Human and General Microbiome

Review: Exploring the Influence of Gut Microbiome on Energy Metabolism in Humans – Julia Montenegro – Advances in Nutrition

Review: Ruminococcus gnavus: friend or foe for human health – Emmanuelle H Crost – FEMS Microbiology Reviews

Uncovering the special microbiota associated with occurrence and progression of gastric cancer by using RNA-sequencing – Bin Ai – Scientific Reports

Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism – Xiangwei Hu – NPJ Biofilms and Microbiomes

The secondary bile acid isoursodeoxycholate correlates with post-prandial lipemia, inflammation, and appetite and changes post-bariatric surgery – Panayiotis Louca – Cell Reports. Medicine

Forging the microbiome to help us live long and prosper – Rachel R Rock – PLoS Biology

Meta-analysis reveals Helicobacter pylori mutual exclusivity and reproducible gastric microbiome alterations during gastric carcinoma progression – Yan Li – Gut Microbes

Beneficial Microbes and Compounds

Lacticaseibacillus rhamnosus Probio-M9 enhanced the antitumor response to anti-PD-1 therapy by modulating intestinal metabolites – Guangqi Gao – EBioMedicine

Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems – Samuel Zimmerman – mSystems

New carbohydrate binding domains identified by phage display based functional metagenomic screens of human gut microbiota – Akil Akhtar – Communications Biology

Animal Microbiome

Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community – Jacob Agerbo Rasmussen – Microbiological Research

Plant Microbiome

Cofunctioning of bacterial exometabolites drives root microbiota establishment – Felix Getzke – PNAS

Environmental Microbiome

Review: Unveiling the role of emerging metagenomics for the examination of hypersaline environments – Kiran Dindhoria – Biotechnology & Genetic Engineering Reviews

Microbiome Analysis: Protocols, Resources, Tools and Techniques

Multi-scale Adaptive Differential Abundance Analysis in Microbial Compositional Data – Shulei Wang – Bioinformatics

The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection – Ruijie Xu – PloS ONE

An in vitro platform for study of the human gut microbiome under an oxygen gradient – James Comolli – Biomedical Microdevices

Machine learning model to predict obesity using gut metabolite and brain microstructure data – Vadim Osadchiy – Scientific Reports

Human and General Microbiome

Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection – Jiarui Li – Microbiome

Population-level impacts of antibiotic usage on the human gut microbiome – Kihyun Lee – Nature Communications

A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem – Toshihiko Katoh – Nature Chemical Biology

Microbiota-derived genotoxin tilimycin generates colonic stem cell mutations – Lisa Pöltl – Cell Reports

Review: Impact of caloric restriction on the gut microbiota – Lara Kern – Current Opinion in Microbiology

Animal Microbiome

Romboutsia lituseburensis JCM1404 supplementation ameliorated endothelial function via gut microbiota modulation and lipid metabolisms alterations in obese rats – Honggang Yin – FEMS Microbiology Letters

Disparate population and holobiont structure of pocilloporid corals across the Red Sea gradient demonstrate species-specific evolutionary trajectories – Carol Buitrago-López – Molecular Ecology

Omics and imaging combinatorial approach reveals butyrate-induced inflammatory effects in the zebrafish gut – Adrià López Nadal – Animal Microbiome

Gut microbiome is linked to functions of peripheral immune cells in transition cows during excessive lipolysis – Fengfei Gu – Microbiome

Maternal effects drive intestinal development beginning in the embryonic period on the basis of maternal immune and microbial transfer in chickens – Haizhou Gong – Microbiome

Mouse mammary tumor virus is implicated in severity of colitis and dysbiosis in the IL-10(-/-) mouse model of inflammatory bowel disease – Heather Armstrong – Microbiome

Microplastics affect arsenic bioavailability by altering gut microbiota and metabolites in a mouse model – Shan Chen – Environmental Pollution 

Substantial viral and bacterial diversity at the bat-tick interface – Ayda Susana Ortiz-Baez – Microbial Genomics

Review: Perturbation of maternal gut microbiota in mice during a critical perinatal window influences early neurobehavioral outcomes in offspring – Cassandre Morel – Neuropharmacology

Plant and Soil Microbiome

Local environment drives rapid shifts in composition and phylogenetic clustering of seagrass microbiomes – Melissa R Kardish – Scientific Reports

Experimental community coalescence sheds light on microbial interactions in soil and restores impaired functions – Sarah Huet – Microbiome

Microbiome Analysis: Tools and Techniques

Infants’ gut microbiome data: A Bayesian Marginal Zero-inflated Negative Binomial regression model for multivariate analyses of count data – Morteza Hajihosseini – Computational and Structural Biotechnology Journal

From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools – Robyn J Wright – Microbial Genomics

Using strain-resolved analysis to identify contamination in metagenomics data – Yue Clare Lou – Microbiome

Preprint: Transkingdom Network Analysis (TkNA): a systems approach inferring causal factors underlying host-microbiota interactions – Nolan K Newman – bioRxiv

Highlights!

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 – Aitor Blanco-Míguez – Nature Biotechnology

Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease – Raaj S Mehta – Nature Medicine

Human and General Microbiome

Interpersonal variability of the human gut virome confounds disease signal detection in IBD – Stephen R Stockdale – Communications Biology

Clinical characteristics, diagnosis, outcomes and lung microbiome analysis of invasive pulmonary aspergillosis in the community-acquired pneumonia patients – Zhi Ao – BMJ Open Respiratory Research

Comparing the gut microbiome of obese, African American, older adults with and without mild cognitive impairment – Andrew McLeod – PloS One

Beneficial Microbes and Compounds

Capacity of a Microbial Synbiotic To Rescue the In Vitro Metabolic Activity of the Gut Microbiome following Perturbation with Alcohol or Antibiotics – Braden T Tierney – Applied and Environmental Microbiology

Animal Microbiome

A microbiota and dietary metabolite integrates DNA repair and cell death to regulate embryo viability and aneuploidy during aging – Robert Sonowal – Science Advances

A longitudinal survey in the wild reveals major shifts in fish host microbiota after parasite infection – Eglantine Mathieu-Bégné – Molecular Ecology

Matrine alleviates depressive-like behaviors via modulating microbiota-gut-brain axis in CUMS-induced mice – Ming Zhang – Journal of Translational Medicine

Variations in gut microbiome and metabolites of dogs with acute diarrhea in poodles and Labrador retrievers – Huasong Bai – Archives of Microbiology

Environmental Microbiome

Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes – Ramona Marasco – Nature Communications

Microbiome Analysis: Tools and Techniques

Review: Computational methods and challenges in analyzing intratumoral microbiome data – Qi Wang – Trends in Microbiology

Robust Bioinformatics Approaches Result in the First Polygenic Risk Score for BMI in Greek Adults – Maria Kafyra – Journal of Personalized Medicine

Development of a tongue image-based machine learning tool for the diagnosis of gastric cancer: a prospective multicentre clinical cohort study – Li Yuan – EClinicalMedicine

Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework – Elie-Julien El Hachem – BMC Bioinformatics

Human and General Microbiome

Review: Controlling the human microbiome – Yang-Yu Liu – Cell Systems

Review: Metabolic models of human gut microbiota: Advances and challenges – Daniel Rios Garza – Cell Systems

The fecal microbiotas of women of Pacific and New Zealand European ethnicities are characterized by distinctive enterotypes that reflect dietary intakes and fecal water content – Nikki Renall – Gut Microbes

Identifying the Novel Gut Microbial Metabolite Contributing to Metabolic Syndrome in Children Based on Integrative Analyses of Microbiome-Metabolome Signatures – Jia Wei – Microbiology Spectrum

Gut Microbiome and Risk of Ischemic Stroke: A Comprehensive Mendelian Randomization Study – Changjiang Meng – European Journal of Preventive Cardiology

Ancient Microbiome

Metagenomic analysis of Ancient Egyptian canopic jars – Enrique Rayo – American Journal of Biological Anthropology

Animal Model Microbiome

Preprint: Vaginal microbial dynamics and pathogen colonization in a humanized microbiota mouse model – Marlyd E Mejia – bioRxiv

Plant Microbiome

Multidisciplinary evaluation of plant growth promoting rhizobacteria on soil microbiome and strawberry quality – Jun Haeng Nam – AMB Express

Environmental Microbiome

Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks – B L D Uthpala Pushpakumara – Scientific Reports

Microbiome Analysis and Techniques

gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota – Victòria Pascal Andreu – Nature Biotechnology

Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach – Andreas Hiergeist – PloS One

Preprint: Impact of experimental bias on compositional analysis of microbiome data – Yingtian Hu – bioRxiv