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Correlation between body mass index and gut concentrations of Lactobacillus reuteri , Bifidobacterium animalis , Methanobrevibacter smithii and Escherichia coli · 10.1038/ijo.2013.20

Name: Verified Rigor Record — Correlation between body mass index and gut concentrations of Lactobacillus reuteri , Bifidobacterium animalis , Methanobrevibacter smithii and Escherichia coli · 10.1038/ijo.2013.20
Item: Correlation between body mass index and gut concentrations of Lactobacillus reuteri , Bifidobacterium animalis , Methanobrevibacter smithii and Escherichia coli · 10.1038/ijo.2013.20
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 data or code availability links were detected to verify.

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 has a clear scientific premise, adequate methods description, and uses appropriate statistical tests. However, it has critical gaps in data/code availability (no repository or data statement), several reporting gaps (no informed consent, no power analysis, no reporting guideline), an internal arithmetic inconsistency in Table 1, and some overstatement of conclusions (e.g., claiming 'specificity of the obese microbiota').

Evaluated on all eight rigor dimensions. Many sub-criteria were not applicable due to the observational, cross-sectional design (randomization, blinding, replicate distinction, trial registration, IACUC). The statistic verification covered 15 tests; 2 showed minor p-value discrepancies (both remained <0.05). One reference was found to be retracted (Million et al. 2012, IJO) and one reference could not be found in the registry. The claim audit identified three overstatements. Reviewers largely converged, with notable divergence on two dimensions (biological variables: Reviewer 3 vs 1/2 on overall pass vs warn; statistical analysis: Reviewer 3 vs 1/2 on pass vs warn).

12 major claims checked against the paper's own evidence: 3 not fully backed by the presented evidence (unsupported or overstated).

Recomputed 15 tests: 13 consistent, 2 inconsistent, 15 via agent-written checks.

4 integrity concerns flagged (1 high).

Rigor

Eight Dimensions4 pass · 3 warn · 1 fail

12 major claims3 overstated4 partial5 supported

The introduction cites numerous studies linking specific bacterial taxa (e.g., Bifidobacterium, Lactobacillus, Methanobrevibacter smithii, Escherichia coli) to obesity or leanness, establishing the premise. The rationale is clearly stated: to test correlations between BMI and the concentrations of these specific species, building on a previous case-control study with an expanded sample size. Limitations of prior research are implicitly addressed by the study's design (e.g., including anorexic and overweight patients, analyzing correlations), but a dedicated section on how the study addresses prior limitations is not explicitly provided.

Sub-criteria

prior work citedADEQUATE

premise rationaleADEQUATE

limitations addressedINADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 95% conf

The paper establishes a clear scientific premise by citing prior work on the gut microbiota's association with obesity and provides a logical rationale for the study.

Evidence

direct quote[Introduction, paragraphs 1-4]

“A decreased Bacteroidetes/Firmicutes ratio was initially shown to be associated with obesity... the Bifidobacterium genus was associated with lean humans in a meta-analysis... we showed that among Lactobacillus species previously associated with obesity... some have also been associated with weight gain...”

direct quote[Introduction, final paragraph]

“Based on our previous case-control study, we have more than doubled the sample size, having included both anorexic and overweight patients in this study, and finally we have analyzed the correlations between the BMI and the considered taxa.”

absence[Introduction]

Limitations of prior research are not explicitly addressed in a dedicated section.

PASSReviewer 2· 95% conf

The study clearly establishes its scientific foundation by citing prior work, providing a logical rationale, and addressing limitations of previous studies.

Evidence

direct quote[Introduction, paragraph 1-3]

“The Bifidobacterium genus was associated with lean humans in a meta-analysis, including studies from Finland, Germany, Spain and China.”

direct quote[Introduction, paragraph 4]

“Here, we looked at the inter-relationships among E. coli, one of the main representatives of the Enterobacteriaceae, Methanobrevibacter smithii, a leading representative of the gut archaea, Bifidobacterium animalis and 5 Lactobacillus species...”

direct quote[Introduction, paragraph 5]

PASSReviewer 3· 90% conf

Clear scientific premise with adequate prior work cited and rationale, though limitations of prior work are only partially addressed.

Evidence

direct quote[Introduction, paragraphs 2-4]

“The Bifidobacterium genus was associated with lean humans in a meta-analysis... we showed that among Lactobacillus species previously associated with obesity and diabetes, some have also been associated with weight gain”

direct quote[Methods, first paragraph]

“Based on our previous case-control study, we have more than doubled the sample size, having included both anorexic and overweight patients in this study”

The study is a cross-sectional observational analysis, so randomization, blinding, and biological replicate distinction are not applicable. Inclusion and exclusion criteria are well-defined. A power analysis is not reported. Outlier handling is not mentioned. The study uses appropriate controls (lean and anorexic groups) and statistical methods (logistic regression, linear regression, Spearman correlation). Independent replication is not applicable for this single cross-sectional study.

Sub-criteria

controlsADEQUATE

power analysisNOT REPORTED

blinding levelsN/A

outlier handlingNOT REPORTED

randomization unitN/A

inclusion exclusionADEQUATE

randomization methodN/A

replicate distinctionN/A

independent replicationN/A

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 85% conf

The study design is observational and cross-sectional, with clear inclusion/exclusion criteria and appropriate statistical methods, but lacks a pre-specified power analysis and does not address outlier handling.

Evidence

direct quote[Methods, Patients section]

“The inclusion criteria were adults for whom the BMI value and a fecal sample were readily available. The exclusion criteria were patients <18 years of age, a history of colon cancer, the presence of an inflammatory bowel disease, an acute or a chronic diarrhea in the previous 4 weeks and an antibiotic administration <6 months before the fecal sampling.”

absence[Methods]

No power analysis is reported.

absence[Methods, Statistical analysis]

Outlier handling is not mentioned.

WARNReviewer 2· 85% conf

The study design lacks a priori power analysis and explicit outlier handling, but inclusion/exclusion criteria are well-defined.

Evidence

absence[Methods]

Power analysis not reported.

direct quote[Methods, Patients subsection]

absence[Methods, Statistical analysis]

Outlier handling not reported.

WARNReviewer 3· 85% conf

The study design is observational cross-sectional; inclusion/exclusion criteria and control group are adequate, but no power analysis or outlier handling is reported.

Evidence

direct quote[Methods, Patients section]

absence[Methods, Statistical analysis]

No power analysis is mentioned.

The study reports age, sex, and BMI for all participants, with a table showing these demographics per group. Health status is implied by the inclusion/exclusion criteria (e.g., no colon cancer, IBD, diarrhea). Race/ethnicity and comorbidities are not reported. Since this is a human study, species/strain/source and housing conditions are not applicable.

Sub-criteria

demographicsINADEQUATE

sex reportedADEQUATE

sex justifiedN/A

age weight healthADEQUATE

housing conditionsN/A

species strain sourceN/A

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 90% conf

The study adequately reports key biological variables for human subjects, including age, sex, and BMI, but does not report race/ethnicity or comorbidities.

Evidence

direct quote[Table 1]

“Age (mean±s.d.) 27.3±10.8 ... Male sex (n (%)) 1 (7%) ... BMI (median, IQR) 13.5 (11.7–14.6)”

absence[Methods, Patients section]

Race/ethnicity and comorbidities are not reported.

PASSReviewer 2· 90% conf

Sex, age, and BMI are reported, but demographics are limited to age and sex (no race/ethnicity or comorbidities).

Evidence

direct quote[Results, paragraph 1]

“138 (52.5%) of them were males.”

direct quote[Results, paragraph 1 and Table 1]

“The average age was 50±s.d. 17 years.”

paraphrase[Methods, Patients subsection]

“Clinical data recorded includes gender, date of birth, clinical history, weight, height, and antibiotic use, but no race/ethnicity is mentioned.”

PASSReviewer 3· 90% conf

Sex, age, and BMI are reported for all groups; both sexes are included so sex justification is not applicable; demographics are partially reported missing ethnicity.

Evidence

paraphrase[Table 1]

“Table 1 lists age (mean±SD), male sex n (%), and BMI (median IQR) for anorexic, lean, overweight, and obese groups.”

direct quote[Methods, Patients section]

“Other factors, such as yogurt (pro- and prebiotics) intake, vegetarian habits, ethnicity or familial obesity, were not taken into consideration”

The paper states it was approved by the local ethics committee with accession number 10-002. However, no information is provided about informed consent from participants or compliance with regulations such as the Declaration of Helsinki.

Sub-criteria

iacuc statementN/A

informed consentNOT REPORTED

irb ethics statementADEQUATE

regulatory complianceNOT REPORTED

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 90% conf

The study reports ethics approval from a named committee and implies informed consent, but the consent process is not explicitly described.

Evidence

direct quote[Methods, Patients section]

“This study was approved by the local ethics committee (accession number 10-002, 2010).”

absence[Methods]

Informed consent is not explicitly described.

WARNReviewer 2· 95% conf

Ethics approval is reported with a protocol number, but informed consent and regulatory compliance are not mentioned.

Evidence

direct quote[Methods, Patients subsection]

“This study was approved by the local ethics committee (accession number 10-002, 2010).”

absence[Methods]

Informed consent not reported.

absence[Methods]

Regulatory compliance not reported.

WARNReviewer 3· 85% conf

Ethics committee approval is documented with a number, but informed consent is not mentioned, and regulatory framework compliance is not stated.

Evidence

direct quote[Methods, Patients section]

“This study was approved by the local ethics committee (accession number 10-002, 2010).”

absence[Methods and entire text]

No informed consent statement is present.

The paper provides primer and probe sequences for E. coli and mentions primers for L. reuteri from a previous study. It does not provide vendor or catalog numbers for these primers/probes. The software used (SPSS, R, XLSTAT) is identified with versions. No antibodies, cell lines, or organisms (beyond human subjects) are used, so those criteria are not applicable. The study does not mention mycoplasma testing.

Sub-criteria

mycoplasma testingN/A

reagents identifiedINADEQUATE

organisms identifiedN/A

antibodies identifiedN/A

cell line authenticationN/A

software tools identifiedADEQUATE

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 85% conf

The study identifies key reagents (primers, probes) and software, but does not provide full details on the source of the bacterial strains used for validation or catalog numbers for reagents.

Evidence

direct quote[Methods, PCR section]

“Forward, 5′-GCTGCGCGTGCAAATGCG-3′ Reverse, 5′-CATGGTCATCGCTTCGGTCT-3′ and probe, 5′-CATCAGAAACTGAACACCAC-3′.”

direct quote[Methods, Statistical analysis]

“The analyses were performed using the SPSS v20.0 (IBM, Paris, France), R version 2.14.0 (R-foundation, Vienna, Austria) and XLSTAT v12 (Addinsoft, Paris, France) software.”

WARNReviewer 2· 85% conf

Software tools are identified with versions, but PCR reagents are not fully specified (no vendor or catalog numbers).

Evidence

direct quote[Methods, PCR subsection]

“Forward, 5′-GCTGCGCGTGCAAATGCG-3′ Reverse, 5′-CATGGTCATCGCTTCGGTCT-3′ and probe, 5′-CATCAGAAACTGAACACCAC-3′.”

direct quote[Methods, Statistical analysis]

“SPSS v20.0 (IBM, Paris, France), R version 2.14.0 (R-foundation, Vienna, Austria) and XLSTAT v12 (Addinsoft, Paris, France).”

WARNReviewer 3· 80% conf

Software tools are well identified with versions, but PCR primer sequences for most species are not provided in full, relying on references to previous work.

Evidence

direct quote[Methods, Statistical analysis]

“The analyses were performed using the SPSS v20.0 (IBM, Paris, France), R version 2.14.0 (R-foundation, Vienna, Austria) and XLSTAT v12 (Addinsoft, Paris, France) software.”

direct quote[Methods, PCR section]

“PCR analysis was performed as previously described except for E. coli, for which the protocol was the same, but the primers and probes were the following: Forward, 5′-GCTGCGCGTGCAAATGCG-3′ Reverse, 5′-CATGGTCATCGCTTCGGTCT-3′ and probe, 5′-CATCAGAAACTGAACACCAC-3′.”

The paper names all statistical tests used (Pearson Chi-square, Barnard exact test, Kruskal-Wallis, Spearman correlation, logistic regression, linear regression). Exact p-values and 95% confidence intervals are reported for key results. The software is identified. Data presentation includes scatter plots and tables with per-group n. Test assumptions (e.g., normality for linear regression) are not explicitly verified, but the use of non-parametric tests (Kruskal-Wallis, Spearman) addresses some concerns. Mathematical plausibility checks are not applicable for continuous data with large N.

Sub-criteria

tests namedADEQUATE

exact p valuesADEQUATE

effect sizes ciADEQUATE

data presentationADEQUATE

software identifiedADEQUATE

assumptions verifiedINADEQUATE

mathematical plausibilityN/A

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 90% conf

The statistical analysis is well-described, with named tests, exact p-values, and effect sizes with confidence intervals, but test assumptions are not explicitly verified.

Evidence

direct quote[Results, L. reuteri section]

“L. reuteri was associated with obesity (odds ratio (OR)=5.31; 95% confidence interval (CI) 1.04–27.1; P =0.04)”

absence[Methods, Statistical analysis]

Test assumptions are not explicitly verified.

PASSReviewer 2· 90% conf

Statistical tests are named, exact p-values and effect sizes with CIs are reported, software is identified, and data presentation is adequate. Assumptions are partially addressed.

Evidence

direct quote[Methods, Statistical analysis]

“bilateral Pearson Chi-square test... bilateral Barnard exact test... Kruskal–Wallis test... Spearman method... linear regression.”

direct quote[Results, various]

“coefficient=0.85; 95% confidence interval (CI) 0.12–1.58; P =0.02”

direct quote[Methods, Statistical analysis]

“Because of a generally non-Gaussian distribution, comparisons were performed using the Kruskal–Wallis test.”

WARNReviewer 3· 85% conf

Statistical tests are appropriately named and many exact p-values are reported, but assumptions are not verified, effect sizes lack CIs for some analyses, data presentation does not show individual points, and a sex percentage in Table 1 is arithmetically implausible.

Evidence

direct quote[Methods, Statistical analysis]

“comparisons were performed using the Kruskal–Wallis test... the correlation was tested using the Spearman method... Linear regression was used to identify bacteria whose concentrations were correlated with BMI”

direct quote[Results sections and abstract]

“coefficient=0.85; 95% confidence interval (CI) 0.12–0.58; P =0.02”

direct quote[Table 1]

“Lean subjects (n=76) ... Male sex 40 (57%)”

No data availability statement is present. The paper does not mention depositing raw data (e.g., qPCR data) in any public repository. No accession numbers are provided. Custom code is not mentioned or shared. This is a clear failure for a study that generated new experimental data.

Sub-criteria

code sharingNOT REPORTED

accession numbersNOT REPORTED

repository depositNOT REPORTED

data availability statementNOT REPORTED

Per reviewer (3) — the votes behind the verdict

FAILReviewer 1· 95% conf

The paper does not provide a data availability statement, repository deposit, accession numbers, or code sharing, which is a significant gap for a study generating new data.

Evidence

absence[Entire paper]

No data availability statement is present.

absence[Entire paper]

No repository deposit or accession numbers are mentioned.

FAILReviewer 2· 95% conf

No data availability statement is provided, and no data or code are deposited in a repository.

Evidence

absence[Entire paper]

No data availability statement.

FAILReviewer 3· 95% conf

No data availability statement is provided; no repository deposit, accession numbers, or code sharing are mentioned.

Evidence

absence[Entire text]

No data availability statement is present in the paper.

absence[Methods and Results]

No repository or accession numbers are mentioned.

The methods section provides sufficient detail for replication. All measured bacterial taxa are reported, including non-significant results. Limitations are discussed, and the conclusions are appropriately cautious. A conflict of interest statement is provided. However, no reporting guideline (e.g., STROBE) is mentioned.

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 has adequate methods, discusses limitations, and has proportional conclusions, but lacks a reporting guideline checklist and does not register the study (not required for observational studies).

Evidence

direct quote[Discussion, paragraph 3]

“A limitation of our study, as it is for most studies, is that the analysis of the digestive microbiota associated with obesity was performed by analyzing stool samples.”

absence[Methods]

No reporting guideline is mentioned.

direct quote[Acknowledgments and Author contributions]

“The authors declare no conflict of interest.”

PASSReviewer 2· 90% conf

Methods are detailed, all outcomes are reported, limitations are discussed, conclusions are proportional, and funding/COI is stated. No reporting guideline is referenced.

Evidence

direct quote[Methods, PCR subsection]

“PCR analysis was performed as previously described except for E. coli, for which the protocol was the same, but the primers and probes were the following:”

direct quote[Results, Bacterial clades associated with obesity]

“L. acidophilus was not detected by our system in any sample, despite the positive amplification of the type strain L. acidophilus CIP7613 in our in silico study.”

direct quote[Discussion, paragraph 2]

“A limitation of our study, as it is for most studies, is that the analysis of the digestive microbiota associated with obesity was performed by analyzing stool samples.”

PASSReviewer 3· 85% conf

Methods are sufficiently detailed, all pre-specified outcomes are reported, limitations are discussed, and conclusions are proportional; however, no reporting guideline is referenced and funding details are imprecise.

Evidence

direct quote[Discussion, paragraph 2]

“A limitation of our study, as it is for most studies, is that the analysis of the digestive microbiota associated with obesity was performed by analyzing stool samples.”

direct quote[Results, paragraph 2]

“L. acidophilus was not detected by our system in any sample”

absence[Methods section]

No reporting guideline is mentioned.

8 copyedit issues flagged (3 major): mostly consistency, clarity, grammar.

Checked 39 references: 37 verified — 1 retracted, 1 unresolved.

Αlpha¹ Rigor Action ItemsFinal pass before journal submission

This published paper has serious reporting gaps. An informed reader should weigh: (1) the absence of any data availability statement—raw data cannot be inspected; (2) the arithmetic inconsistency in Table 1 (lean group percentage), which may indicate a counting error; (3) the retracted citation (Million et al. 2012 IJO) that should have been flagged; and (4) overstated conclusions (e.g., 'specificity of the obese microbiota') that go beyond the correlational evidence. An erratum or correction is warranted to address the Table 1 inconsistency, retracted citation, and the missing data availability and ethics consent statements. A re-analysis by independent researchers would strengthen confidence.

1.
HIGHdata code
Add a data availability statement (e.g., 'The raw qPCR data and de-identified participant data are available from the corresponding author upon reasonable request') and deposit the anonymized data in a public repository (Figshare, Zenodo, etc.) with a DOI.
Without a data availability statement or repository deposit, the study's findings cannot be independently verified or re-used, a major reproducibility gap.
2.
HIGHethics
Add an informed consent statement (e.g., 'Written informed consent was obtained from all participants') and a regulatory compliance statement (e.g., 'conducted in accordance with the Declaration of Helsinki') to the Methods section.
Human subjects research requires documented informed consent and regulatory compliance for ethical and journal requirements.
3.
HIGHother
Correct the arithmetic inconsistency in Table 1: the lean group male sex should be 52.6% (53%), not 57% (40/76).
An internal numerical inconsistency undermines confidence in the data integrity and requires an erratum.
4.
HIGHreporting
Remove or replace the retracted reference (Million et al. 2012, IJO, doi:10.1038/ijo.2011.153) with a current, non-retracted source, and check the reference 'New Test for 2×2 Tables' that could not be located in any registry.
Citing a retracted paper spreads invalidated findings; a reference that cannot be found suggests possible fabrication or an unrecoverable citation error.
5.
HIGHstatistics
Correct the confidence interval in the Abstract for the L. reuteri linear regression coefficient: change '0.12–0.58' to '0.12–1.58' to match Table 2.
The current abstract CI does not contain the reported coefficient (0.85) and is numerically impossible; this is a transcription error that must be fixed.
6.
HIGHreporting
Temper the claim that 'the findings confirm the specificity of the obese microbiota' to acknowledge that the study shows correlations, not defining characteristics.
The term 'specificity' implies a unique or defining feature, which is not supported by correlational data and is overstated per the claim audit.
7.
HIGHreporting
Separate the claims for B. animalis (P=0.03, significant) and M. smithii (P=0.08, not significant) rather than stating both are 'negatively associated with BMI'.
Grouping a non-significant result with a significant one overstates the evidence for M. smithii.
8.
HIGHstatistics
Verify the male sex n and calculate percentages correctly for all groups in Table 1; re-check underlying counts for any other numerical errors.
The detected arithmetic error raises the possibility of other data-handling mistakes that should be ruled out.
9.
MEDIUMreporting
Add a statement that the study adheres to the STROBE reporting guideline for cross-sectional studies in the Methods section.
Adherence to STROBE is standard for observational research and improves completeness and reproducibility.
10.
MEDIUMrigor
Report an a priori power analysis or sample size justification, or at least acknowledge the lack of one as a limitation in the Discussion.
Without a power analysis, readers cannot assess whether the study had sufficient statistical power to detect its hypothesized effects.
11.
MEDIUMstatistics
Describe how outliers in the bacterial concentration data were handled (e.g., Winsorization, exclusion, none) in the Statistical analysis section.
The absence of outlier handling raises concern that undetected extreme values may have influenced results.
12.
MEDIUMreporting
Provide full primer/probe sequences for all targeted species (L. reuteri, M. smithii, B. animalis, etc.) in a supplementary table, rather than only referencing earlier publications.
Relying on references for key reagents makes reproduction more difficult if those articles are behind paywalls or have errors.
13.
MEDIUMreporting
Report vendor names and catalog numbers for all PCR reagents (primers, probes, master mix) in the Methods section.
Full reagent identification is required for reproducibility per most journal guidelines.
14.
LOWcopyedit
Add a serial comma before 'and' in lists (e.g., 'Lactobacillus reuteri, Bifidobacterium animalis, Methanobrevibacter smithii, and Escherichia coli').
Consistent serial comma usage improves clarity and follows many journal style guides.
15.
LOWcopyedit
Change 'bilateral' to 'two-sided' when describing statistical tests in the Methods.
'Two-sided' is the standard term in statistical reporting; 'bilateral' is less common and may cause confusion.

Full text (33,966 chars)Analyzed: Jul 6, 2026

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