P. D. Schloss

Waste not, want not: Revisiting the analysis that called into question the practice of rarefaction

The paper reanalyzes McMurdie and Holmes' 2014 study on rarefaction in microbiome data, showing that rarefaction is more robust for controlling sequencing depth than previously claimed.

Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses

This paper evaluates methods for controlling uneven sequencing effort in amplicon sequencing and finds rarefaction is the most robust approach for accurate diversity metric analysis.

Machine learning classification by fitting amplicon sequences to existing OTUs

The paper evaluates OptiFit, a method to fit new sequences to existing OTUs, finding it performs as well or better than de novo and database-reference-based clustering in classifying colonic screen relevant neoplasia.

Simplified fecal community transplant restores Clostridioides difficile colonization resistance to antibiotic perturbed murine communities

This study shows that a simplified fecal community transplant can restore colonization resistance to antibiotic-perturbed murine gut communities, preventing Clostridioides difficile colonization depending on the community structure.

Intestinal inflammation reversibly alters the microbiota to drive susceptibility to Clostridioides difficile colonization in a mouse model of colitis

This study shows that intestinal inflammation in a mouse model alters microbiota composition, increasing susceptibility to C. difficile colonization, and that reducing inflammation restores colonization resistance.

The gut bacterial community potentiates Clostridioides difficile infection severity

This study shows that gut bacterial communities influence the severity of Clostridioides difficile infections in mice, with certain bacterial groups linked to more or less severe outcomes.

OptiFit: an improved method for fitting amplicon sequences to existing OTUs

OptiFit improves OTU assignment by considering all reference-query sequence pairs, achieving quality similar to de novo methods while maintaining consistency across datasets.

A Goldilocks Principle for the Gut Microbiome: Taxonomic Resolution Matters for Microbiome-Based Classification of Colorectal Cancer

This study finds that optimal taxonomic resolution for microbiome-based colorectal cancer classification is at the family level, with performance decreasing at finer resolutions like ASVs.

An osmotic laxative renders mice susceptible to prolonged Clostridioides difficile colonization and hinders clearance

This study shows that PEG laxative treatment in mice increases susceptibility to C. difficile colonization and delays clearance.

Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research

The paper develops a two-day workshop curriculum for teaching reproducible research using R, Unix, git, and GitHub, addressing content overload and integration challenges in existing curricula.

Protection from lethal Clostridioides difficile infection via intraspecies competition for co-germinant

This study shows pre-colonization with a less virulent C. difficile strain reduces germination of a lethal strain by limiting glycine availability, offering a mechanism for protective intraspecies competition.

Amplicon sequence variants artificially split bacterial genomes into separate clusters

This study shows that ASVs can split a single bacterial genome into multiple clusters, highlighting the risk of over-splitting in microbial community analysis.

Removal of rare amplicon sequence variants from 16S rRNA gene sequence surveys biases the interpretation of community structure data

This paper shows that removing rare ASVs from 16S rRNA gene data distorts community structure analysis and reduces statistical power to detect true differences.

Clearance of Clostridioides difficile colonization is associated with antibiotic-specific bacterial changes

The paper investigates how different antibiotic treatments affect the gut microbiota's ability to clear C. difficile colonization, finding antibiotic-specific community changes associated with clearance.

The initial gut microbiota and response to antibiotic perturbation influence Clostridioides difficile colonization in mice

This study shows that initial gut microbiota composition and response to antibiotic perturbation affect C. difficile colonization in mice from different sources.

A framework for effective application of machine learning to microbiome-based classification problems

This paper evaluates ML models for predicting colonic neoplasias using 16S rRNA data, finding that L2-regularized logistic regression offers a balance of performance, speed, and interpretability.

The proton pump inhibitor omeprazole does not promote Clostridioides difficile colonization in a murine model

This study shows omeprazole does not promote C. difficile colonization in mice, even when combined with clindamycin, suggesting it does not disrupt microbiota resistance to CDI.

Fecal short-chain fatty acids are not predictive of colonic tumor status and cannot be predicted based on bacterial community structure

This study finds that fecal SCFA concentrations are not associated with colonic tumor status and cannot be predicted from bacterial community structure.

The impact of DNA polymerase and number of rounds of amplification in PCR on 16S rRNA gene sequence data

This study evaluates how DNA polymerase fidelity and PCR amplification rounds affect 16S rRNA gene sequencing data quality in mock communities and human stool samples.

The Diagnostic Potential & Interactive Dynamics of the Colorectal Cancer Virome

The paper examines the colorectal cancer virome and identifies differences in virome composition between healthy and cancerous samples, suggesting a potential role for bacteriophages in cancer progression.

Nonsteroidal anti-inflammatory drugs alter the microbiota and exacerbate Clostridium difficile colitis while dysregulating the inflammatory response

This study shows NSAIDs like indomethacin alter gut microbiota and worsen C. difficile colitis by disrupting PG metabolism, epithelial integrity, and immune responses in mice.

Clostridium difficile alters the structure and metabolism of distinct cecal microbiomes during initial infection to promote sustained colonization

This study shows that C. difficile infection alters gut microbiome structure and metabolism in mice pretreated with specific antibiotics, promoting persistent colonization.

Leveraging Existing 16S rRNA Gene Surveys to Identify Reproducible Biomarkers in Individuals with Colorectal Tumors

This paper identifies 8 bacterial taxa associated with colorectal carcinoma using meta-analysis of 16S rRNA gene data and validates them with Random Forest classification models.

Biogeography & environmental conditions shape bacteriophage-bacteria networks across the human microbiome

This study uses network analysis to show how environmental factors shape phage-bacteria interactions across different human body sites and cohorts.

Spatial variation of the native colon microbiota in healthy adults

The paper profiles the microbiota of the healthy colon to identify spatial variations between proximal and distal regions using 16S rRNA gene sequencing and classification models.

Normalization of the microbiota in patients after treatment for colonic lesions

This study examines microbiota changes in patients after treatment for colonic lesions, finding significant normalization in carcinomas but not adenomas or advanced adenomas.

Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut microbiomes

This study shows C. difficile adapts its metabolism to different gut environments caused by antibiotic pretreatment, preferring nitrogen-containing carbon sources and host-derived glycans.

Preprinting Microbiology

This paper discusses the role of preprints in microbiology, highlighting their potential to accelerate knowledge dissemination and enhance peer review.

OptiClust: Improved method for assigning amplicon-based sequence data to operational taxonomic units

OptiClust improves OTU assignment by optimizing MCC, achieving higher accuracy and speed compared to existing methods.