September 25, 2021


Review: Bacterial Translocation as Inflammatory Driver in Crohn’s Disease – Raquel Linares – Frontiers in Cell and Developmental Biology

Review:  The Gut Microbiome and Inflammatory Bowel Diseases – Yue Shan – Annual Review of Medicine

Vegan vs. omnivore diets paradox: A whole-metagenomic approach for defining metabolic networks during the race in ultra-marathoners- a before and after study  design – Aslı Devrim-Lanpir – PloS ONE

The Prebiotic Potential of Inulin-type Fructans: A Systematic Review – Riley L Hughes – Advances in Nutrition

Next-generation prebiotic promotes selective growth of bifidobacteria, suppressing Clostridioides difficile – Rika Hirano – Gut Microbes

timeOmics: an R package for longitudinal multi-omics data integration – Antoine Bodein – Bioinformatics 

Automation of QIIME2 Metagenomic Analysis Platform – Calvin Fung – Current Protocols

Human and General Microbiome

Persistence of functional microbiota composition across generations – Christian Ramos – Scientific Reports

Gastric microbiota in patients with Helicobacter pylori-negative gastric MALT lymphoma. – Takahide Tanaka – Medicine

Lachnospira is a signature of antihistamine efficacy in chronic spontaneous urticarial – Runqiu Liu – Experimental Dermatology

Association of Female Genital Schistosomiasis With the Cervicovaginal Microbiota and Sexually Transmitted Infections in Zambian Women – Amy S Sturt – Open Forum Infectious Diseases

Gut Lactobacillus Level Is a Predictive Marker for Coronary Atherosclerotic Lesions Progress and Prognosis in Patients With Acute Coronary Syndrome – Jing Gao – Frontiers in Cellular and Infection Microbiology

Causal Effects of Gut Microbiome on Systemic Lupus Erythematosus: A Two-Sample Mendelian Randomization Study – Kun Xiang – Frontiers in Immunology

Vaginal microbiome as a tool for prediction of chorioamnionitis in preterm labor: a pilot study – Daichi Urushiyama – Scientific Reports

Genital mycoplasma infection and spontaneous preterm birth outcome: a prospective cohort study. – Giulia Karnauchovas Porto Cunha – BJOG

Endometrial microbiota is more diverse in people with endometriosis than symptomatic controls – Jocelyn M Wessels – Scientific Reports

Periodontitis associates with species-specific gene expression of the oral microbiota – Daniel Belstrøm – NPJ biofilms and microbiomes

Review: Interplay and cooperation of Helicobacter pylori and gut microbiota in gastric carcinogenesis – Seyedeh Zahra Bakhti – BMC Microbiology

Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species – Hassan Zafar – Microbial Physiology

Review: Mass spectrometry-based metabolomics in microbiome investigations – Anelize Bauermeister – Nature Reviews Microbiology

Gut microbiota depletion exacerbates cholestatic liver injury via loss of FXR signalling – Kai Markus Schneider – Nature Metabolism

Review: Chains of evidence from correlations to causal molecules in microbiome-linked diseases. – Snehal N Chaudhari – Nature Chemical Biology

Review: Host and microbiota metabolic signals in aging and longevity – Yue Zhou – Nature Chemical Biology

Fecal filtrate transplantation protects against necrotizing enterocolitis – Anders Brunse – The ISME Journal

High-fat diet increases the severity of Giardia infection in association with low-grade inflammation and gut microbiota dysbiosis – Thibault Allain – Scientific Reports

Beneficial Microbes and Compounds

Effects of konjac glucomannan with different molecular weights on gut microflora with antibiotic perturbance in in-vitro fecal fermentation – Yu-Heng Mao – Carbohydrate Polymers

Review: Interactions between dietary polyphenols and aging gut microbiota: A review – Sergio Davinelli – BioFactors

Safety and efficacy of using heat-killed Lactobacillus plantarum L-137: High-dose and long-term use effects on immune-related safety and intestinal bacterial flora – Hiroko Nakai – Journal of Immunotoxicology

Faecalibacterium prausnitzii Attenuates DSS-Induced Colitis by Inhibiting the Colonization and Pathogenicity of Candida albicans – Xiaqiong Mao – Molecular Nutrition & Food Research

Minireview: Probiotics, Prebiotics, and Synbiotics for the Prevention of Necrotizing Enterocolitis. – Kiera Murphy – Frontiers in Nutrition

Review: Main drivers of (poly)phenol effects on human health: metabolite production and/or gut microbiota-associated metabotypes? – Carlos E Iglesias-Aguirre – Food & Function

Inhibitory effects of Lactobacillus casei Shirota against both Candida auris and Candida spp. isolates that cause vulvovaginal candidiasis and are resistant to antifungals – Aline Lorenzoni Paniágua – BMC Complementary Medicine and Therapies

Fructooligosaccharides: From Breast Milk Components to Potential Supplements. A Systematic Review– Valentina De Cosmi – Advances in Nutrition

Effects of Microbiota-Driven Therapy on Circulating Trimethylamine-N-Oxide Metabolism: A Systematic Review and Meta-Analysis – Lina Miao – Frontiers in Cardiovascular Medicine

Animal Microbiome

The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya. – Rehema Liyai – PeerJ

Marked Seasonal Variation in Structure and Function of Gut Microbiota in Forest and Alpine Musk Deer – Feng Jiang – Frontiers in Microbiology

Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes – Amanda C Perofsky – Molecular Ecology

Association of female reproductive tract microbiota with egg production in layer chickens – Yuan Su – GigaScience

Plant Microbiome

Bacillus subtilis Colonization of Arabidopsis thaliana Roots Induces Multiple Biosynthetic Clusters for Antibiotic Production – Harsh Maan – Frontiers in Cellular and Infection Microbiology

Environmental Microbiome

Review: Prospects for multi-omics in the microbial ecology of water engineering – Elizabeth A McDaniel – Water Research


QSDB-a graphical Quorum Sensing Database – Karsten Klein – Database

Testing microbiome association using integrated quantile regression models – Tianying Wang – Bioinformatics 

timeOmics: an R package for longitudinal multi-omics data integration – Antoine Bodein – Bioinformatics 

Automation of QIIME2 Metagenomic Analysis Platform – Calvin Fung – Current Protocols

September 22, 2021

Grant application (US specific grant)
Call for application for Biocodex Microbiota Foundation’s 2021 research grant ($50,000 US) which can be applied to new or existing research aimed at helping understand gut microbiota and its impact beyond the human digestive system.
Deadline: October 15th, 2021

Human skin microbiome

[Commentary]Food for thought: does host diet affect skin microbes? – Schneider & Nelson – British Journal of Dermatology

Host traits, lifestyle and environment are associated with human skin bacteria – Moitinho-Silva et al – British Journal of Dermatology

Human nearly-sterile sites (blood, organs, brain)

Deciphering the low abundance microbiota of presumed aseptic hip and knee implants – Carr et al. – PLOS One

Human gut microbiome

[REVIEW]Next Generation Microbiome Research: Identification of Keystone Species in the Metabolic Regulation of Host-Gut Microbiota Interplay – Tudela, Claus & Saleh – Front. Cell Dev. Biol.

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

Commensal microbe-derived acetate suppresses NAFLD/NASH development via hepatic FFAR2 signalling in mice – Aoki et al. – Microbiome

Animal microbiome (for animals in the wild)

16 S rRNA gene diversity and gut microbial composition of the Indian white shrimp (Penaeus indicus) – Patil et al. – Antonie van Leeuwenhoek

Plant, root, and soil microbiome

Disease-induced changes in plant microbiome assembly and functional adaptation – Gao et al. – Microbiome

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

Diversity and distribution of viruses inhabiting the deepest ocean on Earth – Jian et al. – The ISME Journal

Deep-sea shipwrecks represent island-like ecosystems for marine microbiomes – Hamdan et al – The ISME Journal

The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole – Martin et al. – Nature Comminications

Phages and viruses

A 2021 taxonomy update for the family Smacoviridae – Krupovic & Varsani – Archives of Virology


[PREPRINT]MIMOSA2: A metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data – Noecker, Eng & Borenstein – bioRxiv

Identifying indicator species in ecological habitats using Deep Optimal Feature Learning – Tsai, Baldwin & Gopaluni – PLOS One

September 15, 2021

Today’s digest is fairly light. It includes an article focused on the protective role of bacterial endosymbionts on soil fungus, a preprint on the indoor environment as a source for human-associated anaerobes, and work demonstrating how protein biosensors can be used to track the effects osmotic stress on cells.

Happy reading!

General microbiome

Preprint: Comprehensive comparative genomics analysis for the emerging human pathogen Streptococcus dysgalactiae subsp. equisimilis (SDSE): A case study and Pan-subspecies genomic analysis – Saeb & Tayeb – bioRxiv

Preprint: The model arbuscular mycorrhizal fungus Rhizophagus irregularis harbours endosymbiotic bacteria with a highly reduce genome – Savary et al. – bioRxiv

Preprint: A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare? – van Vilet et al. – bioRxiv

Animal microbiome (for animals in the wild)

Differences in gut microbiome composition between sympatric wild and allopatric laboratory populations of omnivorous cockroaches – Tinker et al. – Frontiers in Microbiology

Plant, root, and soil microbiome

Bacterial endosymbionts protect beneficial soil fungus from nematode attack – Büttner et al. – Proceedings of the National Academy of Sciences of the United States of America

Built environment

Preprint: The indoor environment – A potential source for intact human-associated anaerobes – Pausan et al. – bioRxiv


Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells – Cuevas-Velazquez et al. – Nature Communications

September 14, 2021

General microbiome

[REVIEW]Host specificity of the gut microbiome – Mallott & Amato – Nature Reviews Microbiology

[COMMENT]Harnessing the power of host–microbe symbioses to address grand challenges – Hentschel – Nature Reviews Microbiology

The intratumoral microbiome: Characterization methods and functional impact – Heymann et al. – Cancer Letters

Human oral microbiome

Oral hygiene and oral microbiota in children and young people with neurological impairment and oropharyngeal dysphagia – Fregatto et al. – Scientific Reports

Human skin microbiome/virome

[PREPRINT]The Application of The Skin Virome for Human Identification – Graham et al. – bioRxiv

Human vaginal microbiome

Vaginal microbiome topic modeling of laboring Ugandan women with and without fever – Movassagh et al. – NPJ Biofilms and Microbes

Human nearly-sterile sites (blood, organs, brain)

Plasma metagenomic sequencing to detect and quantify bacterial DNA in ICU patients suspected of sepsis – Kisat et al. – The Journal of Trauma and Acute Care Surgery

Human gut microbiome

The gut microbiome in konzo – Bramble et al. – Nature Communications

High-salt diet mediates interplay between NK cells and gut microbiota to induce potent tumor immunity – Rizvi et al. – Science Advances

The Firmicutes/Bacteroidetes ratio of the human gut microbiota is associated with prostate enlargement – Takezawa et al. – The Prostate

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

Gut microbiota from green tea polyphenol-dosed mice improves intestinal epithelial homeostasis and ameliorates experimental colitis – Wu et a. – Microbiome

Differential perturbations of gut microbial profiles and co-occurrence networks among phases of methamphetamine-induced conditioned place preference – Wang et al. – Journal of Neuroscience Research

Gut microbiota regulation of P-glycoprotein in the intestinal epithelium in maintenance of homeostasis – Foley et al. – Microbiome

Vitamin A supplementation ameliorates ulcerative colitis in gut microbiota–dependent manner – Pang et al. – Food Research International

Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period – Suriyaphol et al. – Scientific Reports


A statistical model for describing and simulating microbial community profiles – Ma et al. – PLOS Computational Biology

September 11, 2021


Bioaccumulation of therapeutic drugs by human gut bacteria – Martina Klünemann – Nature → In this article, the authors showed new bacteria-drug interactions and observed that some microbe communities bioaccumulate drugs.

Eight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian Permafrost – Katie Sipes – Applied and Environmental Microbiology → Interesting features from a set of eight ≥80% complete MAGs from Siberian permafrost soil. 

Review: Analysis the Link between Periodontal Diseases and Alzheimer’s Disease: A Systematic Review – Leslie Borsa – International Journal of Environmental Research and Public Health → This systematic review found that “an association between periodontal disease and Alzheimer’s disease”, suggesting that “the treatment of periodontal disease could be a way to explore Alzheimer’s disease prevention”.

Transplantation of gut microbiota derived from Alzheimer’s disease mouse model impairs memory function and neurogenesis in C57BL/6 mice – Namkwon Kim – Brain, Behavior, and Immunity → Microbiota transplantation from an Alzheimer mouse model into a healthy model, showing effects in neurological parameters.

General Microbiome 

Controllers of cutaneous regulatory T cells: ultraviolet radiation and the skin microbiome. – Thomas Schwarz – Biological Chemistry

The effects of cigarette smoking on the salivary and tongue microbiome – Nao Suzuki – Clinical and Experimental Dental Research

Review: Oral Microbiota Variation: A Risk Factor for Development and Poor Prognosis of Esophageal Cancer. – Xiaobo Song – Digestive Diseases and Sciences

The gastric microbiota in patients with Crohn’s disease; a preliminary study – Jerzy Ostrowski – Scientific Reports

Saliva-derived microcosm biofilms grown on different oral surfaces in vitro – Xiaolan Li – NPJ biofilms and microbiomes

Plasma Metabolomic and Intestinal Microbial Analyses of Patients With Severe Aplastic Anemia – Yuanyuan Shao – Frontiers in Cell and Developmental Biology

Review: Gastrointestinal mucosal immunity and COVID-19 – Tsvetelina Velikova – World Journal of Gastroenterology

Review: Exploring the global vaginal microbiome and its impact on human health – Linda Abou Chacra – Microbial Pathogenesis

Review: Gut microbiome in acute pancreatitis: A review based on current literature – Bharati Kadamb Patel – World Journal of Gastroenterology

Review: Parkinson’s Disease and Gut Microbiota – Masaaki Hirayama – Annals of Nutrition & Metabolism

Beneficial Microbes, Compounds and Interventions

Dietary Pterostilbene and Resveratrol Modulate the Gut Microbiota Influenced by Circadian Rhythm Dysregulation – Yen-Chun Koh – Molecular Nutrition & Food Research

Lactobacillus rhamnosus Affects Rat Peritoneal Cavity Cell Response to Stimulation with Gut Microbiota: Focus on the Host Innate Immunity – Stanislava Stanojević – Inflammation

Fisetin Improves Hyperuricemia-Induced Chronic Kidney Disease via Regulating Gut Microbiota-Mediated Tryptophan Metabolism and Aryl Hydrocarbon Receptor Activation. – Qian Ren – Journal of Agricultural and Food Chemistry

Comparative effects of alive and pasteurized Akkermansia muciniphila on normal diet-fed mice – Fatemeh Ashrafian – Scientific Reports

Review: Fruits and their impact on the gut microbiota, gut motility and constipation – Zoi Katsirma – Food & Function

Review: Rare sugars: Metabolic Impacts and Mechanisms of Action – a Scoping Review – Alison Smith – The British Journal of Nutrition

Plant Microbiome

Invasive Grass Dominance over Native Forbs Is Linked to Shifts in the Bacterial Rhizosphere Microbiome. – Marina L LaForgia – Microbial ecology

Coupling the endophytic microbiome with the host transcriptome in olive roots – Antonio J Fernández-González – Computational and Structural Biotechnology Journal

Fungi Microbiome

Succession and potential role of bacterial communities during Pleurotus ostreatus production – Renáta Bánfi – FEMS Microbiology Ecology

Wastewater Microbiome

Metagenomic Analysis of Antibiotic Resistance Genes in Untreated Wastewater From Three Different Hospitals – Xiurong Guo – Frontiers in Microbiology


Learning Sparse Log-Ratios for High-Throughput Sequencing Data – Elliott Gordon-Rodriguez – Bioinformatics

gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites – Liang Cheng – Nucleic Acids Research

Experimental Techniques

Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits – Kathrin Janssen – Applications in Plant Sciences


Metagenome-Assembled Genome Sequences Obtained from a Reactivated Kombucha Microbial Community Exposed to a Mars-Like Environment outside the International Space Station – Imchang Lee – Microbiology Resource Announcements

Mon-microbiome picks

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa – Eduan Wilkinson – Science

September 10, 2021

In today’s digest read about a discovery of new Bordetella bronchiseptica-specific temperate and highly abundant siphoviruses that lead to the creation of a new genus Vojvodinavirus, biases in public human microbiome data, infant gut strain persistence, and more. Also, check out a list of upcoming microbiome events. Happy Friday!

Global microbiome

*Public human microbiome data dominated by highly developed countries – Richard J. Abdill – bioRxiv

Gut microbiome

Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization – Jing Lu – npj Biofilms and Microbiomes

Gut microbiota alterations in response to sleep length among African-origin adults – Na Fei – PlosOne

Bioaccumulation of therapeutic drugs by human gut bacteria – Martina Klünemann – Nature

*Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition – Yue Clare Lou – Cell Reports Medicine

Skin microbiome

Cotton and Surgical Face Masks in Community Settings: Bacterial Contamination and Face Mask Hygiene – Lize Delanghe – Frontiers in Medicine

Animal microbiome

The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps? – Chiara Crestani – Microbial Genomics

Viruses and phages

*Are Bordetella bronchiseptica Siphoviruses (Genus Vojvodinavirus) Appropriate for Phage Therapy—Bacterial Allies or Foes? – Aleksandra Petrovic Fabijan – Viruses

Water microbiome

Functional Redundancy in Ocean Microbiomes Controls Trait Stability – Taylor M. Royalty and Andrew D. Steen – bioRxiv


SHOOT: phylogenetic gene search and ortholog inference – David Emms and Steven Kelly – bioRxiv

Ultra-resolution Metagenomics: When Enough Is Not Enough – Falk Hildebrand – mSystems

Computational challenges and opportunities in spatially resolved transcriptomic data analysis – Lyla Atta & Jean Fan – Nature Communications

*BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data – Chenhao Li – Plos Computational Biology

Webinars &c

Conference: Microbiome Virtual International Conference #MVIF – September 14/16 (Atlantic/Pacific)

Course + Symposium: 2021 ISB Virtual Microbiome Series – October 13-15

Webinar: EMBARK Fall Webinars – a webinar series where invited speakers will be presenting their AMR research and be contrasted to EMBARK members presenting the work performed in the project.

For more, check out a collection of microbiome events HERE!

September 7, 2021

Today’s digest features some excellent human and mouse microbiome research, a highly detailed study of human associated Bifidobacterium longum, as well as a non microbiome picks on the history of rhinoceros in Cell and how to write a lab protocol in Nature.

General microbiome

Exploring Microbiome Functional Dynamics through Space and Time with Trait-Based Theory – Bittleston et al. mSystems

Human gut microbiome

Effects of antibiotic duration on the intestinal microbiota and resistome: The PIRATE RESISTANCE project, a cohort study nested within a randomized trial – Leo et al. EBioMedicine

Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals  – Tarallo et al. Gut

Associations between the gut microbiome and metabolome in early life – Nguyen et al. BMC Microbiology

Animal Experiments

The composition of the gut microbiota following early-life antibiotic exposure affects host health and longevity in later life – Lynn et al. Cell Reports

Human gut-derived B. longum subsp. longum strains protect against aging in a D-galactose-induced aging mouse model – Xiao et al. Microbiome

Water Microbiome

Arms race in a cell: genomic, transcriptomic, and proteomic insights into intracellular phage–bacteria interplay in deep-sea snail holobionts – Zhou et al. Microbiome

Soil microbiome

Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil – Starr et al. mSphere


Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ) – Ling et al. Microbiome

Non-microbiome picks

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family – Lie et al. Cell

Five keys to writing a reproducible lab protocol – Nature

September 06, 2021

General microbiome

[PREPRINT]Host-microbiome protein-protein interactions capture mechanisms in human disease – Zhou, Beltran & Brito – bioRxiv

Prognostic correlations with the microbiome of breast cancer subtypes – Banerjee et al. – Cell Death & Disease

Pregnancy and early life

[REVIEW]Composition of the vaginal microbiota during pregnancy in women living in sub-Saharan Africa: a PRISMA-compliant review – Juliana et al. – BMC Pregnancy and Childbirth

Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage – Seki et al. – Cell Host & Microbe

Multi-site human microbiome

[PREPRINT]Comparing Fecal, Saliva, and Chicha Microbiomes Between Mothers and Children in an Indigenous Ecuadorian Cohort – Adams et al. – bioRxiv

Human respiratory microbiome

Alterations of gut microbiota in patients with active pulmonary tuberculosis in China: A pilot study – Shi et al. – International Journal of Infectious Diseases

Human oral microbiome

The effects of periodontitis associated microbiota on the development of oral squamous cell carcinoma – Hu, Shen & Tian – Biochemical and Biophysical Research Communications

Human gut microbiome

Parasites and diet as main drivers of the Malagasy gut microbiome richness and function – Mondot et al. – Scientific Reports

[REVIEW]The second brain: The connection between gut microbiota composition and multiple sclerosis = Farshbafnadi, Agah & Rezaei – Journal of Neuroimmunology

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

Thymic development of gut-microbiota-specific T cells – Zegarra-Ruiz et al – Nature

High-fat diet alters stress behavior, inflammatory parameters and gut microbiota in Tg APP mice in a sex-specific manner – Yanguas-Casas – Neurobiology of Diesease

Sex-dependent effects on the gut microbiota and host metabolome in type 1 diabetic mice – Zhang et al. – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease


Efficient computation of Faith’s phylogenetic diversity with applications in characterizing microbiomes – Armstrong et al. – Genome Research

September 4, 2021

Have a nice weekend! Today we have a good set of papers. Highlights: articles about microbiome crosstalk in acute leukemia, the relationship between trimethylamine N-oxide and hypertension, and the quantification of rapid bacterial evolution in a murine model. 


Altered microbiota-host metabolic crosstalk preceding neutropenic fever in patients with acute leukemia – Armin Rashidi – Blood Advances

Gut microbiota dependent trimethylamine N-oxide aggravates angiotensin II-induced hypertension – Shan Jiang – Redox Biology

Quantifying rapid bacterial evolution and transmission within the mouse intestine – Kimberly S Vasquez – Cell Host & Microbe

Human and General Microbiome

Letter: Human oral microbiome cannot predict Pleistocene starch dietary level, and dietary glucose consumption is not essential for brain growth – Miki Ben-Dor – PNAS

Free threonine in human breast milk is related to infant intestinal microbiota composition – Monika Riederer – Amino Acids

Sickle cell disease children’s gut colonization by extended-spectrum β-lactamase (ESBL)-producing Enterobacterales: an antibiotic prophylaxis effect? – Adriano de Souza Santos Monteiro – Journal of Medical Microbiology

Disruption of the oral microbiota is associated with a higher risk of relapse after allogeneic hematopoietic stem cell transplantation – Vinícius Campos de Molla – Scientific Reports

The bladder microbiome and interstitial cystitis: is there a connection? – Melinda G Abernethy – Current opinion in Obstetrics & Gynecology

Delivery mode and perinatal antibiotics influence the predicted metabolic pathways of the gut microbiome – Petri Vänni – Scientific Reports

Changes in Conjunctival Microbiota Associated With HIV Infection and Antiretroviral Therapy – Qun Liu – Investigative Ophthalmology & Visual Science

Activation of the gut microbiota-kynurenine-liver axis contributes to the development of nonalcoholic hepatic steatosis in nondiabetic adult. – Guoyuan Sui – Aging

Review: Recent progress in research on the gut microbiota and highland adaptation on the Qinghai-Tibet Plateau. – Kui Liu – Journal of Evolutionary Biology

Review: Investigating dairy microbiome: an opportunity to ensure quality, safety and typicity. – Ilario Ferrocino – Current Opinion in Biotechnology

Review: Novel approaches to intervene gut microbiota in the treatment of chronic liver diseases. – Chang Liu – The FASEB journal

Review: Tryptophan-derived serotonin-kynurenine balance in immune activation and intestinal inflammation – Sabah Haq – The FASEB journal

Human gut microbiome impacts skeletal muscle mass via gut microbial synthesis of the short-chain fatty acid butyrate among healthy menopausal women – Wan-Qiang Lv – Journal of Cachexia, Sarcopenia and Muscle

Effects of gut microbiota-derived extracellular vesicles on obesity and diabetes and their potential modulation through diet – Ester Díez-Sainz – Journal of Physiology and Biochemistry

Animal Microbiome

Integrated Bacterial and Fungal Diversity Analysis Reveals the Gut Microbial Alterations in Diarrheic Giraffes – Aoyun Li – Frontiers in microbiology

Comparative study of gut microbiota from captive and confiscated-rescued wild pangolins – Chunbing Liu – Journal of Genetics and Genomics

Sugar feeding protects against arboviral infection by enhancing gut immunity in the mosquito vector Aedes aegypti – Floriane Almire – PLoS pathogens

Bacterial community dynamics on bats and the implications for pathogen resistance – Aoqiang Li – Environmental Microbiology

Draft Genome Sequence of Enterobacter oligotrophicus, Isolated from the Microbiome of a Lizard in the Caribbean. – Matthieu Pot – Microbiology Resource Announcements

Animal Model Microbiome

Gut microbiota and metabolites of α-synuclein transgenic monkey models with early stage of Parkinson’s disease – Yaping Yan – NPJ biofilms and microbiomes

Eugenol Alleviates Dextran Sulfate Sodium-Induced Colitis Independent of Intestinal Microbiota in Mice – Shuai Chen – Journal of Agricultural and Food Chemistry

Integrative analysis of the gut microbiome and metabolome in a rat model with stress induced irritable bowel syndrome – Yue Hu – Scientific Reports

Lycium barbarum polysaccharide attenuates emotional injury of offspring elicited by prenatal chronic stress in rats via regulation of gut microbiota – Feng Zhao – Biomedicine & Pharmacotherapy

Sex-specific effects of the microbiota on adult carbohydrate intake and body composition in a polyphagous fly – Binh Nguyen – Journal of Insect Physiology

Beneficial Microbes and Compounds

Commentary: Targeted diets for the gut microbiota and the potential cardiovascular effects – Gemma Chiva-Blanch – Cardiovascular Research

Review: Galacto-oligosaccharides as infant prebiotics: production, application, bioactive activities and future perspectives – Valentina Ambrogi – Critical Reviews in Food Science and Nutrition

Synbiotics Containing Nanoprebiotics: A Novel Therapeutic Strategy to Restore Gut Dysbiosis. – Liang Hong – Frontiers in Microbiology

Environmental Microbiome

Comparative Metagenomics of the Active Layer and Permafrost from Low-Carbon Soil in the Canadian High Arctic – Xiaofen Wu – Environmental Science & Technology

Microbiome analysis and techniques

Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ) – Wodan Ling – Microbiome

High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts. – Žana Kapustina – Microbial Genomics

September 01, 2021

General microbiome

Circulating microbiome DNA: An emerging paradigm for cancer liquid biopsy – Chen et al. – Cancer letters

Human-associated microbiota suppress invading bacteria even under disruption by antibiotics – Letten et al. – The ISME Journal

[PERSPECTIVE]Crosstalk between γδ T cells and the microbiota – Papotto, Yilmaz & Silva-Santos – Nature Microbiology

Pregnancy and early life

Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life – Tsukuda et al. – The ISME Journal

Deterministic transition of enterotypes shapes the infant gut microbiome at an early age – Xiao et al. – Genome Biology

Human oral microbiome

[REVIEW]Association between metabolic syndrome and periodontitis: The role of lipids, inflammatory cytokines, altered host response, and the microbiome – Pirih et al. – Periodontology 2000

[REVIEW]Fungal diseases: Oral dysbiosis in susceptible hosts – Villar & Dongari-Bagtzoglou – Periodontology 2000

[REVIEW]The oral microbiome: Role of key organisms and complex networks in oral health and disease – Sedghi et al. – Periodontology 2000

Human gut microbiome

Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes – Kim et al. – Genome Medicine

[REVIEW]The promise of the gut microbiome as part of individualized treatment strategies – Schupack et al. – Nature Reviews Gastroenterology & Hepatology

[REVIEW]The gut microbiome and efficacy of cancer immunotherapy – Robiello et al. – Pharmacology & Therapeutics

Integrated analysis of the faecal metagenome and serum metabolome reveals the role of gut microbiome-associated metabolites in the detection of colorectal cancer and adenoma – Chen et al. – Gut

Animal/Insect microbiome

Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes – Gupta et al. – Microbiome

Social networks strongly predict the gut microbiota of wild mice – Raulo et al. – The ISME Journal

Genetic identity and genotype × genotype interactions between symbionts outweigh species level effects in an insect microbiome – Smee, Raines & Ferrari – The ISME Journal

[REVIEW]The effects of raw-meat diets on the gastrointestinal microbiota of the cat and dog: a review – Butowski et al. – New Zealand Veterinary Journal

Plant, root, and soil microbiome

Predicting spatial patterns of soil bacteria under current and future environmental conditions – Mod et al. – The ISME Journal

Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype – Stopnisek & Shade – The ISME Journal

Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota – Wippel et al. – Nature Microbiology


Functional meta-omics provide critical insights into long- and short-read assemblies – Galata et al. – Briefings in Bioinformatics

[PREPRINT]BiomeHorizon: visualizing microbiome time series data in R – Fink et al. – bioRxiv

Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota – Shibata et al. – PLOS ONE

MicFunPred: A conserved approach to predict functional profiles from 16S rRNA gene sequence data – Mongad et al. – Genomics