April 19, 2023

Pregnancy and early life

[REVIEW]The maternal gut microbiome during pregnancy and its role in maternal and infant health – Sinha et al. – Current Opinion in Microbiology

Human oral microbiome

Independent Effects of HIV and Antiretroviral Therapy on the Oral Microbiome Identified by Multivariate Analyses – Beall et al. – mBio

[REVIEW]Oral microbial changes and oral disease management before and after the treatment of hematological malignancies: a narrative review – Lin et al. – Clinical Oral Investigations

Human vaginal microbiome

[REVIEW]Gardnerella Revisited: Species Heterogeneity, Virulence Factors, Mucosal Immune Responses, and Contributions to Bacterial Vaginosis – Shvartsman et al. – Infection and Immunity

Human gut microbiome/virome

[REVIEW]Intrahost evolution of the gut microbiota – Barreta & Gordo – Nature Reviews Microbiology

The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice – Fan et al. – Nature Microbiology

Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori – Wang et al. – Nature Communications

Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem – Spatz et al. – Microbiome

Metabolic independence drives gut microbial colonization and resilience in health and disease – Watson et al. – Microbiome

Development of the gut microbiota in the first 14 years of life and its relations to internalizing and externalizing difficulties and social anxiety during puberty – Ou et al. – European Child & Adolescent Psychiatry

Reconstructing the landscape of gut microbial species across 29,000 diverse individuals – Segota et al. – NAR

Microbiomic profiles of bile in patients with benign and malignant pancreaticobiliary disease – Poudel et al. – PLOS One

Seasonal variations in gut microbiota and disease course in patients with inflammatory bowel disease – Tani et al. – PLOS One

The convergent application of metabolites from Avena sativa and gut microbiota to ameliorate non-alcoholic fatty liver disease: a network pharmacology study – Oh et al. – Journal of Translational Medicine volume

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Effects of Extended Cage Component Sanitation Interval on the Microenvironment, Health, and Gastrointestinal Microbiome of Rats (Rattus norvegicus) – Taylor et al. – Journal of the American Association for Laboratory Animal Science

Music-based interventions in the feeding environment on the gut microbiota of mice – Niu et al. – Scientific Reports

Animal microbiome (for animals in the wild)

Characterisation of the koala (Phascolarctos cinereus) pouch microbiota in a captive population reveals a dysbiotic compositional profile associated with neonatal mortality – Maidment et al. – Microbiome

[PREPRINT]Microbiome variability of mosquito lines is consistent over time and across environments – Accoti et al. – bioRxiv

Differences in the luminal and mucosal gut microbiomes and metabolomes of oriental rat snake (Ptyas mucosus) – Wei et al. – Applied Microbiology and Biotechnology


Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes – Bazant et al. – Microbiome


Functional gene-guided enrichment plus in situ microsphere cultivation enables isolation of new crucial ureolytic bacteria from the rumen of cattle – Liu et al. – Microbiome

April 17, 2023

Human and General Microbiome

Large-scale phage cultivation for commensal human gut bacteria – Juntao Shen – Cell Host & Microbe

On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis – Felix M Key – Cell Host & Microbe

Staphylococcal diversity in atopic dermatitis from an individual to a global scale – Sara Saheb Kashaf – Cell Host & Microbe

A lncRNA from an inflammatory bowel disease risk locus maintains intestinal host-commensal homeostasis – Hongdi Ma – Cell Research

Coliphages of the human urinary microbiota – Elias Crum – PloS ONE

Children with autism show differences in the gut DNA virome compared to non-autistic children: a case control study – Aina Qu – BMC Pediatrics

Aerobic exercise training-induced alteration of gut microbiota composition affects endurance capacity – Masataka Uchida – The Journal of Physiology

Fusobacterium nucleatum aggravates rheumatoid arthritis through FadA-containing outer membrane vesicles – Mukeng Hong – Cell Host & Microbe

Review: Dental caries and their microbiomes in children: what do we do now? – Apoena Aguiar Ribeiro – Journal of Oral Microbiology

Review: Role of the Microbiome in Gut-Heart-Kidney Cross Talk – Griet Glorieux – Circulation Research

Review: Influence of Microbiota on Vaccine Effectiveness: Is the Microbiota the Key to Vaccine-induced Responses? – So-Hee Hong – Journal of Microbiology 

Review: Deciphering the quorum-sensing lexicon of the gut microbiota – Rita A Oliveira – Cell Host & Microbe

Review: The intratumoral microbiota: friend or foe? – Valentina Ferrari – Trends in Cancer

Review: Assembling symbiotic bacterial species into live therapeutic consortia that reconstitute microbiome functions – Rita A Oliveira – Cell Host & Microbe

Review: One population, multiple lifestyles: Commensalism and pathogenesis in the human mycobiome – Diana M Proctor – Cell Host & Microbe

Review: Cross-feeding in the gut microbiome: Ecology and mechanisms – Elizabeth J Culp – Cell Host & Microbe

Minireview: Networking between helminths, microbes, and mammals – P’ng Loke – Cell Host & Microbe

Commentary: The intratumoral microbiota: From microniches to single cells – Susan Bullman – Cell

Perspective: Designer bugs as cancer drugs? – Sairaj M Sajjath – Science

Animal Microbiome

Flagellar Genes Are Associated with the Colonization Persistence Phenotype of the Drosophila melanogaster Microbiota – Sarah J Morgan – Microbiology Spectrum

Integration host factor regulates colonization factors in the bee gut symbiont Frischella perrara – Konstantin Schmidt – eLife

Research Highlight: Urban bees reveal a city’s microbiome – Ashley York – Nature Reviews. Microbiology

Environmental Microbiome

Phyllosphere antibiotic resistome in a natural primary vegetation across a successional sequence after glacier retreat – Jian Li – Environment International

Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring – Shekhar Nagar – Applied Microbiology and Biotechnology

April 14, 2023

Today’s reading recommendation includes microbiome from sites with low anthropogenic impact, drinking water microbiome, and more.

If you have only a minute for reading then your must read is this amazing summary thread on how you should be careful with making assumptions ⬇️

See you at #MVIF next week!

Global resistome

Global trends in antimicrobial resistance on organic and conventional farms – Eldon Ager – bioRxiv

*Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance? – Uli Klümper – bioRxiv

Mother-to-infant microbiome

Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites – Debby Bogaert – Cell Host & Microbe

Human gut microbiome

The Local Tumor Microbiome Is Associated with Survival in Late-Stage Colorectal Cancer Patients – Justine W. Debelius – Microbiology Spectrum

Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy – Ruben Ladeira, Julien Tap, Muriel Derrien – Microbiome Research Reports

Water microbiome

The microbial dark matter and “wanted list” in worldwide wastewater treatment plants – Yulin Zhang – Microbiome

*Microbiome, resistome and mobilome of chlorine-free drinking water treatment systems – David Calderón-Franco – Water Research

Animal experiment

Probiotics of Lacticaseibacillus paracasei SD1 and Lacticaseibacillus rhamnosus SD11 attenuate inflammation and β-cell death in streptozotocin-induced type 1 diabetic mice – Jongdee Nopparat – PlosOne

Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem – Madeleine Spatz – Microbiome

*Experimental Factors Influence Diversity Metrics of the Gut Microbiome in Laboratory Mice – Rikeish R. Muralitharan – bioRxiv

Virome & phages

Expanding known viral diversity in the healthy infant gut – Shiraz A. Shah – Nature Microbiology

Large-scale phage cultivation for commensal human gut bacteria – Juntao Shen – Cell Host & Microbe


Reducing bias in microbiome research: Comparing methods from sample collection to sequencing – Jolanda Kool – Frontiers in Microbiology

In Vitro Modelling of Oral Microbial Invasion in the Human Colon – Lucie Etienne-Mesmin – Microbiology Spectrum


Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes – Wojtek Bazant – Microbiome

April 10, 2023

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

April 3, 2023

Human and General Microbiome

Review: Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome – Stephen R Stockdale – Current Opinion in Microbiology

No evidence for a common blood microbiome based on a population study of 9,770 healthy humans – Cedric C S Tan – Nature Microbiology

Genetic correlations between Alzheimer’s disease and gut microbiome genera – Davis Cammann – Scientific Reports

Limitations of using 16S rRNA microbiome sequencing to predict oral squamous cell carcinoma – Christopher Delaney – APMIS

Mendelian randomization analyses reveal causal relationships between the human microbiome and longevity – Xiaomin Liu – Scientific Reports

Genomics of Invasive Cutibacterium acnes Isolates from Deep-Seated Infections – Anna Both – Microbiology Spectrum

Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition – Kayla A Carter – mSystems

Review: Interspecies Interactions within the Host: the Social Network of Group B Streptococcus – Marlyd E Mejia – Infection and Immunity

Beneficial Microbes and Compounds

Review: Kefir as a therapeutic agent in clinical research: a scoping review – Milena Klippel Bessa – Nutrition Research Reviews

Interaction between β-glucans and gut microbiota: a comprehensive review – Reza Karimi – Critical Reviews in Food Science and Nutrition

Combination of vitamin D and probiotics inhibits chemically induced colorectal carcinogenesis in Wistar rats – Carolina S de Oliveira – Life Sciences

Animal Microbiome

Review: Recent advancements in coral health, microbiome interactions and climate change – Nizam Ashraf – The Science of the Total Environment

Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome – Line Jensen Ostenfeld – PloS One

Microbial Species-Area Relationships on the Skins of Amphibian Hosts – Fan Yang – Microbiology Spectrum

Intestinal microbiota of Nearctic-Neotropical migratory birds vary more over seasons and years than between host species – Heather R Skeen – Molecular Ecology

Food Microbiome

A unique case in which Kimoto-style fermentation was completed with Leuconostoc as the dominant genus without transitioning to Lactobacillus – Kohei Ito – Journal of Bioscience and Bioengineering

Built Environment

Holobiont Urbanism: sampling urban beehives reveals cities’ metagenomes – Elizabeth Hénaff – Environmental Microbiome

Microbiome Analysis: Protocols, Resources, Tools and Techniques

Contamination detection and microbiome exploration with GRIMER – Vitor C Piro – GigaScience

Annotation-free discovery of functional groups in microbial communities – Xiaoyu Shan – Nature Ecology & Evolution

ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis – Jinlong Ru – Gut Microbes

Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition – Line Roager – Microbiology Spectrum

Preprint: Identifying keystone species in microbial communities using deep learning – Xu-Wen Wang – bioRxiv

March 27, 2023

Human and General Microbiome

The genomic landscape of reference genomes of cultivated human gut bacteria – Xiaoqian Lin – Nature Communications

Inhibition of a Microbiota-derived Peptide Ameliorates Established Acute Lung Injury – Valeria Fridman D’Alessandro – The American Journal of Pathology

Eubiotic effect of rifaximin is associated with decreasing abdominal pain in symptomatic uncomplicated diverticular disease: results from an observational cohort study – Vladimir Ivashkin – BMC Gastroenterology

Mucin glycans drive oral microbial community composition and function – Chloe M Wu – NPJ Biofilms and Microbiomes

Changes in gut microbial community upon chronic kidney disease – Wu Liu – PloS One

A Pilot Study Exploring Temporal Development of Gut Microbiome/Metabolome in Breastfed Neonates during the First Week of Life – Imad Awan – Pediatric Gastroenterology, Hepatology & Nutrition

Realising respiratory microbiomic meta-analyses: time for a standardised framework – David Broderick – Microbiome

Vulvovaginal yeast infections during pregnancy and perinatal outcomes: systematic review and meta-analysis – Ranjana M S Gigi – BMC Women’s Health

Preprint: Hadza Prevotella Require Diet-derived Microbiota Accessible Carbohydrates to Persist in Mice – Rebecca H Gellman – bioRxiv

Review: Membrane lipids from gut microbiome-associated bacteria as structural and signalling molecules – Eileen Ryan – Microbiology

Review: Impact of Intermittent Fasting on the Gut Microbiota: A Systematic Review – Theodoro Pérez-Gerdel – Advanced Biology

Animal Microbiome

Wolbachia endosymbiotic bacteria alter the gut microbiome in the fly Drosophila nigrosparsa – Matsapume Detcharoen – Journal of Invertebrate Pathology

A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota – Ren Dodge – Nature Communications

Plant Microbiome

The core metabolome and root exudation dynamics of three phylogenetically distinct plant species – Sarah McLaughlin – Nature Communications

Co-occurrence network analysis unveils the actual differential impact on the olive root microbiota by two Verticillium wilt biocontrol rhizobacteria – Martina Cardoni – Environmental Microbiome

Environmental Microbiome

Investigating the eco-evolutionary response of microbiomes to environmental change – Jennifer B H Martiny – Ecology Letters

Microbiome Analysis: Resources, Tools and Techniques

In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea – Alba Regueira-Iglesias – Microbiome

DeepGeni: deep generalized interpretable autoencoder elucidates gut microbiota for better cancer immunotherapy – Min Oh – Scientific Reports

Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes – Mingqian Zhang – Bioinformatics

Preprint: Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research – Jonathan L Golob – medRxiv

March 22, 2023

Human gut microbiome

NEMoE: a nutrition aware regularized mixture of experts model to identify heterogeneous diet-microbiome-host health interactions – Xu et al. – Microbiome

The gut microbiome in social anxiety disorder: evidence of altered composition and function – Butler et al. – Translational Psychiatry

Analysis of the fecal metagenome in long-term survivors of pancreas cancer – Kharofa et al. – Cancer

Multiomic signatures of body mass index identify heterogeneous health phenotypes and responses to a lifestyle intervention – Watanabe et al. – Nature Medicine

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

New insights into the impact of microbiome on horizontal and vertical transmission of a tick-borne pathogen – Du et al. – Microbiome

Periodontitis exacerbates atherosclerosis through Fusobacterium nucleatum-promoted hepatic glycolysis and lipogenesis – Zhou et al. – Cardiovascular Research

Gut microbiota in a mouse model of obesity and peripheral neuropathy associated with plasma and nerve lipidomics and nerve transcriptomics – Guo et al. – Microbiome

Characterization of Gut Microbiome Composition in Patients with Triple-Negative Breast Cancer Treated with Neoadjuvant Chemotherapy – Vernaci et al. – The Oncologist

Plant, root, and soil microbiome

Environments and host genetics influence the geographic distribution of plant microbiome structure – Wei & Tan – bioRxiv

Gut feelings: associations of emotions and emotion regulation with the gut microbiome in women – Ke et al. – Psychological Medicine

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Core species and interactions prominent in fish-associated microbiome dynamics – Yamjima et al. – Microbiome

March 20, 2023

Human and General Microbiome

Bacteria require phase separation for fitness in the mammalian gut – Emilia Krypotou – Science

Is there a placental microbiota? A critical review and re-analysis of published placental microbiota datasets – Jonathan J Panzer – BMC Microbiology

Gut-microbiome-expressed 3β-hydroxysteroid dehydrogenase degrades estradiol and is linked to depression in premenopausal females – Di Li – Cell Metabolism

Metagenomic association analysis of cognitive impairment in community-dwelling older adults – Jincheng Li – Neurobiology of Disease

Fusobacterium nucleatum promotes esophageal cancer early occurrence through upregulation of IL-32/PRTN3 expression – Jing Lei – Cancer Science

Review: Postbiotics Implication in the Microbiota-Host Intestinal Epithelial Cells Mutualism – Harpreet Kaur – Probiotics and Antimicrobial Proteins

Review: Microbiota and growth among infants and children in low-income and middle-income settings – James M Njunge – Current Opinion in Clinical Nutrition and Metabolic Care

Review: Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective – Mireia Valles-Colomer – Nature Medicine

Review: Oral polymicrobial communities: Assembly, function, and impact on diseases – George Hajishengallis – Cell Host & Microbe

Review: Gut microbiota: a non-target victim of pesticide-induced toxicity – Tusha Sharma – Gut Microbes

Perspective: Human microbiome research: Growing pains and future promises – Jens Puschhof – PLoS Biology

Beneficial Microbes and Compounds

Versatility of bacterial outer membrane vesicles in regulating intestinal homeostasis – Xinyue Wang – Science Advances

Lactobacillus rhamnosus GG cell-free supernatant as a novel anti-cancer adjuvant – Rossella Salemi – Journal of Translational Medicine

Environmental Microbiome

Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy – Eke I Kalu – ISME Communications

Other Microbes

Biointerface mineralization generates ultraresistant gut microbes as oral biotherapeutics – Zhongmin Geng – Science Advances

Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli – Tracy H Hazen – Nature Communications

Microbiome Analysis: Tools and Techniques

Spatial profiling of microbial communities by sequential FISH with error-robust encoding – Zhaohui Cao – Nature Communications

sBGC-hm: An atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome – Huixi Zou – Bioinformatics

Protocol: Bioinformatic and Statistical Analysis of Microbiome Data – Youngchul Kim – Methods in Molecular Biology

Protocol: Multi-omics Data Deconvolution and Integration: New Methods, Insights, and Translational Implications – Xuefeng Wang – Methods in Molecular Biology

March 15, 2023

Pregnancy and early life

The impact of prenatal dog keeping on infant gut microbiota development – Panzer et al. – Clinical & Experimental Allergy

Human oral microbiome

Host microbiome interactions in apical periodontitis: the endodontic microbiome in relation to circulatory immunologic markers – Georgiou et al. – International Endodontic Journal

Human gut microbiome

[REVIEW]Microbiota dysbiosis and myasthenia gravis: Do all roads lead to Rome? – Kapoor et al. – Autoimmunity Reviews

Metabolomic interplay between gut microbiome and plasma metabolome in cardiac surgery-associated acute kidney injury – Bai et al. – Rapid Communications in Mass Spectrometry

A non-antibiotic-disrupted gut microbiome is associated with clinical responses to CD19-CAR-T cell cancer immunotherapy – Stein-Thoeringer et al. – Nature Medicine

The gut microbiome modulates the transformation of microglial subtypes – Huang et al. – Molecular Psychiatry

Multi-omics insights into the interplay between gut microbiota and colorectal cancer in the “microworld” age – Wang et al. – Molecular Omics

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

A Longitudinal Characterization of the Seminal Microbiota and Antibiotic Resistance in Yearling Beef Bulls Subjected to Different Rates of Gain – Webb et al. – Microbiology Spectrum

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Abiotic selection of microbial genome size in the global ocean – Ngugi et al. – Nature Communications


Benchmarking genome assembly methods on metagenomic sequencing data – Zhang et al. – Briefings in Bioinformatics

March 13, 2023

Human and General Microbiome

Dysbiosis of a microbiota-immune metasystem in critical illness is associated with nosocomial infections – Jared Schlechte – Nature Medicine

Altered infective competence of the human gut microbiome in COVID-19 – Laura de Nies – Microbiome

Impact of high altitude on composition and functional profiling of oral microbiome in Indian male population – Manisha Kumari – Scientific Reports

Incidence of Breast Cancer and Enterococcus Infection: A Retrospective Analysis – Matthew Cardeiro – World Journal of Oncology

Multi-omics studies in interpreting the evolving standard model for immune functions – Dipyaman Ganguly – Briefings in Functional Genomics

Understanding the bacterial compositional network associations between oral and gut microbiome within healthy Koreans – Jinuk Jeong – Journal of oral Microbiology

A transcriptomic insight into the human sperm microbiome through next-generation sequencing – Celia Corral-Vazquez – Systems Biology in Reproductive Medicine

Beneficial Microbes and Compounds

Metformin alleviates liver fibrosis in mice by enriching Lactobacillus sp. MF-1 in the gut microbiota – Tao Yang – Biochimica et Biophysica Acta

Animal Microbiome

Microbiota alters the metabolome in an age- and sex- dependent manner in mice – Kirsty Brown – Nature Communications

IL-22 alters gut microbiota composition and function to increase aryl hydrocarbon receptor activity in mice and humans – Jordan S Mar – Microbiome

Decreased Paneth cell α-defensins promote fibrosis in a choline-deficient L-amino acid-defined high-fat diet-induced mouse model of nonalcoholic steatohepatitis via disrupting intestinal microbiota – Shunta Nakamura – Scientific Reports

Plant Microbiome

Microbiota and functional analyses of nitrogen-fixing bacteria in root-knot nematode parasitism of plants – Ye Li – Microbiome

Non-volatile metabolites mediating plant interactions with insect herbivores – Mei Luo – The Plant Journal

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress – Bo Wang – Frontiers in Microbiology

Review: Emerging Pathways for Engineering the Rhizosphere Microbiome for Optimal Plant Health – Shengdie Yang – Journal of Agricultural and food Chemistry

Microbiome Analysis: Tools and Techniques

A bayesian zero-inflated dirichlet-multinomial regression model for multivariate compositional count data – Matthew D Koslovsky – Biometrics

Determining the most accurate 16S rRNA hypervariable region for taxonomic identification from respiratory samples – Ruben López-Aladid – Scientific Reports