Category Archives: Metagenomics & Bioinformatics

February 21, 2022

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Today’s digest features two excellent metagenome – metabolome association studies in Nature Medicine and a great article in Genome Biology showing that the sustained software development is what you should look for in a bioinformatic software, not what journal it was published in.

Human gut microbiome

Metabolomic and microbiome profiling reveals personalized risk factors for coronary artery disease – Talmor-Barkan et al. Nature Medicine. 

Microbiome and metabolome features of the cardiometabolic disease spectrum – Fromentin et al. Nature Medicine

Gut metagenome associations with extensive digital health data in a volunteer-based Estonian microbiome cohort – Aasmets et al. Nature Communications

Animal Microbiome

Drivers of gut microbiome variation within and between groups of a wild Malagasy primate – Rudolph et al. Microbiome

Integrated meta-omics reveals new ruminal microbial features associated with feed efficiency in dairy cattle – Xue et al. Microbiome

The gut microbiome and antibiotic resistome of chronic diarrhea rhesus macaques (Macaca mulatta) and its similarity to the human gut microbiome – Yang et al Microbiome

Virome

Independent host- and bacterium-based determinants protect a model symbiosis from phage predation – Lynch et al. Cell Reports

Virome characterization of game animals in China reveals a spectrum of emerging pathogens – He et al. Cell

Water and extremophile microbiome

Microeukaryotic gut parasites in wastewater treatment plants: diversity, activity, and removal – Freudenthal et al. Microbiome

Bioinformatics

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks – Zhou et al. Microbiome

Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software – Gardner et al. Genome Biology

Non-Microbiome picks

If you’ve listened to The Dropout podcast you might like this editorial.  

The post-Theranos world – Nature Biotechnology. 

February 16, 2022

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Happy Wednesday! Today’s digest includes two gut-brain axis papers from Sarkis Mazmanian’s lab at CalTech. The first article, published in Nature, found that 4-ethylphenol (4EPS) produced by gut microbes from dietary tyrosine was capable of entering the brain and changing gene expression, brain cell interactions, and brain functions. In the second study, published in Nature Medicine, oral administration of the adsorbent AB-2004–which can bind and sequester phenolic compounds–led to reduced levels of gut 4EPS and decreased anxiety in human adolescents with autism spectrum disorder.

I have also included an article published by my thesis lab in The Journal of Allergy and Clinical Immunology looking at the impact of seasons on the respiratory microbiome and asthma exacerbations in children.

Finally, there is an interesting paper by Baranova et al. in which the authors identify a bacterial species ubiquitous across multiple wild animals that appears to have novel functions for pathogen control or microbiome remodeling. Happy reading!

General Microbiome
Scale-dependent tipping points of bacterial colonization resistance. – Karita, Y. et al., PNAS.

Microbial protection favors parasite tolerance and alters host-parasite coevolutionary dynamics. – Rafaluk-Mohr, C. et al., Current Biology.

Human Respiratory Microbiome
Seasonal Airway Microbiome and Transcriptome Interactions Promote Childhood Asthma Exacerbations. – McCauley, K.E. et al., The Journal of Allergy and Clinical Immunology.

Human Skin Microbiome
Secreted Toxins From Staphylococcus aureus Strains Isolated From Keratinocyte Skin Cancers Mediate Pro-tumorigenic Inflammatory Responses in the Skin. – Krueger, A. et al., Frontiers in Microbiology.

Aged related human skin microbiome and mycobiome in Korean women. – Kim, H-J. et al., Scientific Reports.

Human Vaginal Microbiome
Extracellular Vesicles Generated by Gram-Positive Bacteria Protect Human Tissues Ex Vivo From HIV-1 Infection. – Costantini, P.E. et al., Frontiers in Cellular and Infection Microbiology.

Gut-Brain Axis
A gut-derived metabolite alters brain activity and anxiety behavior in mice. – Needham, B.D. et al., Nature.

Safety and target engagement of an oral small-molecule sequestrant in adolescents with autism spectrum disorder: an open-label phase 1b/2a trial. – Campbell, A.S., Needham, B.D., Meyers, C.R. et al., Nature Medicine.

Animal Experiments
Tryptophan-derived microbial metabolites activate the aryl hydrocarbon receptor in tumor-associated macrophages to suppress anti-tumor immunity. – Hezaveh, K. et al., Immunity.

Stochastic microbiome assembly depends on context. – Jones, E.W. et al., PNAS.

IBD-Associated Atg16L1T300A Polymorphism Regulates Commensal Microbiota of the Intestine. – Liu, H. et al., Frontiers in Immunology.

A homeostatic interferon-lambda response to bacterial microbiota stimulates preemptive antiviral defense within discrete pockets of intestinal epithelium. – Van Winkle, J.A. et al. eLife.

Enteric nervous system modulation of luminal pH modifies the microbial environment to promote intestinal health. – Hamilton, M.K. et al., PLoS Pathogens.

Animal Microbiome
Characterization of the Gut Microbiome and Resistomes of Wild and Zoo-Captive Macaques. – Jia, T. et al., Frontiers in Veterinary Science.

Deep Functional Profiling of Wild Animal Microbiomes Reveals Probiotic Bacillus pumilus Strains with a Common Biosynthetic Fingerprint. – Baranova, M.N. et al., International Journal of Molecular Sciences.

Plant, Root, and Soil Microbiome
Plant immunity suppression via PHR1-RALF-FERONIA shapes the root microbiome to alleviate phosphate starvation. – Tang, J. et al., The EMBO Journal.

Extracts from Environmental Strains of Pseudomonas spp. Effectively Control Fungal Plant Diseases. – Librizzi, V. et al., Plants.

Mega-fire in Redwood Tanoak Forest Reduces Bacterial and Fungal Richness and Selects for Pyrophilous Taxa that are Phylogenetically Conserved. – Enright, D.J. et al., Molecular Ecology.

Water and Extremophile Microbiome
Analysis of antibiotic resistance genes reveals its important role in influencing the community structure of ocean microbiome. – Yang, P. et al., The Science of the Total Environment.

Seaweeds influence oyster microbiota and disease susceptibility. – Dugeny, E. et al., The Journal of Animal Ecology.

Air Microbiome
Vertical stratification of the air microbiome in the lower troposphere. – Drautz-Moses, D.I. et al., PNAS.

Bioinformatics
Evaluating supervised and unsupervised background noise correction in human gut microbiome data. – Briscoe, L. et al., PLoS Computational Biology.

February 4, 2022

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Today’s digest is super diverse (read cool!): novel genes from uncultivated prokaryotes, a new Latilactobacillus species isolated from leaves of a strawberry plant (read the full 🍓 story behind the paper!), the benchmarking study of taxonomic profilers for long-read shotgun metagenomic datasets, and more. The first Issue of a new international peer-reviewed, open access, microbiome-oriented journal – the Microbiome Research Reports – is out with one original article, one perspective and four reviews.
And, a bit of shameless self-promotion, check out my preprint on urinary microbiome of healthy European women!
Happy Friday!

Global microbiome

*Functional and evolutionary significance of unknown genes from uncultivated taxa – Alvaro Rodríguez – bioRxiv

Ear microbiome

The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes – Maria Burton – PlosOne

Respiratory microbiome

Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer – Lisa Derosa – Nature Medicine

Associations and recovery dynamics of the nasopharyngeal microbiota during influenza‑like illness in the aging population – Sudarshan A. Shetty – Scientific Reports

Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways – Kasey A. Webb – Microbial Genomics

Gut microbiome

Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project – Esteban A. Lopera-Maya – Nature Genetics


The gut bacterial community potentiates Clostridioides difficile infection severity – Nicholas A Lesniak – bioRxiv

Emergent evolutionary forces in spatial models of microbial growth in the human gut microbiota – Olivia M. Ghosh and Benjamin H. Good – bioRxiv

Review: Microbiome-based therapeutics – Matthew T. Sorbara and Eric G. Pamer – Nature Reviews Microbiology

Review: Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota –Anna E. Lindell – Nature Reviews Microbiology

Review: Gut microbiome and health: mechanistic insights – Willem M de Vos – Gut

Vaginal microbiome

Gardnerella vaginalis induces matrix metalloproteinases in the cervicovaginal epithelium through TLR-2 activation – Kristin D. Gerson – American Journal of Obstetrics & Gynecology/SMFM 42nd Annual Meeting: The Pregnancy Meeting

Urinary microbiome

*Extended bacterial diversity of the urinary microbiome of reproductive-age healthy European women captured by culturomics and long-read amplicon sequencing – Svetlana Ugarcina Perovic – bioRxiv

Phylogenetic analysis and antimicrobial susceptibility profile of uropathogens – Hanif Ullah – PlosOne

Multidrug-resistant Uro-associated Escherichia coli Populations and Recurrent Urinary Tract Infections in Patients Performing Clean Intermittent Self-catheterisation – Catherine Mowbray – European Urology Open Science

Plant microbiome

*Latilactobacillus fragifolii sp. nov., isolated from leaves of a strawberry plant (Fragaria x ananassa) – Marie Legein – International Journal of Systematic and Evolutionary Microbiology

Ecology and potential functions of plant-associated microbial communities in cold environments – Malek Marian – FEMS Microbiology Ecology

Animal microbiome

Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides – Lucelia Cabral – Nature Communications

Review: Pesticide-induced disturbances of bee gut microbiotas – Michelle Z Hotchkiss – FEMS Microbiology Reviews

Animal experiments

Effect of a freeze-dried coffee solution in a high-fat diet-induced obesity model in rats: Impact on inflammatory response, lipid profile, and gut microbiota – Marilia Hermes Cavalcanti – PlosOne

Gut microbiota and butyrate contribute to nonalcoholic fatty liver disease in premenopause due to estrogen deficiency – Limin Liu – PlosOne

Techniques

BIOME-Preserve: A novel storage and transport medium for preserving anaerobic microbiota samples for culture recovery – Embriette R. Hyde – PlosOne

Species-targeted sorting and cultivation of commensal bacteria from the gut microbiome using flow cytometry under anaerobic conditions – Samuel Bellais – Microbiome

Bioinformatics

*Evaluation of taxonomic profiling methods for long-read shotgun metagenomic sequencing datasets – Daniel M Portik – bioRxiv

AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite – Giorgos Skoufos – Genome Biology

McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems – André Bogdanowski – Plos Computational Biology

VeChat: Correcting errors in long reads using variation graphs – Xiao Luo – bioRxiv

ReadBouncer: Precise and Scalable Adaptive Sampling for Nanopore Sequencing – Jens-Uwe Ulrich – bioRxiv

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February 2, 2022

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General microbiome

Genomic structure predicts metabolite dynamics in microbial communities – Gowda et al. – Cell 

Inhalable antibiotic resistomes emitted from hospitals: metagenomic insights into bacterial hosts, clinical relevance, and environmental risks – Wu et al. – Microbiome

Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge – Dai et al. – Microbiome

Understanding microbiome alterations in autism – Nature Medicine

Human gut microbiome

3β-Hydroxysteroid dehydrogenase expressed by gut microbes degrades testosterone and is linked to depression in males – Li et al. – Cell Host & Microbe

Pregnancy and early life

Early-life viral infections are associated with disadvantageous immune and microbiota profiles and recurrent respiratory infections – Piters et al. – Nature Microbiology

Meconium Microbiome of Very Preterm Infants across Germany – Klopp et al. – mSphere

Water and extremophile microbiome

Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts – Zhang et al. – Microbiome

A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss) – Rasmussen et al. – Microbiome

Bioinformatics

MUON: multimodal omics analysis framework – Bredikhin et al. – Genome Biology

Non Microbiome Picks

A Toast to All the Rejects – The Atlantic. An insightful article on celebrating your rejections in academia. 

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 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 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