Microbial Community Ecology and Physiology

Soil bacterial community diversity and composition vary more with elevation than seasons in alpine habitats of western Himalaya

The paper examines soil bacterial community diversity and composition across elevation and seasons in western Himalayan alpine habitats, finding greater variation with elevation than seasons.

Detection of stress functional responses in bacterial populations under dry soil conditions show potential microbial mechanisms to resist drought conditions

Impacts of Desulfobacterales and Chromatiales on sulfate reduction in the subtropical mangrove ecosystem as revealed by SMDB analysis

The paper constructs a sulfur metabolism database (SMDB) to analyze sulfate reduction in subtropical mangroves, identifying Desulfobacterales and Chromatiales as key taxa involved.

Leave no stone unturned: The hidden potential of carbon and nitrogen cycling by novel, highly adapted Thaumarchaeota in the Atacama Desert hyperarid core

The paper identifies a novel Thaumarchaeota genus in the Atacama Desert hyperarid core, revealing its role in carbon and nitrogen cycling through genomic analysis.

Taxonomically and metabolically distinct microbial communities with depth and across a hillslope to riparian zone transect

The paper investigates microbial community structure and metabolic potential along a hillslope to riparian zone transect using genome-resolved metagenomics and stable isotopes, finding distinct communities and functions across depth and landscape position.

Tax4Fun2: a R-based tool for the rapid prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene marker gene sequences

Tax4Fun2 predicts habitat-specific functional profiles and redundancy from 16S rRNA gene sequences using user-defined genomic information.

Revealing ecologically coherent population structure of uncultivated bacterioplankton with POGENOM

POGENOM quantifies population genomic indices from metagenome data, revealing environmental correlates of genomic variation in bacterioplankton across spatial and temporal scales.

Metagenomic analysis suggests broad metabolic potential in extracellular symbionts of the bivalve Thyasira cf. gouldi

This study presents the first metagenomic analysis of a bivalve symbiont, revealing its broad metabolic potential and genomic features.

Metabolic complementarity between a brown alga and associated cultivable bacteria provide indications of beneficial interactions

The paper identifies metabolic complementarities between a brown alga and its associated bacteria, showing that selected bacterial consortia enhance algal growth and metabolite exchange.

Rapid, inexpensive measurement of synthetic bacterial community composition by Sanger sequencing

The paper introduces a method using Sanger sequencing to rapidly and cheaply measure synthetic bacterial community composition, achieving accurate results in under a day for ~$5 per sample.

Ecotype Simulation 2: An improved algorithm for efficiently demarcating microbial species from large sequence datasets

Ecotype Simulation 2 improves the analysis of large sequence datasets to identify ecologically distinct microbial species more efficiently.

Short-range interactions govern cellular dynamics in microbial multi-genotype systems

The paper measures spatial interaction networks in microbial communities and finds that short-range interactions significantly impact system function and metabolic processes.

Pangenomics reveal diversification of enzyme families and niche specialization in globally abundant SAR202 bacteria

The paper analyzes SAR202 bacterial genomes to show paralog expansions correlate with metabolic specialization and niche adaptation across ocean depths and regions.

Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples

Machine learning to predict microbial community functions: An analysis of dissolved organic carbon from litter decomposition.

The paper develops a machine learning tool to predict dissolved organic carbon from soil microbiome data and finds that it performs comparably to traditional methods.

A New Method to Correct for Habitat Filtering in Microbial Correlation Networks

The paper introduces an algorithm to correct habitat filtering in microbial correlation networks, improving accuracy on simulated and real data.

Rarity of microbial species: In search of reliable associations

The paper investigates how rare microbial species affect the reliability of association tests in microbiota data and suggests dataset trimming to improve inference.

Machine learning reveals missing edges and putative interaction mechanisms in microbial ecosystem networks

The paper uses machine learning to infer missing edges and interaction mechanisms in microbial networks using trait-level data.

Alpha diversity metrics for noisy OTUs

This paper introduces two new alpha diversity estimators for OTU tables generated from NGS data, showing they are effective under limited conditions but face practical challenges.

TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution

TaxAss improves fine-resolution taxonomic classification of freshwater microbial communities by combining a comprehensive database with an ecosystem-specific database.

Octave plots for visualizing diversity of microbial OTUs

This paper introduces octave plots to visualize microbial OTU abundance distributions, revealing insights into diversity metrics and experimental artifacts.

ampvis2: an R package to analyse and visualise 16S rRNA amplicon data

ampvis2 unifies 16S amplicon count tables, taxonomy, and sample metadata in one R object, feeding ggplot2 heatmaps at any taxonomic rank and single-call ordination (seven methods).

Methods in Description and Validation of Local Metagenetic Microbial Communities

The paper compares MinHash and NMF methods for metagenetic sample similarity and evaluates clustering quality using ecological metadata.

HTSSIP: an R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments

The paper introduces HTSSIP, an R package for analyzing HTS-SIP data, addressing the lack of accessible and well-documented tools for this task.

DirtyGenes: significance testing for gene or bacterial population composition changes using the Dirichlet distribution

DirtyGenes tests the significance of changes in bacterial populations or gene composition using the Dirichlet distribution, applied to microbiome data from environmental and animal samples.

A new multi-genomic approach for the study of biogeochemical cycles at global scale: the molecular reconstruction of the sulfur cycle

The paper introduces a method to analyze the sulfur cycle using genomic data, producing a sulfur score that classifies microorganisms and identifies key environments.

UNBIAS: An attempt to correct abundance bias in 16S sequencing, with limited success

16S amplicon read frequencies correlate poorly with true microbial species abundances, and the UNBIAS correction method for copy number and primer mismatches yields only modest improvements when reference identity drops.