Category Archives: Pregnancy and birth

March 3, 2022

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Today’s digest is heavy on studies focused on the gut and soil microbiomes. It also includes articles focused on microbial indoor air quality as well as bacterial vaginosis and aerobic vaginitis among pregnant women. If you’d still like more, I’ve also included several preprints.

Happy reading!


Human vaginal microbiome

Prevalence of bacterial vaginosis and aerobic vaginitis and their associated risk factors among pregnant women from northern Ethiopia: A cross-sectional study – Yalew et al. – PLOS One

Human gut microbiome

Systematically assessing microbiome–disease associations identifies drivers of inconsistency in metagenomic research – Tierney et al. – PLOS Biology

Preprint: Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation – Venzon et al. – bioRxiv

Hydrogen-producing small intestinal bacterial overgrowth is associated with hepatic encephalopathy and liver function – Yokoyama et al. – PLOS One

Plant, root, and soil microbiome

Preprint: Deciphering the potential niche of two novel black yeast fungi from a biological soil crust based on their genomes, phenotypes, and melanin regulation – Carr et al. – bioRxiv

Bacterial age distribution in soil—Generational gaps in adjacent hot and cold spots – Borer & Or – PLOS Computational Biology

Deciphering the influence of Bacillus subtilis strain Ydj3 colonization on the vitamin C contents and rhizosphere microbiomes of sweet peppers – Liang et al. – PLOS One

Antimicrobial effect and mechanism of bovine lactoferrin against the potato common scab pathogen Streptomyces scabiei – Nakamura et al. – PLOS One

Preprint: Arbuscular mycorrhizal fungal composition across US citrus orchards, management strategies, and disease severity spectrum – Xi et al. – bioRxiv

Built environment

Comprehensive health risk assessment of microbial indoor air quality in microenvironments – Kumar et al. – PLOS One

Phages and viruses

Preprint: Modelling the synergistic effect of bacteriophage and antibiotics on bacteria: killers and drivers of resistance evolution – Leclerc et al. -bioRxiv

Bioinformatics

Preprint: Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution – Kiefl et al. – bioRxiv

March 02, 2022

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General microbiome

Bacterial-Fungal Interactions and Their Impact on Microbial Pathogenesis – MacAlpine, Robbins & Cowen – Molecular Ecology

Pregnancy and early life

Influence of timing of maternal antibiotic administration during caesarean section on infant microbial colonisation: a randomised controlled trial – Dierikx et al. – Gut

Human skin microbiome

Predominance of Staphylococcus correlates with wound burden and disease activity in dystrophic epidermolysis bullosa: a prospective case-control study – Reimer-Taschenbrecker et al. – Journal of Investigative Dermatology

[REVIEW]Towards standardized and reproducible research in skin microbiomes – Ruuskanen et al. – Environmental Microbiology

Human oral microbiome

Comparability of microbiota of swabbed and spit saliva – Kaan et al. – Oral Sciences

Human gut microbiome

A multiple-dimension model for microbiota of patients with colorectal cancer from normal participants and other intestinal disorders – Shen et al. – Applied Microbial and Cell Physiology

Associations between Drinking Water Source and Gut Microbiota Composition in the American Gut Project Database – Vanhaecke – Annals of Nutrition and Metabolism

Rethinking Parkinson Disease: Exploring Gut-Brain Interactions and the Potential Role of Exercise – Zapanta et al. – Physical Therapy & Rehabilitation Journal

[PREPRINT]Mucosal microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients – Tran et al. – bioRxiv

How to Maintain a Healthy Gut Microbiome in Children with Cancer? Gut Microbiome Association with Diet in Children with Solid Tumors Postchemotherapy – Zhou et al. – OMICS: A Journal of Integrative Biology

[REVIEW]The potential utility of fecal (or intestinal) microbiota transplantation in controlling infectious diseases – Ghani et al. – Gut Microbes

Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma – Lee et al. – Nature Medicine

Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1 – McCulloch et al. – Nature Medicine

Establishing the role of the gut microbiota in susceptibility to recurrent urinary tract infections – Worby et al. – JCI

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

High environmental temperature: Insights into behavioural, neurodevelopmental and gut microbiome changes following gestational exposure in rats – Adebiyi – Neuroscience

Animal microbiome (for animals in the wild)

Unraveling the microbiota of the fish parasite Pseudoterranova decipiens in codfish (Gadus morhua) reveals a fish-related bacterial community – Saelens & Houf – International Journal of Food Microbiology

Microbial biogeography of the wombat gastrointestinal tract – Eisenhofer et al. – PeerJ

Intrinsic variation in the vertically transmitted core virome of the mosquito Aedes aegypti – Coatsworth et al. – Molecular Ecology

Plant, root, and soil microbiome

Multiomics Reveals the Effect of Root Rot on Polygonati Rhizome and Identifies Pathogens and Biocontrol Strain – Pang et al. – Microbiology Spectrum

Long-term effect of epigenetic modification in plant–microbe interactions: modification of DNA methylation induced by plant growth-promoting bacteria mediates promotion process – Chen et al. – Microbiome

Bioinformatics

[PREPRINT]Achieving pan-microbiome biological insights via the dbBact knowledge base – Amir et al. – bioRxiv

January 26, 2022

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General microbiome

[PREPRINT]Arresting microbiome development limits immune system maturation and resistance to infection – Lubin et al. – bioRxiv

Pregnancy and early life

Transcription shifts in gut bacteria shared between mothers and their infants – Vatanen et al. – Scientific Reports

Human urinary tract microbiome

Immune milieu and microbiome of the distal urethra in Ugandan men: impact of penile circumcision and implications for HIV susceptibility – Galwango et al. – Microbiome

Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states – Adu-Oppong et al. – Microbiome

Longitudinal variability in the urinary microbiota of healthy premenopausal women and the relation to neighboring microbial communities: A pilot study – Biehl et al. – PLOS One

Human vaginal microbiome

molBV reveals immune landscape of bacterial vaginosis and predicts human papillomavirus infection natural history – Usyk et al. – Nature Communications

Human gut microbiome

Differences in gut microbiome by insulin sensitivity status in Black and White women of the National Growth and Health Study (NGHS): A pilot study – Price et al. – PLOS One

Changes in the gut microbiota and risk of colonization by multidrug-resistant bacteria, infection and death in critical care patients – Rubio et al. – Clinical Microbiology and Infection

[PREPRINT]Gut Microbiome of Helminth Infected Indigenous Malaysians Is Context Dependent – Tee et al. – bioRxiv

Assessing the joint effects of brain aging and gut microbiota on the risks of psychiatric disorders – Zhang et al. – Brain Imaging and Behavior

Animal microbiome

Investigation of fiber utilization in the rumen of dairy cows based on metagenome-assembled genomes and single-cell RNA sequencing – Xue et al. – Microbiome

The influence of food processing methods on serum parameters, apparent total-tract macronutrient digestibility, fecal microbiota and SCFA content in adult beagles – Cai et al. – PLOS One

Kaempferol acts on bile acid signaling and gut microbiota to attenuate the tumor burden in ApcMin/+ mice – Li et al. – European Journal of Pharmacology

[PREPRINT]Diet outweighs genetics in shaping gut microbiomes in Asian honeybee – Su et al. – bioRxiv

Changes of Gut Microbiota by Natural mtDNA Variant Differences Augment Susceptibility to Metabolic Disease and Ageing – Künstner et al. – Int. J. Mol. Sci.

Diet Prevents Social Stress-Induced Maladaptive Neurobehavioural and Gut Microbiota Changes in a Histamine-Dependent Manner – Costa et al. – Int. J. Mol. Sci.

Gut microbe-targeted choline trimethylamine lyase inhibition improves obesity via rewiring of host circadian rhythms – Schugar et al. – eLife

Limited Evidence for Microbial Transmission in the Phylosymbiosis between Hawaiian Spiders and Their Microbiota – Perez-Lamarque – mSystems

Parkinson’s Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats – van Kessel et al. – mSystems

Multi-omics Analysis Revealed Coordinated Responses of Rumen Microbiome and Epithelium to High-Grain-Induced Subacute Rumen Acidosis in Lactating Dairy Cows – Mu et al. – mSystems

Predicting fungal infection rate and severity with skin-associated microbial communities on amphibians – Chen et al. – Molecular Ecology

Commensal oral microbiota induces osteoimmunomodulatory effects separate from systemic microbiome in mice – Hathaway-Schrader et al. – JCI insight

Plant, root, and soil microbiome

Shared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota – Duran et al. – Nature Communications

[PREPRINT]Biodiversity of the Genus Trichoderma in the Rhizosphere of Coffee (Coffea arabica) Plants in Ethiopia and their Potential Use in Biocontrol of Coffee Wilt Disease – Mulatu et al. – bioRxiv

Built environment (subways, indoor surfaces)

A biogeographic 16S rRNA survey of bacterial communities of ureolytic biomineralization from California public restrooms – Lim et al. – PLOS One

Techniques

[PREPRINT]Choice of 16S ribosomal RNA primers impacts urinary microbiota profiling – Heidrich et al. – bioRxiv

January 12, 2022

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General microbiome

[PERSPECTIVE]It’s the Economy, Stupid: Applying (Micro)economic Principles to Microbiome Science – Kashtan, Bushong and Leveau – mSystems

[PERSPECTIVE]Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes – Pfister et al. – mSystems

Human endometrial microbiome

Endometrial microbiota composition is associated with reproductive outcome in infertile patients – Moreno et al. – Microbiome

Human oral microbiome

[REVIEW]Temporal development of the infant oral microbiome – Blum et al. – Critical Reviews in Microbiology

Human gut microbiome

Effect of antibiotic pretreatment on bacterial engraftment after Fecal Microbiota Transplant (FMT) in IBS-D – Singh et al. – Gut Microbes

[REVIEW]The gut microbiota can orchestrate the signaling pathways in colorectal cancer – Bennedsen et al. – Journal of Pathology, Microbiology and Immunology

Age-Associated Gut Dysbiosis, Marked by Loss of Butyrogenic Potential, Correlates With Altered Plasma Tryptophan Metabolites in Older People Living With HIV – Ghare et al. – Journal of Acquired Immune Deficiency Syndrome

Intestinal Microbiota and Host Cooperate for Adaptation as a Hologenome – Zhou et al. – mSystems

The bacterial density of clinical rectal swabs is highly variable, correlates with sequencing contamination, and predicts patient risk of extraintestinal infection – Chanderraj et al. – Microbiome

Animal microbiome

Consistent changes in the intestinal microbiota of Atlantic salmon fed insect meal diets – Li et al. – Animal Microbiome

Maternal regulation of biliary disease in neonates via gut microbial metabolites – Jee et al. – Nature Communications

Reduced calorie diet combined with NNMT inhibition establishes a distinct microbiome in DIO mice – Dimet-Wiley et al. – Scientific Reports

Comparison of Gut Microbiota and Metabolic Status of Sows With Different Litter Sizes During Pregnancy – Chen et al. – Front. Vet. Sci.

Modulation of gut microbiota impacts diet-induced and drug-induced alopecia in mice – Lam et al. – Gut

Sex-specific differences in the gut microbiota and fecal metabolites in an adolescent valproic acid-induced rat autism model – Gu et al. – Frontiers in Bioscience Landmark

Host tp53 mutation induces gut dysbiosis eliciting inflammation through disturbed sialic acid metabolism – Lee et al. – Microbiome

Plant, root, and soil microbiome

Whole-Genome Duplication and Host Genotype Affect Rhizosphere Microbial Communities – Ponsford et al. – mSystems

Bioinformatics

A Goldilocks Principle for the Gut Microbiome: Taxonomic Resolution Matters for Microbiome-Based Classification of Colorectal Cancer – Armour et al. – mBio

Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer – Casimiro-Soriguer et al. – Scientifi Reports

Techniques

[PREPRINT]Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes – Poulsen et al. – bioRxiv

October 8, 2021

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Today’s digest features a metagenomic meta-study on faecal microbiota transplantation, RibDif for count and compare 16S rRNA genes within a genus, and more. Also, there is a new FEMS Microbiology Letters collection of articles highlighting the evolution of education during the COVID-19 pandemic.

There is still time to join in the second 🌎 Microbiome Virtual International Forum 🌏. Recordings from previous MVIF can be found here.

And, the #Microber2021 just started! Check out this microbe edition of #Inktober drawing challenge – during October, every day a new scientific art on microbiology topic.

Global microbiome

Cultivating Healthy Connections: Exploring and Engineering the Microbial Flow That Shapes Microbiomes – Travis J. Wiles – mSystems

Neonatal microbiome

Presence of distinctive microbiome in the first-pass meconium of newborn infants – Jenni Turunen – Scientific Reports

Respiratory microbiome

Divergence of bacterial communities in the lower airways of CF patients in early childhood – John B. O’Connor – PlosOne

Gut microbiome

Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation – Thomas Schmidt – bioRxiv

Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth–gut axis – Vishnu Prasoodanan P. K. – npj Biofilms and Microbiomes

Animal microbiome

Phylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate vast taxonomic diversity, open genomes and an abundance of carbohydrate-active enzyme family isoforms – Sara E. Pidcock – Microbial Genomics

Animal experiment

Metabolic modulation of tumours with engineered bacteria for immunotherapy – Fernando P. Canale – Nature

Citrobacter amalonaticus Inhibits the Growth of Citrobacter rodentium in the Gut Lumen – Caroline Mullineaux-Sanders – mBio

Regulation of blood–brain barrier integrity by microbiome-associated methylamines and cognition by trimethylamine N-oxide – Lesley Hoyles – bioRxiv

Effects of prebiotic oligofructose-enriched inulin on gut-derived uremic toxins and disease progression in rats with adenine-induced chronic kidney disease – Ebru Melekoglu – PlosOne

Plant microbiome

Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria – Claudia Sanchis-López – mSystems

Food

Bacteriocinogenic lactic acid bacteria in the traditional cereal-based beverage Boza: a genomic and functional approach – Luciano Lopes Queiroz – bioRxiv

Bioinformatics

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes – Francisco Zorrilla – Nucleic Acids Research

RibDif: can individual species be differentiated by 16S sequencing? – Mikael Lenz Strube – Bioinformatics Advances

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale – Carlos P Cantalapiedra – Molecular Biology and Evolution

Sequencing DNA with nanopores: Troubles and biases – Clara Delahaye and Jacques Nicolas – PlosOne

Webinars &c

Conference: Microbiome Virtual International Conference #MVIF – October 14 (Pacific Live)/15 (Atlantic Reply)

Webinar: EMBARK Fall Webinars – a webinar series focused on AMR research

Microscopy Live! – Geology – an hour of live electron microscopy, guided by the audience – Plymouth Electron Microscopy Centre (October 29)

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

Happy #Microber2021, sci-art October!

October 06, 2021

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General microbiome

The intestinal 3M (microbiota, metabolism, metabolome) Zeitgeist – from fundamentals to future challenges – Dey et al. – Free Radical Biology and Medicine

Pregnancy and early life

Gut microbiota changes in preeclampsia, abnormal placental growth and healthy pregnant women – Huang et al. – BMC Microbiology

Human respiratory microbiome

Refinement of microbiota analysis of specimens from patients with respiratory infections using next-generation sequencing – Ikegami et al. – Scientific Reports

Human skin microbiome

Experimental Dermatology Special Issue with Focus on ‘Skin microbiome and antimicrobial peptides’

Human gut microbiome

[REVIEW]Gut microbiome in pediatric acute leukemia: from predisposition to cure – Masetti et al. – Blood Advances

Animal microbiome

Effects of moderate exercise on hepatic amino acid and fatty acid composition, liver transcriptome, and intestinal microbiota in channel catfish (Ictalurus punctatus) – Zhang et al. – Comparative Biochemistry and Physiology Part D: Genomics and Proteomics

Metagenomic Sequencing Reveals that High-Grain Feeding Alters the Composition and Metabolism of Cecal Microbiota and Induces Cecal Mucosal Injury in Sheep – Xie, Wang & Mao – mSystems

Plant, root, and soil microbiome

Biodegradable and conventional microplastics exhibit distinct microbiome, functionality, and metabolome changes in soil – Sun et al. – Journal of Hazardous Materials

Soil microbiota and microarthropod communities in oil contaminated sites in the European Subarctic – Melekhina et al. – Scientific Reports

Fast and persistent responses of alpine permafrost microbial communities to in situ warming – Perez-Mon et al. – Science of The Total Environment

Built environment (subways, indoor surfaces)

Environmental dynamics of hospital microbiome upon transfer from a major hospital to a new facility – Ashokan et al. – Journal of Infection

Bioinformatics

[Commentary]Predicting Microbiome Metabolism and Interactions through Integrating Multidisciplinary Principles – Schmidt, Ghadermazi & Chan – mSystems

Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data – Armstrong et al. – mSystems

September 06, 2021

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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

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 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