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

August 28, 2021


Free Webinar: Convergence Of Circadian Rhythms And Gut Microbes: Maintaining The Metronome Of Life – September 7, 2021 (10:00 am – 11:00 am) – Organized by The Institute for the Advancement of Food and Nutrition Sciences


Review: The importance of Faecalibacterium prausnitzii in human health and diseases – M Parsaei – New Microbes and New Infections

Review: The gut microbiome in feast and famine – Hannah D Holscher – Nature Reviews Gastroenterology & Hepatology

Prophylactic Administration of a Bacteriophage Cocktail Is Safe and Effective in Reducing Salmonella enterica Serovar Typhimurium Burden in Vivo – Quentin Lamy-Besnier – Microbiology Spectrum

Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users – Divya Gopinath – Clinical Oral Investigations

Cross-sectional comparisons of subgingival microbiome and gingival fluid inflammatory cytokines in periodontally healthy vegetarians versus non-vegetarians – Ahmed Khocht – Journal of Periodontal Research

Human and General Microbiome

Review: Gut microbiota as the critical correlation of polycystic ovary syndrome and type 2 diabetes mellitus. – Liyun Duan – Biomedicine & Pharmacotherapy

Review: The Gut Microbiome, Metformin, and Aging – Sri Nitya Reddy Induri – Annual Review of Pharmacology and Toxicology

Review: Microbe defines the efficacy of chemotherapeutic drug: A complete paradigm – P Dalal – FEMS Microbiology Letters

Review: Gut Microbiota Profiles in Early- and Late-Onset Colorectal Cancer: A Potential Diagnostic Biomarker in the Future – Murdani Abdullah – Digestion

Review: Manipulating the neonatal gut microbiome: current understanding and future perspectives. – Emma Wong – Archives of Disease in Childhood

Review: Dietary advanced glycation end-products elicit toxicological effects by disrupting gut microbiome and immune homeostasis – Yingjia Chen – Journal of Immunotoxicology

Perspective: The microbiome extends host evolutionary potential – Lucas P Henry – Nature Communications

Perspective: How microbiota improve immunotherapy – Eduard Ansaldo – Science

Alterations in microbiota and their metabolites are associated with beneficial effects of bile acid sequestrant on icteric primary biliary Cholangitis – Bo Li – Gut Microbes

The gut microbiome in sickle cell disease: Characterization and potential implications – Hassan Brim – PloS ONE

Bacterial resistance to CRISPR-Cas antimicrobials – Ruben V Uribe – Scientific Reports

Depression: A Gut Microbiome Feeling! – Ahmed Naguy – The Journal of Nervous and Mental Disease

The potential prebiotic effect of 2-Butyloctanol on the human axillary microbiome – Min Li – International Journal of Cosmetic Science

Fecal Bacteria as Non-Invasive Biomarkers for Colorectal Adenocarcinoma – Biao Yuan – Frontiers in Oncology

Beneficial Compounds and Microbes

Review: Molecular genetics for probiotic engineering: dissecting lactic acid bacteria – Ronit Suissa – Trends in Microbiology

The effect of probiotic supplementation on the gut microbiota of preterm infants – Erica L Plummer – Journal of Medical Microbiology

Noni (Morinda citrifolia L.) Fruit Polysaccharides Regulated IBD Mice Via Targeting Gut Microbiota: Association of JNK/ERK/NF-κB Signaling Pathways – Ming-Yu Jin – Journal of Agricultural and Food Chemistry

Long-term personalized low FODMAP diet improves symptoms and maintains luminal Bifidobacteria abundance in irritable bowel syndrome – Heidi M Staudacher – Neurogastroenterology and Motility

New Lactiplantibacillus plantarum and Lacticaseibacillus rhamnosus strains: well tolerated and improve infant microbiota – Gunilla Önning – Pediatric Research

Multi-targeted properties of the probiotic Saccharomyces cerevisiae CNCM I-3856 against enterotoxigenic Escherichia coli (ETEC) H10407 pathogenesis across human gut models – Charlène Roussel – Gut Microbes

Animal Microbiome 

Review: A role for bacterial experimental evolution in coral bleaching mitigation? – Justin Maire – Trends in Microbiology

Microbial bioindicators of Stony Coral Tissue Loss Disease identified in corals and overlying waters using a rapid field-based sequencing approach – Cynthia C Becker – Environmental Microbiology

Assessing age, breeding stage, and mating activity as drivers of variation in the reproductive microbiome of female tree swallows – Jessica Hernandez – Ecology and Evolution

Study in Drosophila: Activation of innate immunity during development induces unresolved dysbiotic inflammatory gut and shortens lifespan – Kyoko Yamashita – Disease Models & Mechanisms

Study in Mice: The composition of the gut microbiota following early-life antibiotic exposure affects host health and longevity in later life – Miriam A Lynn – Cell Reports

Study in Mice: Redundant cytokine requirement for intestinal microbiota-induced Th17 cell differentiation in draining lymph nodes – Teruyuki Sano – Cell reports

Honeybee intestines retain low yeast titers, but no bacterial mutualists, at emergence. – James P Tauber – Yeast (Wiley)

The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans – Jaelle C Brealey – Current Biology

Breed differences in the expression levels of gga-miR-222a in laying hens influenced H(2)S production by regulating methionine synthase genes in gut bacteria – Si-Cheng Xing – Microbiome

Unveiling the Gut Microbiota and Resistome of Wild Cotton Mice, Peromyscus gossypinus, from Heavy Metal- and Radionuclide-Contaminated Sites in the  Southeastern United States – Jesse C Thomas IV – Microbiology spectrum

Ingestion of Lactobacillus rhamnosus modulates chronic stress-induced feather pecking in chickens – Claire Mindus – Scientific Reports

Wolves, dogs and humans in regular contact can mutually impact each other’s skin microbiota. – Stefanie Urimare Wetzels – Scientific Reports

Label-free proteomic analysis reveals differentially expressed Wolbachia proteins in Tyrophagus putrescentiae: Mite allergens and markers reflecting population-related  proteome differences – Tomas Erban – Journal of Proteomics

Teaching old mice new tricks: the utility of aged mouse models of C. difficile infection to study pathogenesis and rejuvenate immune response – Jae Hyun Shin – Gut Microbes

Soil and Plant Microbiome

Review: A review of root exudates and rhizosphere microbiome for crop production – Haishu Sun – Environmental Science and Pollution Research International

The biodiversity effect of reduced tillage on soil microbiota – Tobias Guldberg Frøslev – Ambio

Microbiome-mediated response to pulse fire disturbance outweighs the effects of fire legacy on plant performance – Daniel Revillini – The New Phytologist

Interactions between soil compositions and the wheat root microbiome under drought stress: From an in silico to in planta perspective – Jiyeon Si – Computational and Structural Biotechnology Journal

Environmental Science

Review: Temporal and Spatial Signaling Mediating the Balance of the Plankton Microbiome – Yun Deng – Annual Review of Marine Science

Protocols, Methods and Techniques

Archive for Research in Child Health (ARCH) and Baby Gut: Study Protocol for a Remote, Prospective, Longitudinal Pregnancy and Birth Cohort to Address Microbiota  Development and Child Health – Eliot N Haddad – Methods and Protocols

Benchmarking laboratory processes to characterise low-biomass respiratory microbiota – Raiza Hasrat – Scientific Reports

Simultaneous feature selection and outlier detection with optimality guarantees – Luca Insolia – Biometrics

SMDI: An Index for Measuring Subgingival Microbial Dysbiosis – T Chen – Journal of dental researchTrends in inflammatory bowel disease treatment in the past two decades-a high-level text mining analysis of PubMed publications – Eyal Klang – United European Gastroenterology Journal

August 25, 2021

General microbiome

[REVIEW]The longitudinal and cross-sectional heterogeneity of the intestinal microbiota – Miller et al. – Current Opinion in Microbiology

Pregnancy and early life

Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California – Alderete et al. – Gut Microbes

Human respiratory microbiome

Characterization of the Human Oropharyngeal Microbiomes in SARS-CoV-2 Infection and Recovery Patients – Gao et al. – Advanced Science

Human gut microbiome

Metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in Japanese – Tomofuji et al. – Annals of the Rheumatic Diseases

Gut microbes participate in food preference alterations during obesity – d’Oplinter et al. – Gut Microbes

Altered gut microbiome compositions are associated with the severity of asthma – Wang et al. – Journal of Thoracic Disease

Evolution in a Community Context: towards Understanding the Causes and Consequences of Adaptive Evolution in the Human Gut Microbiota over Short Time Scales – Scanlan – mSystems

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

Propamocarb exposure has the potential to accelerate the formation of atherosclerosis in both WT and ApoE−/− mice accompanied by gut microbiota dysbiosis – Jin et al. – Science of The Total Environment

Inflammation-relevant microbiome signature of the stroke brain, gut, spleen, and thymus and the impact of exercise – Kingsbury et al. – Journal of Cerebral Blood Flow & Metabolism

Animal microbiome (for animals in the wild)

Comparative Analysis of Skin Bacterial Diversity and Its Potential Antifungal Function Between Desert and Pine Forest Populations of Boreal Toads Anaxyrus boreas – Basanta et al. – Host Microbe Interactions

Plant, root, and soil microbiome

Herbivory shapes the rhizosphere bacterial microbiota in potato plants – Malacrino et al. – Environmental Microbiology Reports

[PREPRINT]Teasing apart the host-related, nutrient-related and temperature-related effects shaping the phenology and microbiome of the tropical seagrass Halophila stipulacea – Szitenberg et al. – bioRxiv


The Effect of Common Viral Inactivation Techniques on 16S rRNA Amplicon-Based Analysis of the Gut Microbiota – McAdams et al. – Cells

Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies – Ammer-Herrmenau et al. – mSystems