Category Archives: General Microbiome

August 15, 2021

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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.   

Highlights!

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

Techniques

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

August 11, 2021

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General microbiome

[REVIEW]Spot-light on microbiota in obesity and cancer – Marzullo et al. – International Journal of Obesity

Microbiome analysis, the immune response and transplantation in the era of next generation sequencing – Kanangat & Skaljic – Human Immunology

Pregnancy and early life

Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome – Roth-Schulze et al. – Microbiome

Human gut microbiome

[PREPRINT]Metataxonomic review to elucidate the role of the microbiome in Celiac disease across the gastrointestinal tract – Arcila et al. – bioRxiv

Microbiota and sleep: awakening the gut feeling – Sen et al. – Trends in Molecular Medicine

Effects of Smoking on Inflammatory Markers in a Healthy Population as Analyzed via the Gut Microbiota – Yan et al. – Front. Cell. Infect. Microbiol.

[REVIEW]The link between the gut microbiota and Parkinson’s Disease: A systematic mechanism review with focus on α-synuclein transport – Nielsen, Pearson & Seidler – Brain Research

[REVIEW]Gut brain axis: an insight into microbiota role in Parkinson’s disease – Moustafa et al. – Metabolic Brain Disease

Describing the intestinal microbiota of Holstein Fasciola-positive and -negative cattle from a hyperendemic area of fascioliasis in central Colombia – Ramirez et al. – PLOS Neglected Tropical Diseases

The gut microbiome of healthy Vietnamese adults and children is a major reservoir for resistance genes against critical antimicrobials – Pereira-Dias et al. – Journal of Infectious Diseases

Characteristics of gut microbiota in people with obesity – Duan et al. – PLOS One

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

Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes – Gaio et al. – Microbial Genomics

Effects of dietary rosemary extract supplementation on growth performance, nutrient digestibility, antioxidant capacity, intestinal morphology and microbiota of weaning pigs – Yang et al. – Journal of Animal Science

Changes in the gut microbiota: a possible factor influencing peripheral blood immune indexes in non-obese diabetic mice – Wu et al. – Antonie van Leeuwenhoek

Animal microbiome (for animals in the wild)

[PREPRINT]The gut bacteria of an invasive amphibian respond to the dual challenges of range-expansion and parasite attack – Zhou et al. – bioRxiv

Fishing for the Virome of Tropical Tuna – Gadoin et al. – Viruses

Plant, root, and soil microbiome

Colonization by the Red Imported Fire Ant, Solenopsis invicta, Modifies Soil Bacterial Communities – Travanty et al. – Host Microbe Interactions

Techniques

[PREPRINT]Shotgun proteomic profiling of dormant, ‘non-culturable’ Mycobacterium tuberculosis – Nikitushkin et al. – bioRxiv

[PREPRINT]A clinically validated human saliva metatranscriptomic test for global systems biology studies – Toma et al. – bioRxiv

Sample Preparation for Detection of Different Bacterial Strains by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry – Chac et al. – Current Protocols

August 6, 2021

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Today’s digest features a detailed temporal profiling of the rhizosphere and endosphere microbiomes of rice plants exposed to different drought durations, a review on microbiome and recurrent urinary tract infections, a new therapeutic strategy for treating pregnancy disorders via modulation of the maternal gut microbiome in mice, and more. Also, check out a collection of microbiome podcasts. Happy Friday!

First, important NEWS:
If you've recently published an Open-Access paper or Green-OA in peer-reviewed journals or a preprint on a publicly available repository, you can SUBMIT it as Open-Access Paper Highlight and present your work to the worldwide audience at the Microbiome Virtual International Forum!
And, today you can join the 2021 NSURP Closing Ceremony or later you can check out the presentations by NSURP students and their summer internship work on microbiology and immunology here!
New studies:

Global microbiome

A Scale-Free, Fully Connected Global Transition Network Underlies Known Microbiome Diversity – Gongchao Jing – mSystems

Gut microbiome

Perspective: Crosstalk between γδ T cells and the microbiota – Pedro H. Papotto – Nature Microbiology

Opinion: Microbiota and sleep: awakening the gut feeling – Paromita Sen – Trends in Molecular Medicine

Structural and quantitative alterations of gut microbiota in experimental small bowel obstruction – Jiali Mo – PlosOne

Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle – Hilary P. Browne – Genome Biology

Urinary microbiome

*Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs – Jonathan Josephs-Spaulding – Frontiers in Cellular and Infection Microbiology

Vaginal microbiome

The association between the vaginal microenvironment and fecundability: a register-based cohort study among Chinese women – X Hong – BJOG

Animal experiments

*Maternal microbiota Bifidobacterium promotes placental vascularization, nutrient transport and fetal growth in mice – Jorge Lopez-Tello – bioRxiv

Early invasion of the bladder wall by solitary bacteria protects UPEC from antibiotics and neutrophil swarms in an organoid model – Kunal Sharma – Cell Reports

Root microbiome

*Prolonged drought imparts lasting compositional changes to the rice root microbiome – Christian Santos-Medellín – Nature Plants

Bioinformatics

COPLA, a taxonomic classifier of plasmids – Santiago Redondo‑Salvo – BMC Bioinformatics

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

STRONG: metagenomics strain resolution on assembly graphs – Christopher Quince – Genome Biology

HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data – Pranvera Hiseni – Microbiome

YouTube Tutorial: How to Critically Evaluate Machine Learning Methods – Thomas P. Quinn

Webinars &c

Conference: Microbiome Virtual International Conference #MVIF – September 14

Hackathon: Petabyte-Scale Sequence Search: Metagenomics Benchmarking Codeathon – Application deadline August 20; Event Dates: Sept. 27-Oct. – The National Institutes of Health (NIH) Office of Data Science Strategy, the National Center for Biotechnology and Information at the National Library of Medicine, and the Department of Energy’s (DOE) Office of Biological and Environmental Research.

Conference: Microbiome Superheroes Connect – September 8 – Australasian Human Microbiome Research Network

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 EMBARK project.

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

Podcasts

August 4, 2021

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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

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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

July 24, 2021

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Have a nice weekend! Today in this Digest, we have a set of papers covering different aspects of the human microbiome in health and disease. For example, connections between gut microbiota and different clinical parameters in patients with inflammatory bowel disease, and another study showing a relationship between TMAO and heart damage.  

Human and General Microbiome

Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease – Jonathan Wei Jie Lee – Cell Host & Microbe

Gut Microbiota-generated Metabolite, Trimethylamine-N-oxide, And Subclinical myocardial damage: a multicenter study from Thailand – Vichai Senthong – Scientific Reports

Association Between The Urogenital Microbiome And Surgical Treatment Response In Women Undergoing Mid-urethral Sling Surgery for Mixed Urinary Incontinence – Holly E Richter – American Journal Of Obstetrics And Gynecology

Review: Personalized Approach To Childhood Obesity: Lessons From Gut Microbiota And Omics studies. Narrative review and insights from the 29th European childhood obesity congress – Aneta Gawlik – Pediatric Obesity

Review: The complex interplay of gut microbiota with the five most common cancer types: from carcinogenesis to therapeutics to prognosis – Kayla Jaye – Critical Reviews In Oncology/hematology

Clostridium culturomicium sp. nov. and Clostridium jeddahitimonense sp. nov., Novel members of the Clostridium genus isolated from the stool of an obese Saudi Arabian. – Hoang Thong Kieu – Current Microbiology

Effect Of Intestinal Microbiota Imbalance Associated With Chronic Hepatitis B Virus infection on the expression of microRNA‑192 and GLP‑1 – Yinghui Liu – Molecular Medicine Reports

Variations In The Oral Microbiome Are Associated With Depression In Young Adults – Benjamin Wingfield – Scientific Reports

Comparative Analysis Of The Bronchoalveolar Microbiome In Portuguese Patients With different chronic lung disorders – Susana Seixas – Scientific Reports

Microbiome and COVID19

Review: Recent Advance Of ACE2 And Microbiota Dysfunction In COVID-19 Pathogenesis – Zhidan Yu – Heliyon

Animal Microbiome

Review: T Cell Subsets And Environmental Factors In Citrobacter rodentium Infection – Brigitta Stockinger – Current Opinion In Microbiology

Chitinibacter bivalviorum sp. nov., Isolated From The Gut Of The Freshwater Mussel Anodonta arcaeformis – Jee-Won Choi – International Journal Of Systematic And Evolutionary Microbiology

Beneficial Microbes and Compounds

Nanocapsule-mediated Sustained H2 Release In The Gut Ameliorates Metabolic dysfunction-associated fatty liver disease – Zhaokui Jin – Biomaterials

Aryl Hydrocarbon Receptor Activation By Lactobacillus reuteri Tryptophan Metabolism alleviates Escherichia coli-induced mastitis in mice – Caijun Zhao – PLoS Pathogens

Grape Seed Proanthocyanidins Reduced The Overweight Of C57BL/6J Mice through modulating adipose thermogenesis and gut microbiota. – Haiping Du – Food & Function

Plant Microbiome

Distribution Of The Potential Pathogenic Alternaria On Plant Leaves Determines foliar fungal communities around the disease spot – Jiemeng Tao – Environmental Research

Prolonged Drought Imparts Lasting Compositional Changes To The Rice Root Microbiome – Christian Santos-Medellín – Nature Plants

News & Views: Drought Dampens Microbiome Development – Yi Song – Nature Plants

Built Environment

Factors Associated With Elevated Levels Of Antibiotic Resistance Genes In Sewer sediments and wastewater – Eramo Alessia – Environmental Science

Microbiome Techniques and Analysis

A Novel, Scalable, And Modular Bioreactor Design For Dynamic Simulation Of The digestive tract – Salam Habib – Biotechnology And Bioengineering

Assessment Of Biolog Ecoplate(TM) Method For Functional Metabolic Diversity Of aerotolerant pig fecal microbiota – A Checcucci – Applied Microbiology And Biotechnology

Structural Identifiability Of The Generalized Lotka-Volterra Model For Microbiome studies – Christopher H Remien – Royal Society Open Science

Validation Of The MYChrOme™ Culture Plate For Detection And Differentiation Of Rapid-Growing Nontuberculous Mycobacteria in potable and non-potable water: AOAC  Performance Tested MethodSM 062101 – Katherine E Fisher – Journal Of AOAC International

July 23, 2021

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Happy Friday!

It’s an exciting day here because I’m packing for fieldwork! In just a few short days I’ll be sampling from a saline aquifer in Illinois. For those of you who aren’t lucky enough to be going into the field, today’s digest is packed with a wide range of articles. Topics covered include the wild spider gut microbiome, the presence of antibiotic resistance genes in an Ohio river, the mosquito virome, the plant rhizosphere, and more.

Happy reading!

Human gut microbiome

Preprint: Phenotypic and genomic diversification in complex carbohydrate degrading human gut bacteria – Pudlo et al. – bioRxiv

Animal experiments

Effect of biochanin A on the rumen microbial community of Holstein steers consuming a high fiber diet and subjected to a subacute acidosis challenge – Harlow et al. – PLOS ONE

Ear wound healing in MRL/MpJ mice is associated with gut microbiome composition and is transferable to non-healer mice via microbiome transplantation – Velasco et al. – PLOS ONE

Animal microbiome

Preprint: Increased microbial diversity and decreased prevalence of common pathogens in the gut microbiomes of wild turkeys compared to domestic turkeys – Craft et al. – bioRxiv

Interspecific variation and functional traits of the gut microbiome in spiders from the wild: The largest effort so far – Tyagi et al. – PLOS ONE

Plant, root, and soil microbiome

Preprint: Tillage intensity and plant rhizosphere selection shape bacterial-archaeal assemblage diversity and nitrogen cycling genes – Cloutier et al. – bioRxiv

Water and extremophile microbiome

Preprint: An Ohio State Scenic River Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent – Murphy – bioRxiv

Biogeochemistry of the Antrim Shale Natural Gas Reservoir – Stemple et al. – ACS Earth and Space Chemistry

Built environment

Preprint: Novel municipal sewage-associated bacterial genomes and their potential in source tracking – Linder et al. – bioRxiv

Preprint: Structure of bacterial communities in Japanese-style bathrooms: Comparative sequencing of bacteria in shower water and showerhead biofilms using a portable nanopore sequencer – Fujiyoshi et al. – bioRxiv

Phages and viruses

Preprint: Dynamic surveillance of mosquitoes and their viromes in Wuhan during 2020 – Ren et al. – bioRxiv

Techniques

Simple mapping-based quantification of a mock microbial community using total RNA-seq data – Moriya – PLOS ONE

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

July 22, 2021

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Human and General Microbiome

The Change Of Gut Microbiota In MDD Patients Under SSRIs Treatment – Yang Shen – Scientific Reports

Minimal-moderate Variation Of Human Oral Virome And Microbiome In IgA Deficiency – Maria José de la Cruz Peña – Scientific Reports

Weight Shapes The Intestinal Microbiome In Preterm Infants: Results Of A Prospective observational study – Fardou H Heida – BMC Microbiology

Functional Heterogeneity In The Fermentation Capabilities Of The Healthy Human Gut microbiota – Thomas Gurry – PloS One

Characterization Of The Blood And Neutrophil-specific Microbiomes And Exploration Of potential bacterial biomarkers for sepsis in surgical patients – Chenyang Wang – Immunity, Inflammation And Disease

Cognitive Function Improvement After Fecal Microbiota Transplantation In In Alzheimer’s dementia patient: a case report – Soo-Hyun Park – Current Medical Research And Opinion

Amplicon And Metagenomic Analysis Of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS – Waleed Aljabr – mSphere

Dental Plaque Microbial Resistomes Of Periodontal Health And Disease And Their Changes after Scaling and Root Planing Therapy – Yutong Kang – mSphere

Archaea Are Rare And Uncommon Members Of The Mammalian Skin Microbiome – Alexander K Umbach – mSystems

Association Between Human Genetic Variants And The Vaginal Bacteriome Of Pregnant Women – Wei Fan – mSystems

Population-wide Diversity And Stability Of Serum Antibody Epitope Repertoires against human microbiota – Thomas Vogl – Nature Medicine

Dynamic Colonization Of Microbes And Their Functions After Fecal Microbiota Transplantation for Inflammatory Bowel Disease – Nathaniel D Chu – mBio

Review: Tryptophan Metabolites Modulate Inflammatory Bowel Disease And Colorectal Cancer By affecting immune system – Moein Ala – International Reviews Of Immunology

Review: From Gut Microbiota To Host Appetite: Gut Microbiota-derived Metabolites As Key regulators – Hui Han – Microbiome

The Roles Of Cytoplasmic Lipid Droplets In Modulating Intestinal Uptake Of Dietary Fat – Alyssa S Zembroski – Annual Reviews Of Nutrition

Review: Intestinal Microbiota In The SARS-CoV-2 Infection: What Is Known? – Patrícia Brito Rodrigues – Advances In Experimental Medicine And Biology

Review: The Microbiota-Gut-Brain Axis And Epilepsy – Qiang Yue – Cellular And Molecular Neurobiology

In Brief: Microbiota Links To Immunotherapy Toxicity – Sarah Seton-Rogers – Nature Reviews Cancer

Opinion: Forming Consensus To Advance Urobiome Research – Linda Brubaker – mSystems

Beneficial Microbes and Compounds

A High-protein Diet Containing Inulin/oligofructose Supports Body Weight Gain associated with lower energy expenditure and carbohydrate oxidation, and alters faecal microbiota in C57BL/6 mice – Franziska Koch – Journal Of Nutritional Science

Immunosuppressive Activity Is Attenuated By Astragalus polysaccharides Via remodeling the gut microenvironment in melanoma mice – Guiqing Ding – Cancer Science

Review: The Interaction Effect Between Tea Polyphenols And Intestinal Microbiota: Role In ameliorating neurological diseases – Mengyu Hong – Journal Of Food Biochemistry

Review: Nutritional Interventions And The Gut Microbiome In Children – Saurabh Mehta – Annual Reviews Of Nutrition

Animal Microbiome and Animal Models

Interspecific Variation And Functional Traits Of The Gut Microbiome In Spiders From the wild: The largest effort so far. – Kaomud Tyagi – PloS One

Vibrio vulnificus Induces The Death Of A Major Bacterial Species In The Mouse Gut via cyclo-Phe-Pro. – Jeong-A Kim – Microbiome

Maternal Cecal Microbiota Transfer Rescues Early-life Antibiotic-induced Enhancement of type 1 diabetes in mice. – Xue-Song Zhang – Cell Host & Microbe

Comprehensive Cultivation Of The Swine Gut Microbiome Reveals High Bacterial Diversity and Guides Bacterial Isolation in Pigs. – Xiaofan Wang – mSystems

Plant Microbiome

Drought Stress And Plant Ecotype Drive Microbiome Recruitment In Switchgrass – Tie-Yuan Liu – Journal Of Integrative Plant Biology

Microbe-dependent Heterosis In Maize – Maggie R Wagner – Proceedings Of The National Academy Of Sciences Of The United States Of America

Review: Prioritizing Host Phenotype To Understand Microbiome Heritability In Plants – Maggie R Wagner – The New Phytologist

Microbiome Analysis and Techniques

On The Robustness Of Inference Of Association With The Gut Microbiota In Stool, rectal swab and mucosal tissue samples – Shan Sun – Scientific Reports

Amplicon Sequence Variants Artificially Split Bacterial Genomes Into Separate Clusters. – Patrick D Schloss – MSphere

Linking Plasmid-based Beta-lactamases To Their Bacterial Hosts Using Single-cell fusion PCR – Peter J Diebold – eLife

An Integrated Machine Learning Framework For A Discriminative Analysis Of schizophrenia using multi-biological data. – Peng-Fei Ke – Scientific Reports

An Intestinal Gut Organ Culture System For Analyzing Host-Microbiota Interactions – Shalhevet Azriel – Journal Of Visualized Experiments (JoVE)

July 16, 2021

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Today’s digest features studies on environmental contamination of carbapenem-resistant Klebsiella pneumoniae in China (spoiler: extensive contamination, but has negligible impact on patient colonisation), the dynamic change and correlation of microbiome from different body sites to the treatment response as well as immune-related adverse events of immunotherapy in lung cancer patients, and more.

Also, check out a regularly-updated collection of FREE, ONLINE microbiome events. Happy Friday!

Human microbiome

*Prospective correlation between the patient microbiome with response to and development of immune-mediated adverse effects to immunotherapy in lung cancer – Justin Chau – BMC Cancer

Gut microbiome

Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner – Emmanuel Montassier – Nature Microbiology

Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects – Sandeep Verma – PlosOne

Differences in the individual curative effect of acupuncture for obese women with polycystic ovary syndrome based on metagenomic analysis: study protocol for a randomized controlled trial – Huaying Fan – Trials

Comparative Analysis of 16S rRNA Gene and Metagenome Sequencing in Pediatric Gut Microbiomes – Danielle Peterson – Frontiers in Microbiology

Resistome

*Spread of Carbapenem-Resistant Klebsiella pneumoniae in an Intensive Care Unit: A Whole-Genome Sequence-Based Prospective Observational Study – Li Wei – Microbiology Spectrum

*Linezolid- and multidrug-resistant enterococci in raw commercial dog food, Europe, 2019–2020 – Ana R. Freitas – Emerging Infectious Diseases

Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study – Huan Chen – PeerJ

Predicting antibiotic resistance gene abundance in activated sludge using shotgun metagenomics and machine learning – Yuepeng Sun – Water Research

Animal microbiome

Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers – Déborah Romaskevis Gomes Lopes – Journal of Animal Science and Biotechnology

Animal experiment

An osmotic laxative renders mice susceptible to prolonged Clostridioides difficile colonization and hinders clearance – Sarah Tomkovich – bioRxiv

Bioinformatics

Critical Assessment of Metagenome Interpretation – the second round of challenges – F. Meyer – bioRxiv

Disentangling environmental effects in microbial association networks – Maria Deutschmann – bioRxiv

Webinars &c

Microbiome Virtual International Conference #MVIF – September 14

July 14, 2021

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General microbiome

Bacteriophage-Bacteria Interactions in the Gut: From Invertebrates to Mammals – Kirsch et al. – Annual Review of Virology

Helicobacter pylori infection has a detrimental impact on the efficacy of cancer immunotherapies – Oster et al. – Gut

Pregnancy and early life

Cervicovaginal microbiota and metabolome predict preterm birth risk in an ethnically diverse cohort – Flaviani et al. – JCI Insight

[REVIEW][Early-life gut microbiota and its connection to metabolic health in children: Perspective on ecological drivers and need for quantitative approach – Jian et al. – EBBioMedicine

Associations of air pollution and greenness with the nasal microbiota of healthy infants: A longitudinal study – Gisler et al. – Environmental Research

Human respiratory microbiome

Multi-omics profiling predicts allograft function after lung transplantation – Watzenböck et al. – European Respiratory Journal

Metagenomic Analysis Reveals A Possible Association Between Respiratory Infection and Periodontitis – Liu et al. – Genomics, Proteomics & Bioinformatics

Human skin microbiome

[REVIEW]Novel mechanisms of microbial crosstalk with skin innate immunity – Chinnappan & Harris-Tyron – Experimental Dermatology

Shifts in the skin bacterial and fungal communities of healthy children transitioning through puberty – Park et al. – Journal of Investigative Dermatology

Human gut microbiome

Gut-microbiota-targeted diets modulate human immune status – Wastyk et al. – Cell

[REVIEW]Silent hypoxia in COVID-19: a gut microbiota connection – Gopal et al. – Current Opinion in Physiology

[REVIEW]The Athlete and Gut Microbiome: Short-chain Fatty Acids as Potential Ergogenic Aids for Exercise and Training – Bongiovanni, Yin & Heaney

Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects – Verma et al. – PLOS One

Kefir Ameliorates Specific Microbiota-Gut-Brain Axis Impairments in a Mouse Model Relevant to Autism Spectrum Disorder – van de Wouw et al. – Brain, Behavior, and Immunity

Animal microbiome

Comparative analysis of oral-gut microbiota between captive and wild long-tailed macaque in Thailand – Sawaswong et al. – Scientific Reports

Impact of the dietary inclusion of dried food residues on the apparent nutrient digestibility and the intestinal microbiota of dogs – Paßlack et al. – Archives of Animal Nutrition

Triphenyltin exposure causes changes in health-associated gut microbiome and metabolites in marine medaka – He et al. – Environmental Pollution

The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota – Bermudez-Martin et al. – Microbiome

Microbes in space

Seven years of Progress in Determining Fungal Diversity and Characterization of Fungi Isolated from the Japanese Experiment Module KIBO, International Space Station – Satoh et al. – Microbiology and Immunology

Food microbiology

[REVIEW]Virome studies of food production systems: time for ‘farm to fork’ analyses – Mahony & van Sinderen – Current Opinion in Biotechnology

Bioinformatics

D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies – Chen & Zhang – Bioinformatics

Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model – Hosoda, Fukunaga & Hamada – Bioinformatics

[PREPRINT]Stool Studies Don’t Pass the Sniff Test: A Systematic Review of Human Gut Microbiome Research Suggests Widespread Misuse of Machine Learning – Quinn – arXiv

Techniques

Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost – Harrison, Randolph & Buerkle – mSystems

Two-Target Quantitative PCR To Predict Library Composition for Shallow Shotgun Sequencing – Cho et al. – mSystems

Statistical approaches for differential expression analysis in metatranscriptomics – Zhang et al. – Bioinformatics

Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1–V2 and V3–V4 primer sets – Kameoka et al. – BMC Genomics

In vitro models of gut digestion across childhood: current developments, challenges and future trends – Fournier et al. – Biotechnology Advances