Category Archives: General Microbiome

January 28, 2022

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Human and General Microbiome

Diet leaves a genetic signature in a keystone member of the gut microbiota – Tanja Dapa – Cell Host & Microbe

Multi-omics investigation of Clostridioides difficile-colonized patients reveals pathogen and commensal correlates of C. difficile pathogenesis – Skye Rs Fishbein – eLife

Large-scale characterization of the macrolide resistome reveals high diversity and several new pathogen-associated genes – David Lund – Microbial Genomics

The small bowel microbiome changes significantly with age and aspects of the ageing process – Gabriela Leite – Microbial Cell

Intestinal microbiota profiles in a genetic model of colon tumorigenesis correlates with colon cancer biomarkers – Francesco Vitali – Scientific Reports

Skin microbiome profile of healthy Cameroonians and Japanese – Kazuhiro Ogai – Scientific Reports

Interactions between human milk oligosaccharides, microbiota and immune factors in milk of women with and without mastitis – Irma Castro – Scientific Reports

Microbiota of the prostate tumor environment investigated by whole-transcriptome profiling – Paul Vinu Salachan – Genome Medicine

Preview: Microbiome engineering: Taming the untractable – James W Marsh – Cell

Review: Microbiomes in physiology: Insights into 21(st) century global medical challenges – Emad Shehata – Experimental Physiology

Respiratory Tract Microbiome – Highlights

Gut microbiota dynamics in a prospective cohort of patients with post-acute COVID-19 syndrome – Qin Liu – Gut

Characteristics of Lung Microbiota in Children’s Refractory Mycoplasma pneumoniae Pneumonia Coinfected with Human Adenovirus B – Wenxiang Zhou – The Canadian Journal of Infectious Diseases & Medical Microbiology

The lung microbiota in children with cystic fibrosis captured by induced sputum sampling – Rebecca Weiser – Journal of Cystic Fibrosis 

Beneficial Microbes and Compounds

Bifidobacterium animalis subsp. lactis BB-12 Has Effect Against Obesity by Regulating Gut Microbiota in Two Phases in Human Microbiota-Associated Rats – Kemin Mao – Frontiers in Nutrition

Effects of a 10-Strain Oral Probiotic on Parameters of Vaginal Health and Microbial Community: A Pilot Clinical Study – Christopher J Martoni – International Journal of Women’s Health

A randomised, double-blind, placebo-controlled trial of Bifidobacterium bifidum CCFM16 for manipulation of the gut microbiota and relief from chronic constipation – Luyao Wang – Food & Function

Vaginal states: detection of conversion processes in women using contraception and characterization of vaginal Lactobacillus species – Sonia Elena María Fosch – Infectious Disorders Drug Targets

The probiotic properties and potential of vaginal Lactobacilli spp. isolated from healthy women against some vaginal pathogens – Arezoo Asadi – Letters in Applied Microbiology

Review: Protective Effects of Natural Polysaccharides on Intestinal Barrier Injury: A Review – Jiaying Huo – Journal of Agricultural and Food Chemistry

Animal Microbiome

Nitrogen recycling via gut symbionts increases in ground squirrels over the hibernation season – Matthew D Regan – Science

Robust host source tracking building on the divergent and non-stochastic assembly of gut microbiomes in wild and farmed large yellow croaker – Jun Zhu – Microbiome

Evaluation of three Bacillus spp. isolated from the gut of giant freshwater prawn as potential probiotics against pathogens causing Vibriosis and Aeromonosis – Muhamad Firdaus Syahmi Sam-On – Microbial Pathogenesis

Gut Microbial Trimethylamine is Elevated in Alcohol-Associated Hepatitis and Contributes to Ethanol-Induced Liver Injury in Mice – Robert N Helsley – eLife

Intestinal gluconeogenesis shapes gut microbiota, fecal and urine metabolome in mice with gastric bypass surgery – Justine Vily-Petit – Scientific Reports

Food Microbiome

To culture or not to culture: careful assessment of metabarcoding data is necessary when evaluating the microbiota of a modified-atmosphere-packaged vegetarian meat alternative throughout its shelf-life period – E Duthoo – BMC Microbiology

Plant Microbiome

Root Morphogenesis of Arabidopsis thaliana Tuned by Plant Growth-Promoting Streptomyces Isolated From Root-Associated Soil of Artemisia annua – Wenbo Fu – Frontiers in Plant Science

Environmental Microbiome

Soil microbial community development across a 32-year coastal wetland restoration time series and the relative importance of environmental factors – Katherine M Abbott – The Science of the Total Environment

Emerging frontiers in microbe mediated pesticide remediation: Unveiling role of omics and In silico approaches in engineered environment – Muneer Ahmad Malla – Environmental Pollution 

Review: Emerging investigator series: microplastic sources, fate, toxicity, detection, and interactions with micropollutants in aquatic ecosystems – a review of reviews – Mohamed Ateia – Environmental Science. Processes & Impacts

Techniques

Alternating Dual-Collision Energy Scanning Mass Spectrometry Approach: Discovery of Novel Microbial Bile-Acid Conjugates – Quan-Fei Zhu – Analytical Chemistry

Genetic tools for the redirection of the central carbon flow towards the production of lactate in the human gut bacterium Phocaeicola (Bacteroides) vulgatus – Rebecca Lück – Applied Microbiology and Biotechnology

Lipidomics Analysis of Outer Membrane Vesicles and Elucidation of the Inositol Phosphoceramide Biosynthetic Pathway in Bacteroides thetaiotaomicron – Mariana G Sartorio – Microbiology Spectrum

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 21, 2022

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Human and General Microbiome

Metabolite-based dietary supplementation in human type 1 diabetes is associated with microbiota and immune modulation – Kirstine J Bell – Microbiome

GWAS-associated bacteria and their metabolites appear to be causally related to the development of inflammatory bowel disease – Zhenhuang Zhuang – European Journal of Clinical Nutrition

The vaginal Torquetenovirus titer varies with vaginal microbiota composition in pregnant women – Tania Regina Tozetto-Mendoza – PloS ONE

Can the Acid-formation Potential of Saliva Detect a Caries-related Shift in the Oral Microbiome? – Cornelia Frese – Oral Health & Preventive Dentistry

Gut microbiome alterations and gut barrier dysfunction are associated with host immune homeostasis in COVID-19 patients – Zhonghan Sun – BMC Medicine

Predicting Treatment Nonresponse in Hispanic/Latino Children Receiving Silver Diamine Fluoride for Caries Arrest: A Pilot Study Using Machine Learning – Ryan Richard Ruff – Frontiers in Oral Health

The Gut Microbiome of Adults With Type 1 Diabetes and Its Association With the Host Glycemic Control – Smadar Shilo – Diabetes Care

Evaluation of Bacterial Diversity and Evolutionary Dynamics of Gut Bifidobacterium longum Isolates Obtained from Older Individuals in Hubei Province, China – Zhendong Zhang – Microbiology Spectrum

Review: Frontiers in Oral Mucosal Immunity and the Microbiome – Georgios N Belibasakis – Frontiers in Oral Health

Review: The microbiota-gut-brain axis: pathways to better brain health. Perspectives on what we know, what we need to investigate and how to put knowledge into practice – Anirikh Chakrabarti – Cellular and Molecular Life Sciences

Meta-Analysis: Predictors of Fecal Microbiota Transplant Failure in Clostridioides difficile Infection: An Updated Meta-analysis – Azizullah Beran – Journal of Clinical Gastroenterology

Systematic Review: The Role of Gut Microbiota-Brain Axis in Pathophysiology of ADHD: A Systematic Review – Salman Shirvani-Rad – Journal of Attention Disorders

Systematic Review: Meta-Analysis Using NGS Data: The Veillonella Species in Dental Caries – Naile Dame-Teixeira – Frontiers in Oral Health

Beneficial Microbes and Compounds

Peppermint oil effects on the gut microbiome in children with functional abdominal pain – Santosh Thapa – Clinical and Translational Science

SER-109, an Oral Microbiome Therapy for Recurrent Clostridioides difficile Infection – Paul Feuerstadt – The New England Journal of Medicine

Lactiplantibacillus plantarum CCFM1019 attenuate polycystic ovary syndrome through butyrate dependent gut-brain mechanism – Yufeng He – Food & Function

Causal relationship between gut microbiota and serum vitamin D: evidence from genetic correlation and Mendelian randomization study – Xiaolin Yang – European Journal of Clinical Nutrition

Review: Modulation of Gut Microbiota and Immune System by Probiotics, Pre-biotics, and Post-biotics – Yue Liu – Frontiers in Nutrition

Review: Outlook on next-generation probiotics from the human gut – Francesca De Filippis – Cellular and Molecular Life Sciences

Animal Microbiome

Seasonal shift of the gut microbiome synchronizes host peripheral circadian rhythm for physiological adaptation to a low-fat diet in the giant panda – Guangping Huang – Cell Reports

Seasonal variations in the composition and functional profiles of gut microbiota reflect dietary changes in plateau pikas – Chao Fan – Integrative Zoology

N-acyl-homoserine lactone produced by Rahnella inusitata isolated from the gut of Galleria mellonella influences Salmonella phenotypes – Leonardo Luiz de Freitas – Brazilian Journal of Microbiology

Comparative 16S Metabarcoding of Nile Tilapia Gut Microbiota from the Northern Lakes of Egypt – Ahmed M Serag – Applied Biochemistry and Biotechnology

Diversity and Distribution of Microbial Communities Associated with Reef Corals of the Malay Peninsula – Dhivya P Kanisan – Microbial Ecology

The Harris’ hawk (Parabuteo unicinctus) as a source of pathogenic human yeasts: a potential risk to human health – Gustavo Dornelles – Future Microbiology

Increased microbial diversity and decreased prevalence of common pathogens in the gut microbiomes of wild turkeys compared to domestic turkeys – Julia Craft – Applied and Environmental Microbiology

Comparative Evaluation of the Effect of Metformin and Insulin on Gut Microbiota and Metabolome Profiles of Type 2 Diabetic Rats Induced by the Combination of Streptozotocin and High-Fat Diet – Nan Hu – Frontiers in Pharmacology

Plant Microbiome

Modulating the rhizosphere microbiome by altering the cocktail of root secretions – Wei Zhang – Plant Physiology

Book Chapter: Characterization of Tobacco Microbiome by Metagenomics Approach – R Suresh Kumar – Methods in Molecular Biology 

Bioinformatics and Genomics

Incorporating genome-based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes – Nicholas D Youngblut – Environmental Microbiology

Single-cell Microbiomics Unveils Distribution and Patterns of Microbial Symbioses in the Natural Environment – Vittorio Boscaro – Microbial Ecology

Adaptive and powerful microbiome multivariate association analysis via feature selection – Kalins Banerjee – NAR Genomics and Bioinformatics

Metabolic modeling of host-microbe interactions for therapeutics in colorectal cancer – Prerna Bhalla – NPJ Systems Biology and Applications

January 19, 2022

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Human oral and skin microbiome

Oral HPV associated with differences in oral microbiota beta diversity and microbiota abundance – Zhang et al. – The Journal of Infectious Diseases

The Skin and Nose Microbiome and Its Association with Filaggrin Gene Mutations in Pediatric Atopic Dermatitis – van Mierlo et al. – Dermatology

Human gut microbiome

Associations of Childhood and Perinatal Blood Metals with Children’s Gut Microbiomes in a Canadian Gestation Cohort – Shen et al. – Environmental Health Perspectives

Patient knowledge of gut microbiota and acceptability of fecal microbiota transplantation in various diseases – Benech et al. – Neurogastroenterology & Motility

[PREPRINT]Comprehensive assessment of functional effects of commonly used sweeteners on ex vivo human gut microbiome – Sun et al. – bioRxiv

Fusobacterium nucleatum and Bacteroides fragilis detection in colorectal tumours: Optimal target site and correlation with total bacterial load – Rye et al. – PLOS One

Human gut microbiome aging clocks based on taxonomic and functional signatures through multi-view learning – Chen et al. – Gut Microbes

[REVIEW]The gut microbiome can be a potential regulator and treatment target of bone metastasis – Contino, Yadav & Shiozawa – Biochemical Pharmacology

Animal microbiome

Comparative analysis of gut microbial composition and potential functions in captive forest and alpine musk deer – Jiang et al. – Environmental Biotechnology

Effects of dietary antimicrobial peptides on intestinal morphology, antioxidant status, immune responses, microbiota and pathogen disease resistance in grass carp Ctenopharyngodon idellus – Liu et al. – Microbial Pathogenesis

[PREPRINT]Microbiomes of hadal fishes contain similar taxa, obligate symbionts, and known piezophiles across trench habitats – Blanton et al. – bioRxiv

Association of human disturbance and gastrointestinal parasite infection of yellow baboons in western Tanzania – Mason et al. – PLOS One

Bacterial recognition by PGRP-SA and downstream signalling by Toll/DIF sustain commensal gut bacteria in Drosophila – Bahuguna et al. – PLOS Genetics

[PREPRINT]Meta-analysis of the black soldier fly (Hermetia illucens) microbiota based on 16S rRNA gene amplicon sequencing – Idema et al. – bioRxiv

Groundwater microbiome

Vertical stratification of microbial communities and isotope geochemistry tie groundwater denitrification to sampling location within a nitrate-contaminated aquifer – Chakraborty et al. – Science of The Total Environment

Techniques / Bioinformatics

Microbiome differential abundance methods produce different results across 38 datasets – Nearing et al. – Nature Communications

[PREPRINT]Using strain-resolved analysis to identify contamination in metagenomics data – Lou et al. – bioRxiv

Revealing General Patterns of Microbiomes That Transcend Systems: Potential and Challenges of Deep Transfer Learning – David et al. – mSystems

January 18, 2022

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Today’s digest contains interesting gut-brain axis articles, developments in bioinformatic multi-omic analyses, and some recent developments in long COVID research highlighted under non microbiome picks below. 

General microbiome

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

Human gut microbiome

Gut Ruminococcaceae levels at baseline correlate with risk of antibiotic-associated diarrhea – Gu et al. – iScience

Home or hospital birth: the neonatal microbiota perspective – Stojanov et al. – The Lancet Microbe

A pilot exploration of multi-omics research of gut microbiome in major depressive disorders – Zhao et al – Translational Psychiatry

Post-ischemic protein restriction induces sustained neuroprotection, neurological recovery, brain remodeling, and gut microbiota rebalancing – de Carvalho et al. – Brain Behavior and Immunity

Bifidobacterium breve CCFM1025 attenuates major depression disorder via regulating gut microbiome and tryptophan metabolism: A randomized clinical trial – Tian et al.  – Brain Behavior and Immunity

Gestational insulin resistance is mediated by the gut microbiome-indoleamine 2,3-dioxygenase axis – Priyadarshini et al. – Gastroenterology

A natural polyphenol exerts antitumor activity and circumvents anti-PD-1 resistance through effects on the gut microbiota – Messaoudene et al. – Cancer Discovery

Virome

[Research Highlight] Virome holds back a vaccine – York – Nature Reviews Microbiology

Plant & Soil microbiome

Genome-Resolved Metagenomics Reveals Distinct Phosphorus Acquisition Strategies between Soil Microbiomes – Wu et al. – mSystems

Bioinformatics

M&Ms: a versatile software for building microbial mock communities – García-García et al. – Bioinformatics

GraphOmics: an interactive platform to explore and integrate multi-omics data – Wandy & Daly – BMC Bioinformatics

Aristotle: stratified causal discovery for omics data – Mansouri et al.  – BMC Bioinformatics

Non Microbiome Picks

The last few weeks has seen several big studies of ‘long COVID’ published, as well as a letter in The Guardian, which I wanted to highlight

Immunological dysfunction persists for 8 months following initial mild-to-moderate SARS-CoV-2 infection – Phetsouphanh et al. – Nature Immunology

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

Post-acute neurological consequences of COVID-19: an unequal burden – Nolen et al. – Nature Medicine 

Long COVID in children – Gurdasani et al. – The Lancet Child Adolescent Health
I’m leading a long Covid trial – it’s clear Britain has underestimated its impact – Amitava Banerjee – The Guardian

January 17, 2022

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Human and General Microbiome

Exploring the universal healthy human gut microbiota around the World – Samuel Piquer-Esteban – Computational and Structural Biotechnology Journal

An Investigation into the Effects of Outer Membrane Vesicles and Lipopolysaccharide of Porphyromonas gingivalis on Blood-Brain Barrier Integrity, Permeability, and Disruption of Scaffolding Proteins in a Human in vitro Model – Anna Barlach Pritchard – Journal of Alzheimer’s Disease

Evolution of fluoroquinolone-resistant Escherichia coli in the gut after ciprofloxacin treatment – V de Lastours – International Journal of Medical Microbiology

Impact of Helicobacter pylori infection on fluid duodenal microbial community structure and microbial metabolic pathways – Tadashi Maeda – BMC Microbiology

Human and General Microbiome – Reviews

Review: Implications of the Gut Microbiome in Sports – Gerardo Miranda-Comas – Sports Health

Review: Gut microbiome effects on neuronal excitability & activity: Implications for epilepsy – Henry Darch – Neurobiology of Disease

Review: The interplay between Sleep and Gut Microbiota – Mengqi Han – Brain Research Bulletin

Animal Microbiome

High-sugar, high-fat, and high-protein diets promote antibiotic resistance gene spreading in the mouse intestinal microbiota – Rong Tan – Gut Microbes

Determinants for antimicrobial resistance genes in farm dust on 333 poultry and pig farms in nine European countries – Roosmarijn Ec Luiken – Environmental Research

In vitro models of the canine digestive tract as an alternative to in vivo assays: Advances and current challenges – Charlotte Deschamps – ALTEX

Review: Do gastrointestinal microbiomes play a role in bats’ unique viral hosting capacity? – Devin N Jones – Trends in Microbiology

Beneficial Microbes and Compounds

A natural polyphenol exerts antitumor activity and circumvents anti-PD-1 resistance through effects on the gut microbiota – Meriem Messaoudene – Cancer Discovery

Amino acid intake and plasma concentrations and their interplay with gut microbiota in vegans and omnivores in Germany – Stefan Dietrich – European Journal of Nutrition

Plant Microbiome

Cytokinin-microbiome interactions regulate developmental functions – Rupali Gupta – Environmental Microbiome

Bioinformatics / Techniques

Quantitative metaproteomics and activity-based protein profiling of patient fecal microbiome identifies host and microbial serine-type endopeptidase activity associated with ulcerative colitis – Peter S Thuy-Boun – Molecular & Cellular Proteomics

Preprint: ProtFinder: finding subcellular locations of proteins using protein interaction networks – Aayush Grover – BioRxiv

January 14, 2022

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Human and General Microbiome

Intestinal commensal microbiota and cytokines regulate Fut2(+) Paneth cells for gut defense – Mariko Kamioka – PNAS

Gut microbiota promotes cholesterol gallstone formation by modulating bile acid composition and biliary cholesterol secretion – Hai Hu – Nature Communications

Non-typeable Haemophilus influenzae–Moraxella catarrhalis vaccine for the prevention of exacerbations in chronic obstructive pulmonary disease: a multicentre, randomised, placebo-controlled, observer-blinded, proof-of-concept, phase 2b trial – Stefan Andreas – The Lancet. Respiratory Medicine

PET microplastics affect human gut microbiota communities during simulated gastrointestinal digestion, first evidence of plausible polymer biodegradation during human digestion – Alba Tamargo – Scientific Reports

Ear microbiota and middle ear disease: a longitudinal pilot study of Aboriginal children in a remote south Australian setting – Steven L Taylor – BMC Microbiology

Comparative analysis of DNA extraction and PCR product purification methods for cervicovaginal microbiome analysis using cpn60 microbial profiling – Elinor Shvartsman – PloS ONE

Microbial hydrogen economy alleviates colitis by reprogramming colonocyte metabolism and reinforcing intestinal barrier – Li Ge – Gut Microbes

Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome – Dalong Hu – Cell Reports

Draft Genome Sequence of Bifidobacterium adolescentis 4-2, Isolated from Healthy Human Feces – Hend Altaib – Microbiology Resource Announcements

Preview: Diet, microbe, and autism: Cause or consequence? – Guanjian Li – Cell Host & Microbe

Human and General Microbiome – Reviews

Systematic review: Gut microbiota in patients with Alzheimer’s disease spectrum: a systematic review and meta-analysis – Chun-Che Hung – Aging

Systematic review: Characteristics of the gut microbiome in women with gestational diabetes mellitus: A systematic review – Louise Søndergaard Rold – PloS ONE

Systematic review: Respiratory tract infections and gut microbiome modifications: A systematic review – Claire A Woodall – PloS ONE

Systematic review: Repercussions of intermittent fasting on the intestinal microbiota community and body composition: a systematic review – Flaydson C S Pinto – Nutrition Reviews

Review: Skin Deep: The Role of the Microbiota in Cutaneous Autoimmunity – Márcia S Pereira – The Journal of Investigative Dermatology

Review: Current advances in the anti-inflammatory effects and mechanisms of natural polysaccharides – Dan Yuan – Critical Reviews in Food Science and Nutrition

Animal Microbiome

The gut microbiota of environmentally enriched mice regulates visual cortical plasticity – Leonardo Lupori – Cell Reports

Characterization of the juvenile koala gut microbiome across wild populations – Michaela D J Blyton – Environmental Microbiology

Specific gut bacterial responses to natural diets of tropical birds – Kasun H Bodawatta – Scientific Reports

Effect of dietary supplementation of lauric acid on growth performance, antioxidative capacity, intestinal development and gut microbiota on black sea bream (Acanthopagrus schlegelii) – Sami Ullah – PloS ONE

Establishment and resilience of transplanted gut microbiota in aged mice – Ying Wang – iScience

Identification of Gut Bacteria such as Lactobacillus johnsonii that Disseminate to Systemic Tissues of Wild Type and MyD88-/- Mice – Sreeram Udayan – Gut Microbes

Responsive changes of rumen microbiome and metabolome in dairy cows with different susceptibility to subacute ruminal acidosis – Tao Zhang – Animal Nutrition

Torula yeast in the diet of Atlantic salmon Salmo salar and the impact on growth performance and gut microbiome – Alexandra Leeper – Scientific Reports

Distinct gut microbiomes in two polar bear subpopulations inhabiting different sea ice ecoregions – Megan Franz – Scientific Reports

Microbiome Resilience despite a Profound Loss of Minority Microbiota following Clindamycin Challenge in Humanized Gnotobiotic Mice – Lin Liu – Microbiology Spectrum

Review: Bovine respiratory microbiota of feedlot cattle and its association with disease – Jianmin Chai – Veterinary Research

Plant Microbiome

Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome – Kyle M Meyer – The ISME Journal

Environmental Microbiome

Sulfate-dependant microbially induced corrosion of mild steel in the deep sea: a 10-year microbiome study – Pauliina Rajala – Microbiome

Microbial community composition and glyphosate degraders of two soils under the influence of temperature, total organic carbon and pH – Angelica M Muskus – Environmental Pollution

Increased Tea Saponin Content Influences the Diversity and Function of Plantation Soil Microbiomes – Shouke Zhang – Microbiology Spectrum

Bioinformatics

Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO – Britta Velten – Nature Methods

Review: Inferring microbiota functions from taxonomic genes: a review – Christophe Djemiel – GigaScience

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

January 10, 2022

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Today’s digest features studies on glycosaminoglycans degradation by urinary microbiome, social network of honeybees, improved DNA extraction for low biomass samples, the LotuS2 tool for amplicon sequencing analysis, and more. Happy Monday!

Gut microbiome

Review: The role of the microbiota in the management of intensive care patients – Piotr Szychowiak – Annals of Intensive Care

Review: The Gut Microbiome in Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS) – Rahel S. König – Frontiers in Immunology

Review: Opioid Use, Gut Dysbiosis, Inflammation, and the Nervous System – Richa Jalodia – Journal of Neuroimmune Pharmacology

Urinary microbiome

*A Semi-Quantitative Assay to Measure Glycosaminoglycan Degradation by the Urinary Microbiota – Vivian H. Nguyen – Frontiers in Cellular and Infection Microbiology

Vaginal microbiome

Composition and Stability of the Vaginal Microbiota of Pregnant Women With Inflammatory Bowel Disease – Janet E Hill – Inflammatory Bowel Diseases

Skin microbiome

*Anatomy promotes neutral coexistence of strains in the human skin microbiome – Arolyn Conwill – Cell Host & Microbe

Water microbiome

Tenets of a Holistic Approach to Drinking Water-Associated Pathogen Research, Management, and Communication – Caitlin Proctor – Water Research

Animal microbiome

Review: Possibilities and limits for using the gut microbiome to improve captive animal health – Jessica Diaz & Aspen T. Reese – Animal Microbiome

The mosquito microbiome includes habitat-specific but rare symbionts – Hans Schrieke – Computational and Structural Biotechnology Journal

*The gut microbiota affects the social network of honeybees – Joanito Liberti – bioRxiv

Techniques and methods

Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome – Guoshun Xu – BMC Genomics

Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics – Anna Pryszlak – Cell Report Methods

When to suspect contamination rather than colonization – lessons from a putative fetal sheep microbiome – Simone Bihl – Gut Microbes

*Microvolume DNA extraction methods for microscale amplicon and metagenomic studies – Anna R. Bramucci – ISME Communications

Bioinformatics

*LotuS2: An ultrafast and highly accurate tool for amplicon sequencing analysis – Ezgi Özkurt – bioRxiv

Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities – Derek M. Bickhart – Nature Biotechnology

January 7, 2022

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Today’s digest covers a range of topics including a duplex qPCR assay to detect lung infections, an investigation into sand fly symbionts, and a characterization of a fermented soybean food (Pe poke). If you want to end the week on a good note, I’d suggest reading the two articles I’ve highlighted below. One demonstrates that flooding and ecological restoration of former cranberry farmland also restores wetland microbial communities and soil function. The second provides a new barcoding strategy for the phenotypic screening of mosquitos that can be applied towards malaria research.

Happy reading!

General microbiome

Controlled spatial organization of bacterial growth reveals key role of cell filamentation preceding Xylella fastidiosa biofilm formation – Anbumani et al. – npj Biofilms and Microbiomes

Bacteria can be selected to help beneficial plasmids spread – Dimitriu et al. – PLOS Biology

Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network – Urchueguía et al. – PLOS Biology

Human respiratory microbiome

Detection of Pneumocystis jirovecii and Toxoplasma gondii in patients with lung infections by a duplex qPCR assay – Wu et al. – PLOS Neglected Tropical Diseases

Animal experiments

***Barcoded Asaia bacteria enable mosquito in vivo screens and identify novel systemic insecticides and inhibitors of malaria transmission – Sturm et al. – PLOS Biology

Molecular phylogeny of heritable symbionts and microbiota diversity analysis in phlebotominae sand flies and Culex nigripalpus from Colombia – Vivero-Gomez – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar – Tamang et al. – PLOS One

***Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland – Rubin et al. – PLOS One

Water and extremophile microbiome

Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment – Remple et al. – npj Biofilms and Microbiomes