September 01, 2021

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General microbiome

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

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

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

Pregnancy and early life

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

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

Human oral microbiome

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

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

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

Human gut microbiome

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

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

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

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

Animal/Insect microbiome

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

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

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

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

Plant, root, and soil microbiome

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

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

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

Bioinformatics/Techniques

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

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

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

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

August 28, 2021

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Events

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

Highlights!

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

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

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

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

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

Human and General Microbiome

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

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

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

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

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

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

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

Perspective: How microbiota improve immunotherapy – Eduard Ansaldo – Science

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

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

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

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

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

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

Beneficial Compounds and Microbes

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

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

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

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

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

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

Animal Microbiome 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Soil and Plant Microbiome

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

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

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

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

Environmental Science

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

Protocols, Methods and Techniques

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

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

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

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

August 25, 2021

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General microbiome

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

Pregnancy and early life

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

Human respiratory microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

Animal microbiome (for animals in the wild)

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

Plant, root, and soil microbiome

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

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

Techniques/Bioinformatics

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

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

August 22nd, 2021

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Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a selection of really interesting preprints and published studies. If you are interested in soil microbiology, take a look at the preprint by Nelson and collaborators, who characterized the soil microbiome across a wildfire burn severity gradients in coniferous forests and made their dataset available in the Fire Responding Ecogenomic database (FiRE-db).

Looking at a large variety of ecosystems, Rodriguez-Gijon and collaborators used a vast collection of Metagenomes Assembled Genomes (MAGs), to investigate the genomes size of prokaryotes in these ecosystems. They show that, while the environment of origin can be linked to genome size, it seems like evolutionary phylogenetic history is in many cases a stronger predictor.

Finally, today’s non-microbiology pick is a great “10 simples rules” paper reviewing best practices on organizing bioinformatics workshops in low and middle-income countries.

Have a great Weekend!

General microbiome

Preprint: A genomic perspective across Earth’s microbiomes reveals that genome size in Archaea and Bacteria is linked to ecosystem type and trophic strategy – Rodriguez-Gijon et al. – BioRXiV

Multi-site human microbiome

Review : Host-Microbe Metagenomics: a Lens To Refocus Our Perspective
on Infectious and Inflammatory Diseases – Kalantar and Langelier – mSystems

Human gut microbiome

Rectal bacteriome and virome signatures and clinical outcomes in community-acquired pneumonia: An exploratory study – Kullberg et al. – EClinicalMedicine

Review: The important role of fungi in inflammatory bowel diseases – Wang et al. – Scandinavian Journal of Gastroenterology

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

Preprint: A bacterial genome and culture collection of gut microbial in weanling piglet – Dong et al. – BioRXiV

Characterization of the fecal microbiota of sows and their offspring from German commercial pig farms – Lührmann et al. – Plos One

Plant, root, and soil microbiome

Preprint: Does plant diversity determine the diversity of the rhizosphere microbial community? – Zverev et al. – BioRXiV

Preprint: Playing with FiRE: A genome resolved view of the soil microbiome responses to high severity forest wildfire – Nelson et al. – BioRXiV

Peatland microbial community responses to plant functional group and drought are depth-dependent – Lamit et al. – Molecular ecology

Soil pH determines bacterial distribution and assembly processes in natural mountain forests of eastern China – Ni et al. – Global ecology and Biogeography

Water and extremophile microbiome

Preprint: The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments – Nishimura et al. – BioRXiV

Food microbiology

Preprint: Mixed culture metagenomics of the microbes making sour beer – Piraine et al. – BioRXiV

Preprint: Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh – Tanzina et al. – BioRXiV

Preprint: Microbial communities in retail draft beers and the biofilms they produce – Bose et al. – BioRXiV

Bioinformatics

Book chapter: Bioinformatics Tools and Software – Gupta et al. – Advances in Bioinformatics, Springer, Singapore

MiDSystem: A comprehensive online system for de novo assembly and analysis of microbial genomes – Lee et al. – New biotechnology

My non-microbiology picks

Ten simple rules for organizing a bioinformatics training course in low– and middle-income countries – Moore et al. – PLOS computational biology

August 18, 2021

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Call for Papers

Cells is calling for papers for a special issue on “Interplay of Gene Expression Regulation and Microbiome”. Deadline for paper submission: 30th of November 2021

General microbiome

[REVIEW]The Cancer Microbiome: Recent Highlights and Knowledge Gaps – Knippel, Drewes & Sears – Cancer Discoveries

[REVIEW]Healthy Patients Are Not the Best Controls for Microbiome-Based Clinical Studies: Example of Sjögren’s Syndrome in a Systematic Review – Doare et al. – Frontiers in Immunology

[REVIEW]The varying effects of antibiotics on gut microbiota – Yang et al. – AMB Express

[REVIEW]Prevotella diversity, niches and interactions with the human host – Tett et al. – Nature Reviews Microbiology

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

Long-term biodiversity intervention shapes health-associated commensal microbiota among urban day-care children – Roslund et al. – Environment International

Multi-site human microbiome

Different responses of the oral, nasal and lung microbiomes to cigarette smoke – Pfeiffer et al. – Thorax

Human skin microbiome

[REVIEW]The power and potential of BIOMAP to elucidate host-microbiome interplay in skin inflammatory diseases – Alenius et al. – Experimental Dermatology

[PREPRINT]Bacterial DNA on the skin surface overrepresents the viable skin microbiome – Acosta et al. – bioRxiv

Human oral microbiome

[REVIEW]The role of oral bacteria in inflammatory bowel disease – Read, Curtis & Neves

Inflammation-type dysbiosis of the oral microbiome associates with the duration of COVID-19 symptoms and long-COVID – Haran et al. – JCI insight

Human gut microbiome

[REVIEW]Phage Diversity in the Human Gut Microbiome: a Taxonomist’s Perspective – Adriaenssens – mSystems

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

IL-10 Deficiency Accelerates Type 1 Diabetes Development via Modulation of Innate and Adaptive Immune Cells and Gut Microbiota in BDC2.5 NOD Mice – Huang et al. – Frontiers in Immunology

Genetically determined hypertensive phenotype affects gut microbiota composition, but not vice versa – Konopelski et al. – Journal of Hypertension

Plant, root, and soil microbiome

Plant developmental stage drives the differentiation in ecological role of the maize microbiome – Xiong et al. – Microbiome

Bioinformatics

ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach – Dovrolis et al. – PLOS Computational Biology

[PREPRINT]SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs) – Pan et al. – bioRxiv

[PREPRINT]Network analysis of ten thousand genomes shed light on Pseudomonas diversity and classification – Passarelli-Araujo, Franco & Venancio – bioRxiv

Techniques

[PREPRINT]The clinical utility of two high-throughput 16S rRNA gene sequencing workflows for taxonomic assignment of unidentifiable bacterial pathogens in MALDI-TOF MS – Lao et al. – bioRxiv

August 17, 2021

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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.

COVID-19 

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

Bioinformatics

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

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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

Posted on by

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