October 16, 2021


Parallelism of intestinal secretory IgA shapes functional microbial fitness – Tim Rollenske – Nature → By using recombinant IgAs, researchers showed that IgA may shape the metabolism of intestinal bacteria, and in some cases IgA molecules against a same target have a different effect on the activity.

Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period – Frank Maixner – Current Biology → From the analysis of paleofeces, researchers suggest that people from the Austrian zone of Hallstatt could retain a non-westernized diet for centuries; in some cases, a high consumption of blue cheese and beer is suggested by the detection of Penicillium roqueforti and Saccharomyces cerevisiae DNA in the samples.  

In vitro study of the effect of quinoa and quinoa polysaccharides on human gut microbiota – Hitache Zeyneb – Food Science & Nutrition → quinoa, a very nutritious Andean cereal,  contains polysaccharides with potential prebiotic (health-promoting) properties.

Metagenomic analysis of gut microbiome reveals a dynamic change in Alistipes onderdonkii in the preclinical model of pancreatic cancer, suppressing its  proliferation – Kihak Lee – Applied Genetics and Molecular Biotechnology → RNA-seq analysis in a preclinical model revealed that the A. onderdonkii medium induced unique transcriptomic alterations in the pancreatic cancer cells, suggesting an special role in this disease.

Human and General Microbiome

Review: Biomarkers of geroprotection and cardiovascular health: An overview of omics studies and established clinical biomarkers in the context of diet – Riccardo Secci – Critical Reviews in Food Science and Nutrition

Unravelling the collateral damage of antibiotics on gut bacteria – Lisa Maier – Nature

Direct on-swab metabolic profiling of vaginal microbiome host interactions during pregnancy and preterm birth – Pamela Pruski – Nature Communications

Brain development in premature infants: A bug in the programming system? – Gerard Clarke – Cell Host & Microbe

A colon cancer prequel – John T Wren – Cell Host & Microbe

Metagenomic Analysis of Saliva Reveals Disease-Associated Microbiotas in Patients With Periodontitis and Crohn’s Disease-Associated Periodontitis – Boyang Sun – Frontiers in Cellular and Infection Microbiology

Antibiotic use but not gastrointestinal infection frequently precedes first diagnosis of functional gastrointestinal disorders – Michael P Jones – United European Gastroenterology Journal

Impact of Helicobacter pylori eradication on the gastric microbiome – Li-Qi Mao – Gut Pathogens

Baseline co-medications may alter the anti-tumoural effect of checkpoint inhibitors as well as the risk of immune-related adverse events – Marie Kostine – European Journal of Cancer

Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota – Elizabeth Fleming – BMC Microbiology

Effect of chewing betel nut on the gut microbiota of Hainanese – Li Ying – PloS ONE

Animal Models

Transplantation of fecal microbiota from patients with inflammatory bowel disease and depression alters immune response and behavior in recipient mice – Hyo-Min Jang – Scientific Reports

Temporal relationship between alterations in the gut microbiome and the development of polycystic ovary syndrome-like phenotypes in prenatally androgenized female mice – Akari Kusamoto – The FASEB Journal

Gut microbiota dysbiosis of type 2 diabetic mice impairs the intestinal daily rhythms of GLP-1 sensitivity – Estelle Grasset – Acta Diabetologica

Non-Model Animal Microbiome

Diurnal oscillations in gut bacterial load and composition eclipse seasonal and lifetime dynamics in wild meerkats – Alice Risely – Nature Communications

Diet diversity and environment determine the intestinal microbiome and bacterial pathogen load of fire salamanders – Yu Wang – Scientific Reports

The structure of the cereal leaf beetle (Oulema melanopus) microbiome depends on the insect’s developmental stage, host plant, and origin – Beata Wielkopolan – Scientific Reports

Beneficial Microbes and Compounds

Review: Does probiotics work for bacterial vaginosis and vulvovaginal candidiasis – Yue Han – Current Opinion in Pharmacology

Characterization of a new bacteriocin-like inhibitory peptide produced by Lactobacillus sakei B-RKM 0559 – Gulyaim K Abitayeva – Biotechnology Letters

Probiotic Interventions Alleviate Food Allergy Symptoms Correlated With Cesarean Section: A Murine Model – Bi-Ying Jin – Frontiers in Immunology

Selenium-enriched Bifidobacterium longum DD98 attenuates irinotecan-induced intestinal and hepatic toxicity in vitro and in vivo – Hui Zhu – Biomedicine & Pharmacotherapy


Novel lytic bacteriophage vB_GEC_EfS_9 against Enterococcus faecium – S Rigvava – Virus Research

Environmental Microbiome

Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy – Lei Liu – Microbiome


PBK model-based prediction of intestinal microbial and host metabolism of zearalenone and consequences for its estrogenicity – Diana M Mendez-Catala – Molecular Nutrition & Food Research

October 9, 2021


Commensal microbiota divergently affect myeloid subsets in the mammalian central nervous system during homeostasis and disease – Roman Sankowski – The EMBO Journal → This study shows how perturbations in the microbiota drive changes in gene expression profiles in the CNS-associated macrophages, with concomitant effects on the  CNS myeloid cells, including Alzheimer-associated repercussions in a specialized murine model.

Coordination of root auxin with the fungus Piriformospora indica and bacterium Bacillus cereus enhances rice rhizosheath formation under soil drying – Feiyun Xu – The ISME Journal → In this study, authors report a cooperative effect of an endophytic fungus and a plant growth-promoting bacterium in rhizosheath formation when moderate soil drying, an agricultural technique used to improve water utilization, is performed.

Human and General Microbiome

Review: The role of Akkermansia muciniphila in obesity, diabetes and atherosclerosis – Alka Hasani – Journal of Medical Microbiology

Review: How can probiotic improve irritable bowel syndrome symptoms? – Indira Benjak Horvat – World Journal of Gastrointestinal Surgery

Meta-Analysis of the Composition of Human Intestinal Gases – Andre Modesto – Digestive Diseases and Sciences

Effectiveness of Probiotics and Prebiotics Against Acute Liver Injury: A Meta-Analysis – Sheng Xu – Frontiers in Medicine

The bacterial gut microbiome of probiotic-treated very-preterm infants: changes from admission to discharge – Jacob A F Westaway – Pediatric Research

Discovery of β-N-acetylglucosaminidases from screening metagenomic libraries and their use as thioglycoligase mutants – Gregor Tegl – Organic & Biomolecular Chemistry

Animal Microbiome

Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents – Jason L Anders – Scientific Reports

Changes in rumen microbial community composition in yak in response to seasonal variations – Xiaodan Huang – Journal of Applied Microbiology

Faecalicatena faecalis sp. nov., a moderately alkaliphilic bacterial strain isolated from swine faeces – Byeong Seob Oh – Antonie van Leeuwenhoek

Plant Microbiome

Capacity of soil bacteria to reach the phyllosphere and convergence of floral communities despite soil microbiota variation – Julien Massoni –  PNAS

Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds – Flavia Tarquinio – Frontiers in Microbiology

Fungi Microbiome

Widespread bacterial diversity within the bacteriome of fungi – Aaron J Robinson – Communications Biology

Environmental Microbiome

Preprint: Genomic and metabolic adaptations of biofilms to ecological windows of opportunities in glacier-fed streams – Susheel Bhanu Busi – Biorxiv

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 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 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

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 17, 2021

Today’s digest covers a variety of topics including an interesting preprint on how the maternal immune system shapes offspring immunity in a microbiota dependent fashion and a large human study of the Rotavirus vaccine and gut microbiota. Non microbiology picks cover some recent COVID-19 advances and a very interesting article in Science investigating energy expenditure through the human life course.


No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing – Smits et al. Cell Reports

Ultrapotent antibodies against diverse and highly transmissible SARS-CoV-2 variants. Wang et al. Science 

Long-term perturbation of the peripheral immune system months after SARS-CoV-2 infection -Ryan et al. MedRxiv

General microbiome

Bacterial colonization dynamics and antibiotic resistance gene dissemination in the hospital environment after first patient occupancy: a longitudinal metagenetic study – Klassert et al. Microbiome

Acute SARS-CoV-2 infection is associated with an increased abundance of bacterial pathogens, including Pseudomonas aeruginosa in the nose – Rhoades et al. Cell Reports 

Meta-analysis of Clinical Microbiome Studies in Urolithiasis Reveal Age, Stone Composition, and Study Location as the Predominant Factors in Urolithiasis-Associated Microbiome Composition – mBio. Kachroo et al. 

Human gut microbiome

The fecal microbiome and rotavirus vaccine immunogenicity in rural Zimbabwean infants – Robertson et al. Vaccine

Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors – Brown et al. Cell Host & Microbe

Pregnancy and Early-Life

Maternal γδ T Cells Shape Offspring Pulmonary Type-2 Immunity In A Microbiota-Dependent Manner – Papotto et al. BioRxiv

Food Microbiology

Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures – Somerville et al. ISME

Water Microbiome

Ecogenomics and Adaptation Strategies of Southern Ocean Viral Communities – Alarcón-Schumacher et al. mSystems

Soil microbiome

Bog ecosystems as a playground for plant–microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria – Wicaksono et al. Microbiome


HoPhage: an ab initio tool for identifying hosts of phage fragments from metaviromes. Tan et al. Bioinformatics

Sparse least trimmed squares regression with compositional covariates for high dimensional data. Monti and Filzmoser. Bioinformatics. 

Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation. Schaffer et al. BMC Bioinformatics.

Non-microbiome picks

Daily energy expenditure through the human life course – Pontzer et al. Science

Analysis of scientific society honors reveals disparities – Le et al. Cell Systems

August 15, 2021

Have a nice Sunday! Today in this Digest, we want to highlight a study that found the effect of human gastric microbiota on premalignant lesions in mice; additionally, new studies about microbiome and Alzheimer’s, relationships between Oxalobacter formigenes and oxalate excretion. Also, we highlight two studies about the role of the coral microbiome and the metapangenome of the significantly ubiquitous SAR324 lineage.   


Human Gastric Microbiota Transplantation Recapitulates Premalignant Lesions In germ-free mice – Soon-Kyeong Kwon – Gut

Effect Of Antibiotic Treatment On Oxalobacter formigenes Colonization Of The Gut microbiome and urinary oxalate excretion – Lama Nazzal – Scientific Reports

Disturbed Microbial Ecology In Alzheimer’s Disease: Evidence From The Gut Microbiota and fecal metabolome – Jianxiong Xi – BMC Microbiology

The Impact Of Enriched Resistant Starch Type-2 Cookies On The Gut Microbiome In Hemodialysis Patients: A Randomized Controlled Trial – Julie Ann Kemp – Molecular Nutrition & Food Research

Coral Microbiome Manipulation Elicits Metabolic And Genetic Restructuring To Mitigate Heat Stress And Evade Mortality – Erika P Santoro – Science Advances

Metapangenomics Reveals Depth-dependent Shifts In Metabolic Potential For The ubiquitous marine bacterial SAR324 lineage – Dominique Boeuf – Microbiome

A. muciniphila Suppresses Colorectal Tumorigenesis By Inducing TLR2/NLRP3-Mediated M1-Like TAMs – Lina Fan – Cancer Immunology Research

Human and General Microbiome

Review: Genes, Environment, And Developmental Timing: New Insights From Translational Approaches To Understand Early Origins Of Respiratory Diseases – Maria J Gutierrez – Pediatric Pulmonology

Review: Contribution Of Biotransformations Carried Out By The Microbiota, Drug-metabolizing Enzymes, And Transport Proteins To The Biological Activities Of Phytochemicals Found In The Diet – Anna Boronat – Advances In Nutrition

Review: The Power And Potential Of Biomap To Elucidate Host-microbiome Interplay In Skin Inflammatory Diseases – Harri Alenius – Experimental Dermatology

Review: Colliding And Interacting Microbiomes And Microbial Communities And Consequences For Human Health – Susan Mills – Environmental Microbiology

Review: Tralokinumab In Atopic Dermatitis – Andreas Wollenberg –Journal Of The German Society of Dermatology 

Review: Skin Microbiome-The Next Frontier For Probiotic Intervention – Isabella J McLoughlin – Probiotics And Antimicrobial Proteins

Minireview: Pathogenic Mechanisms Of Trimethylamine N-oxide-induced Atherosclerosis And Cardiomyopathy – Youjing Zheng – Current Vascular Pharmacology

Gut Microbiome Diversity And Composition Are Associated With Habitual Dairy Intakes: A Cross-sectional Study In Men – Hajara Aslam – The Journal Of Nutrition

Gut Microbiota Profiles And The Role Of Anti-CdtB And Anti-vinculin Antibodies In Patients with FGID – Riccardo Vasapolli – European Journal Of Clinical Investigation

Small Intestinal Bacterial Overgrowth In Patients With Inflammatory Bowel Disease: A case-control study – Uday C Ghoshal – Indian Journal Of Gastroenterology

Position paper: Dangerous Liaisons: Bacteria, Antimicrobial Therapies And Allergic Diseases – Gerdien Tramper-Stranders – Allergy

PD-L1(+) And XCR1(+) Dendritic Cells Are Region-specific Regulators Of Gut Homeostasis – Thais G Moreira – Nature Communications

Simulated Digestion And Fecal Fermentation Behaviors Of Exopolysaccharides From Paecilomyces cicadae Tjj1213 And Its Effects On Human Gut Microbiota – Juanjuan Tian – International Journal Of Biological Macromolecules

Beneficial Microbes, Compounds, and Interventions

Gut Microbiome-short-chain Fatty Acids Interplay In The Context Of Iron Deficiency anaemia – Ana Soriano-Lerma – European Journal Of Nutrition

Chicory Inulin Enhances Fermentation Of 2′-fucosyllactose By Infant Fecal Microbiota and differentially influences immature dendritic cell and T-cell cytokine responses  under normal and Th2-polarizing condition – Renate Akkerman – Food & Function

The Gut Microbiota Mediates The Protective Effects Of Anserine Supplementation On hyperuricaemia and associated renal inflammation. – Jiaojiao Han – Food & Function

Review: Monoterpenes: Current Knowledge On Food Source, Metabolism, And Health Effects – José Fernando Rinaldi de Alvarenga – Critical Reviews In Food Science And Nutrition

Review: Mushrooms On The Plate: Trends Towards NAFLD Treatment, Health Improvement And sustainable diets – Adriana Fontes – European Journal Of Clinical Investigation

Review: Low-Dose Lactulose As A Prebiotic For Improved Gut Health And Enhanced Mineral Absorption. – Tarkan Karakan – Frontiers In Nutrition

Animal Microbiome

Probiotic Lactobacilli Administration Induces Changes In The Fecal Microbiota Of Preweaned Dairy Calves – Sofía Fernández-Ciganda – Probiotics And Antimicrobial Proteins

Metformin Alleviates Choline Diet-induced TMAO Elevation In C57BL/6J Mice By influencing gut-microbiota composition and functionality – Chunyan Su – Nutrition & Diabetes

Phylosymbiotic Structures Of The Microbiota In Mollitrichosiphum Tenuicorpus (Hemiptera: Aphididae: Greenideinae). – Man Qin – Microbial Ecology

Impaired Skeletal Muscle Hypertrophy Signaling And Amino Acid Deprivation Response In ApoE Knockout Mice With An Unhealthy Lipoprotein Distribution – Jakob Agergaard – Scientific Reports

Effect Of Black Ginseng And Silkworm Supplementation On Obesity, The Transcriptome, and the gut microbiome of diet-induced overweight dogs – Miey Park – Scientific Reports

Juvenile Social Defeat Stress Exposure Favors In Later Onset Of Irritable Bowel syndrome-like symptoms in male mice – Kenjiro Matsumoto – Scientific Reports

Plant Microbiome

Plant Developmental Stage Drives The Differentiation In Ecological Role Of The Maize microbiome. – Chao Xiong – Microbiome

Impact Of Biocontrol Microbes On Soil Microbial Diversity In Ginger (Zingiber officinale Roscoe). – Zhiqiang Huang – Pest Management Science

Environmental Microbiome

16S rRNA Gene Metabarcoding Indicates Species-Characteristic Microbiomes In Deep-Sea Benthic Foraminifera – Iines S Salonen – Frontiers In Microbiology

Microbial Community Composition Controls Carbon Flux Across Litter Types In Early Phase Of Litter Decomposition – Marie E Kroeger – Environmental Microbiology

Contribution Of Stochastic Processes To The Microbial Community Assembly On Field-collected Microplastics – Yuanze Sun – Environmental Microbiology


Review: Simultaneous Ribosome Profiling Of Hundreds Of Microbes From The Human Microbiome – Brayon J Fremin – Nature Protocols

August 4, 2021

Have a nice day!! Today, in this Digest: a study of the microbiome structure and host relationship in a Korean population, Microbiome and vitamin D3, microbiome and cystic fibrosis, a study about Faecalibacterium prausnitzii diversity under liver cirrhosis, and more! 

Human and General Microbiome

Review: Clostridioides difficile Infection in Pediatric Inflammatory Bowel Disease: A Clinician’s Dilemma – Máire A Conrad – Journal of the Pediatric Infectious Diseases Society

Minireview: The Gut-Lung Axis in Cystic Fibrosis – Courtney E Price – Journal of Bacteriology

Comprehensive Strain-Level Analysis of the Gut Microbe Faecalibacterium prausnitzii in Patients with Liver Cirrhosis – Yaowen Chen – mSystems

Gut Microbiome Structure and Association with Host Factors in a Korean Population – Mi Young Lim – mSystems

Pilot trial of vitamin D3 and calcifediol in healthy vitamin D deficient adults: does it change the fecal microbiome? – Albert Shieh – The Journal of Clinical Endocrinology and Metabolism

Deciphering the role of skin surface microbiome in skin health: an integrative multi-omics approach reveals three distinct metabolite-microbe clusters – Pierre-François Roux – The Journal of Investigative Dermatology

Preprint: Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation. – Mericien Venzon – Research Square

Novel microbiota-related gene set enrichment analysis identified osteoporosis associated gut microbiota from autoimmune diseases – Rong-Rong Cao – Journal of Bone and Mineral Metabolism

Sulfation of Arabinogalactan Proteins Confers Privileged Nutrient Status to Bacteroides plebeius – Jose Munoz-Munoz – mBio

Beneficial Microbes, Compounds, and Interventions

Review: Bifidobacterium longum: Protection against Inflammatory Bowel Disease – Shunyu Yao – Journal of Immunology Research

Gluten-free diet can ameliorate the symptoms of non-celiac autoimmune diseases – Aaron Lerner – Nutrition Reviews

Protein supplementation during an energy-restricted diet induces visceral fat loss and gut microbiota amino acid metabolism activation: a randomized trial – Pierre Bel Lassen – Scientific Reports

Food Microbiome

Metabolic Features of Ganjang (a Korean Traditional Soy Sauce) Fermentation Revealed by Genome-Centered Metatranscriptomics – Byung Hee Chun – mSystems

Animal Microbiome

Variation in Microbial Exposure at the Human-Animal Interface and the Implications for Microbiome-Mediated Health Outcome. – Sahana Kuthyar – mSystems

Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance – Christian R Voolstra – Molecular Ecology

Plant Microbiome

Site and Organ-Specific Culture-Dependent Endophytic Diversity of Crocus sativus L (Saffron) in Kashmir Himalaya, India. – Bushra Jan – Microbial ecology

Microbiome and Environment

Biodegradation of metoprolol in oxic and anoxic hyporheic zone sediments: unexpected effects on microbial communities – Cyrus Rutere – Applied Microbiology and Biotechnology

Microbial assemblages and methanogenesis pathways impact methane production and foaming in manure deep-pit storages – Fan Yang – PloS One

Preprint: Multi-plasmid clash in a bacterial community: plasmid viability depends on the ecological setting of hosts – Cindy Given – bioRxiv

Preprint: Genomic remnants of ancestral hydrogen and methane metabolism in Archaea drive anaerobic carbon cycling – Panagiotis S. Adam – bioRxiv

Microbiome and Forensic Research

Touch microbiome as a potential tool for forensic investigation: A pilot study – Noemi Procopio – Journal of Forensic and Legal Medicine

July 27, 2021

Have a nice day! Before presenting the Digest for today, I want to highlight that in few hours the ISME-LatinAmerica 2021 meeting will start. Additionally, I also want to highlight a Call from the Institut Pasteur for the creation of new groups (applications available until next November 30). Now, enjoy this digest!

Human and General Microbiome

Review: Discovery and mining of enzymes from the human gut microbiome – Baolei Jia – Trends in Biotechnology

Review: Antimicrobial peptides and proteins: Interaction with the skin microbiota – Franziska Rademacher – Experimental Dermatology

Review: Malnutrition and the microbiome as modifiers of early neurodevelopment – Elena J L Coley – Trends in Neurosciences

Review: Predictors of multidrug resistant Pseudomonas aeruginosa involvement in bloodstream infections – Sabina Herrera – Current Opinion in Infectious Diseases

Review: Diet Interventions for Irritable Bowel Syndrome: Separating the Wheat from the Chafe. – Emily Haller – Gastroenterology Clinics of North America

Review: Emerging Role of the Gut Microbiome in Irritable Bowel Syndrome – Prashant Singh – Gastroenterology Clinics of North America

Review: The Types and Proportions of Commensal Microbiota Have a Predictive Value in Coronary Heart Disease. – Lin Chen – Journal of Clinical Medicine

Review: Association of Microbiome with Oral Squamous Cell Carcinoma: A Systematic Review of the Metagenomic Studies. – Lee Su Mun – International Journal of Environmental Research and Public Health

Book Chapter: The Role of H(2)S in the Gastrointestinal Tract and Microbiota – Ailin Xiao – Advances in Hydrogen Sulfide Biology 

Research Highlight: CNMa-CNMa receptor at microbiome-gut-brain axis: novel target to regulate feeding decision – Liyuan Peng – Signal Transduction and Targeted Therapy

Household environmental microbiota influences early-life eczema development – Le Duc Huy Ta – Environmental Microbiology

Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment – Morteza Roodgar – Genome Research

Combined mechanical and oral antibiotic bowel preparation is associated with prolonged recurrence-free survival following surgery for colorectal cancer – Lindsey M Zhang – Journal of Surgical Oncology

Field evaluation of the gut microbiome composition of pre-school and school-aged children in Tha Song Yang, Thailand, following oral MDA for STH infections. – Katharina Stracke – PLoS Neglected Tropical Diseases

Characteristics of the bacterial microbiota in the upper respiratory tract of children – Wei Cao – European archives of Oto-rhino-laryngology

Exploring Gut Microbiota in Patients with Colorectal Disease Based on 16S rRNA Gene Amplicon and Shallow Metagenomic Sequencing – Yuanfeng Liu – Frontiers in Molecular Biosciences

The Intestinal Microbiome Predicts Weight Loss on a Calorie-Restricted Diet and Is Associated With Improved Hepatic Steatosis – Tien S Dong – Frontiers in Nutrition

16S rRNA gene amplicon sequencing of gut microbiota in gestational diabetes mellitus and their correlation with disease risk factors – J Wei – Journal of Endocrinological Investigation

Analyses of publicly available Hungatella hathewayi genomes revealed genetic distances indicating they belong to more than one species – Laura E Hernández-Juárez – Virulence

Estrogen-related receptor alpha (ERRα) is a key regulator of intestinal homeostasis and protects against colitis – Allan Tran – Scientific Reports

Predicting dental caries increment using salivary biomarkers in a remote Indigenous Australian child population – Surani Fernando – BMC Oral Health

Beneficial Microbes, Treatments, and Compounds

Human milk oligosaccharide 2′-fucosyllactose supplementation improves gut barrier function and signaling in the vagal afferent pathway in mice – Sunhye Lee – Food & Function

Lactobacillus casei LC89 exerts antidiabetic effects through regulating hepatic glucagon response and gut microbiota in type 2 diabetic mice – Yongli Zhang – Food & Function

The roles of different Bacteroides fragilis strains in protecting against DSS-induced ulcerative colitis and related functional genes – Chen Wang – Food & Function

Probiotics Fermentation Technology, a Novel Kefir Product, Ameliorates Cognitive Impairment in Streptozotocin-Induced Sporadic Alzheimer’s Disease in Mice – Nesrine S El Sayed – Oxidative Medicine and Cellular Longevity

Vaccarin enhances intestinal barrier function in type 2 diabetic mice – Jiang-Nan Sun – European Journal of Pharmacology

Personalized Postprandial Glucose Response-Targeting Diet Versus Mediterranean Diet for Glycemic Control in Prediabetes – Orly Ben-Yacov – Diabetes Care

Animal Microbiome

Dietary supplementation of alpha-lipoic acid mitigates the negative effects of heat stress in broilers – Sanjeev Wasti – PloS One

On the move: sloths and their epibionts as model mobile ecosystems – Maya Kaup – Biological reviews of the Cambridge Philosophical Society

Plant Microbiome

The discovery of pivotal fungus and major determinant factor shaping soil microbial community composition associated with rot root of American ginseng. – Lixia Tian – Plant Signaling & Behavior

Environmental Microbiome

Description of Microbial Communities of Phosphate Mine Wastes in Morocco, a Semi-Arid Climate, Using High-Throughput Sequencing and Functional Prediction. – Najoua Mghazli – Frontiers in Microbiology

Characterization of eukaryotic microbiome and associated bacteria communities in a drinking water treatment plant – Patricia Soler – The Science of the Total Environment

Dynamics of bacterial and archaeal communities along the composting of tannery sludge – Ademir Sergio Ferreira Araujo – Environmental Science and Pollution Research International

Other Microbes

Prioritization of potential drug targets and antigenic vaccine candidates against Klebsiella aerogenes using the computational subtractive proteome-driven approach. – Vijina Chakkyarath – Journal of proteins and proteomics

Genomic evolution of antimicrobial resistance in Escherichia coli – Pimlapas Leekitcharoenphon – Scientific Reports

Microbiome Analysis Tools and Techniques

Strainberry: automated strain separation in low-complexity metagenomes using long reads. – Riccardo Vicedomini – Nature Communications

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging – Katharine M Ng – Journal of Visualized Experiments (JoVE)

A newly developed PCR-based method revealed distinct Fusobacterium nucleatum subspecies infection patterns in colorectal cancer – Dexi Bi – Microbial Biotechnology

A protocol for characterization of extremely preterm infant gut microbiota in double-blind clinical trials – Magalí Martí – STAR Protocols

Transformation and differential abundance analysis of microbiome data incorporating phylogeny – Chao Zhou – Bioinformatics