September 14, 2021

General microbiome

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

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

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

Human oral microbiome

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

Human skin microbiome/virome

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

Human vaginal microbiome

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

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

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

Human gut microbiome

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

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

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

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

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

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

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

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

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

Bioinformatics

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

September 10, 2021

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

Global microbiome

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

Gut microbiome

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

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

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

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

Skin microbiome

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

Animal microbiome

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

Viruses and phages

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

Water microbiome

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

Bioinformatics

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

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

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

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

Webinars &c

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

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

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

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

September 7, 2021

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

General microbiome

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

Human gut microbiome

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

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

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

Animal Experiments

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

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

Water Microbiome

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

Soil microbiome

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

Bioinformatics

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

Non-microbiome picks

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

Five keys to writing a reproducible lab protocol – Nature

September 06, 2021

General microbiome

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

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

Pregnancy and early life

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

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

Multi-site human microbiome

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

Human respiratory microbiome

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

Human oral microbiome

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

Human gut microbiome

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

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

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

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

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

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

Bioinformatics

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

September 01, 2021

General microbiome

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

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

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

Pregnancy and early life

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

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

Human oral microbiome

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

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

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

Human gut microbiome

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

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

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

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

Animal/Insect microbiome

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

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

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

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

Plant, root, and soil microbiome

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

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

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

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 25, 2021

General microbiome

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

Pregnancy and early life

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

Human respiratory microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

Animal microbiome (for animals in the wild)

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

Plant, root, and soil microbiome

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

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

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

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

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 11, 2021

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

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