict of interest statement at the end of the manuscript.
A missing COI statement is a standard reporting requirement that is easily fixed.
7.
HIGHreporting
Provide a demographic table (age, sex, health status) for the main set of 943 stool samples in the main text or a clearly referenced supplementary table.
Age and sex are key biological variables whose absence limits assessment of generalizability and reproducibility.
8.
HIGHreporting
Clarify the inclusion/exclusion criteria for the overall set of 943 stool samples beyond the broad categories of 'healthy individuals' and 'patients with diverse diseases'.
Transparent inclusion/exclusion criteria are essential for study replicability and are currently only reported for specific sub-cohorts.
9.
MEDIUMreporting
Provide catalog numbers (or RRIDs) for all key reagents and culture media (e.g., Trypticase Soy Broth, blood culture bottles, antibiotics) in the Methods.
Complete reagent identification is critical for reproducibility; currently vendor names are given but catalog numbers are often missing.
10.
MEDIUMreporting
Include version numbers for all software tools (e.g., MALDI-TOF software, QIIME, USEARCH, PEAR, Pandaseq, BLAST) used in the analysis.
Software versioning is standard for method reproducibility.
11.
MEDIUMreporting
Add a statement on the handling of outliers or missing data (e.g., for samples that failed to grow any colonies or produced ambiguous identifications).
Outlier handling is a standard element of rigorous methodology reporting that is currently absent.
12.
MEDIUMreporting
Reference a relevant reporting guideline (e.g., STROBE for observational microbiome studies) in the Methods.
Referencing a reporting guideline demonstrates adherence to community standards and may improve manuscript evaluation.
13.
LOWcopyedit
Fix the grammatical error in the Abstract: 'Metagenomics revolutionized' should be 'Metagenomics has revolutionized'.
Minor grammatical correction for clarity.
14.
LOWcopyedit
Remove the duplicate sentence about supplementary information in the Abstract.
Duplicate text is a minor formatting issue.
15.
LOWcopyedit
Remove the bibliographic metadata line ('23 11 2016 Nat Rev Gastroenterol Hepatol ...') at the start of the Introduction.
This appears to be an artifact from the source and should not appear in the manuscript text.
16.
LOWcopyedit
Fix the extra space before the period in the Methods/Culturomics section: 'aerobically and anaerobically .'
Minor typographical correction.
17.
LOWcopyedit
Ensure consistent italicization of species names (e.g., Methanobrevibacter oralis) throughout the manuscript.
Consistency in taxonomic formatting is a standard copyediting expectation.
18.
LOWcopyedit
Rephrase the sentence beginning with 'Analysing our previously published studies' to avoid the dangling participle (e.g., 'We analyzed our previously published studies and observed that...').
Grammatical improvement for sentence clarity.

Full text (51,100 chars)Analyzed: Jul 6, 2026

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