Category Archives: Metagenomics & Bioinformatics

March 3, 2022

Posted on by

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

Posted on by

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

February 28, 2022

Posted on by

Human and General Microbiome

Fusobacterium nucleatum promotes colorectal cancer cells adhesion to endothelial cells and facilitates extravasation and metastasis by inducing ALPK1/NF-κB/ICAM1 axis – Ying Zhang – Gut Microbes

Oral and Intestinal Bacterial Substances Associated with Disease Activities in Patients with Rheumatoid Arthritis: A Cross-Sectional Clinical Study – Kaori Kitamura – Journal of Immunology Research

Cervicovaginal Microbiota Predicts Neisseria gonorrhoeae Clinical Presentation – Angela Lovett – Frontiers in Microbiology

Gut microbiota from Mexican patients with metabolic syndrome and HIV infection: an inflammatory profile – Fernando Amador-Lara – Journal of Applied Microbiology

Dysbiosis of skin microbiome and gut microbiome in melanoma progression – Chahrazed Mekadim – BMC Microbiology

Whole Genome Analysis of 335 New Bacterial Species from Human Microbiota Reveals a Huge Reservoir of Transferable Antibiotic Resistance Determinants – Sami Khabthani – International Journal of Molecular Sciences

Dynamics of the Gut Bacteria and Fungi Accompanying Low-Carbohydrate Diet-Induced Weight Loss in Overweight and Obese Adults – Dan Yu – Frontiers in Nutrition

The Gut Microbiome as a Biomarker of Cancer Progression Among Female Never-smokers With Lung Adenocarcinoma – Takehiro Otoshi – Anticancer Research

Impact Of The Ileal Microbiota On Surgical Site Infections In Crohn’s Disease: A Nationwide Prospective Cohort – Clément Julien – Journal of Crohn’s & Colitis

A multiple-dimension model for microbiota of patients with colorectal cancer from normal participants and other intestinal disorders – Jian Shen – Applied Microbiology and Biotechnology

Gut Microbiota Regulate Pancreatic Growth, Exocrine Function and Gut Hormones – Khyati Girdhar – Diabetes

Respiratory dysfunction three months after severe COVID-19 is associated with gut microbiota alterations – Beate Vestad – Journal of Internal Medicine

Gut microbiota and BMI throughout childhood: the role of firmicutes, bacteroidetes, and short-chain fatty acid producers – Timothy A Houtman – Scientific Reports

Review: Cross-reactivity between microbial and tumor antigens – Laurence Zitvogel – Current Opinion in Immunology

Review: The role of nutrition in inflammaging – Paolo Di Giosia – Ageing Research Reviews

Review: Impact of antibiotics on the human microbiome and consequences for host health – Dhrati V Patangia – MicrobiologyOpen

Beneficial Microbes and Compounds

Randomized, Double-blind, Placebo-controlled Study to Assess the Effect of Two Probiotics on the Preterms’ Gut Microbiota – Bárbara Moreno-Sanz – Journal of Pediatric Gastroenterology and Nutrition

Streptococcus strain C17(T) as a potential probiotic candidate to modulate oral health – Wen Xiao Zhang – Letters in Applied Microbiology

Animal Microbiome

Antimicrobial resistance profile of gram-positive isolates belonging to the microbiota of non-human primates – Melissa M Zaniolo – Journal of Medical Primatology

Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish – Lasse Nyholm – PeerJ

An experimental test of disease resistance function in the skin-associated bacterial communities of three tropical amphibian species – Myra C Hughey – FEMS Microbiology Ecology

Gut Microbiome Characteristics in feral and domesticated horses from different geographic locations – Li Ang – Communications Biology

Plant Microbiome

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

Changes in root microbiome during wheat evolution – Somayeh Gholizadeh – BMC Microbiology

Plant organ and sampling time point determine the taxonomic structure of microbial communities associated to apple plants in the orchard environment – Claudia Maria Oliveira Longa – Microbiological Research

Commensal Pseudomonas strains facilitate protective response against pathogens in the host plant – Or Shalev – Nature Ecology & Evolution

Review: Major Biological Control Strategies for Plant Pathogens – Manisha Arora Pandit – Pathogens

Bioinformatics

ADDAGMA: A database for domestic animal gut microbiome atlas – Yueren Xu – Computational and Structural Biotechnology Journal

To rarefy or not to rarefy: robustness and efficiency trade-offs of rarefying microbiome data – Johnny Hong – Bioinformatics

Techniques

Human Stool Preservation Impacts Taxonomic Profiles in 16S Metagenomics Studies – Anne Plauzolles – Frontiers in Cellular and Infection Microbiology

February 21, 2022

Posted on by

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

Posted on by

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

Posted on by

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

📻

February 2, 2022

Posted on by

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

Posted on by

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

Posted on by

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

Posted on by

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