May 6, 2022

Happy Friday! Today’s microbiome digest is a grab bag of articles on topics such as antibiotic cycling and bacterial contamination in surgery, phage isolated from diseased seafood, and microbial communities in snuff. I was particularly interested to see the article focused on degradation genes found in steel industrial soil communities. Finally, I enjoyed checking out two preprints on oral microbiota in Agta, a group of hunter-gatherers from the Philippines.

General microbiome

Preprint: The making of the oral microbiome in Agta hunter-gatherers – Dobon et al. – bioRxiv

Preprint: Microbial population dynamics decouple nutrient affinity from environmental concentration – Fink et al. – bioRxiv

Beneath the surface: Amino acid variation underlying two decades of dengue virus antigenic dynamics in Bangkok, Thailand – Huang et al. – PLOS Pathogens

Preprint: Hunter-gatherer oral microbiomes are shaped by contact network structure – Muscitto et al. – bioRxiv

Which vaccine attributes foster vaccine uptake? A cross-country conjoint experiment – Stöckli et al. – PLOS ONE

Associations between microbial communities and key chemical constituents in U.S. domestic moist snuff – Tyxobert et al. – PLOS ONE

Multi-site human microbiome

Mycobacterium tuberculosis infection, immune activation, and risk of HIV acquisition – Bender Ignacio et al. – PLOS ONE

The effects of antibiotic cycling and mixing on acquisition of antibiotic resistant bacteria in the ICU: A post-hoc individual patient analysis of a prospective cluster-randomized crossover study – van Duijin et al. – PLOS ONE

Human gut microbiome

Efficacy of laparotomy sponges to reduce bacterial contamination using an in vitro gastrointestinal surgery model – Bezhentseva et al. – PLOS ONE

Animal experiments

Virulence and antimicrobial resistance gene profiles of Staphylococcus aureus associated with clinical mastitis in cattle – Neelam et al. – PLOS ONE

Preexisting Trichinella spiralis infection attenuates the severity of Pseudomonas aeruginosa-induced pneumonia – Rong Long et al. – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Metagenomic analysis for taxonomic and functional potential of Polyaromatic hydrocarbons (PAHs) and Polychlorinated biphenyl (PCB) degrading bacterial communities in steel industrial soil – Sandhu et al. – PLOS ONE

Water and extremophile microbiome

Transcriptomic analysis of chloride tolerance in Leptospirillum ferriphilum DSM 14647 adapted to NaCl – Rivera-Araya et al. – PLOS ONE

Food microbiology

Sole and combined effect of foliar zinc and arbuscular mycorrhizae inoculation on basmati rice growth, productivity and grains nutrient – Mehmood et al. – PLOS ONE

Characterization and complete genome sequence analysis of a newly isolated phage against Vibrio parahaemolyticus from sick shrimp in Qingdao, China – Tian et al. – PLOS ONE


Financial incentives to increase stool collection rates for microbiome studies in adult bone marrow transplant patients – Thompson et al. – PLOS ONE

May 5, 2022

Today’s digest features a review on the role of bacterial translocation (especially oral-gut axis) in health and disease, a proof-of-concept study on probiotics on processing of negative emotions in humans, and more. Happy reading!

Let’s talk microbiome science at the next #MVIF!

Sterile (?) environment

Comprehensive human amniotic fluid metagenomics supports the sterile womb hypothesis – HanChen Wang – Scientific Reports


Lactobacillus acidophilus, L. plantarum, L. rhamnosus, and L. reuteri Cell-Free Supernatants Inhibit Candida parapsilosis Pathogenic Potential upon Infection of Vaginal Epithelial Cells Monolayer and in a Transwell Coculture System In Vitro – Luca Spaggiari – Microbiology Spectrum

*Probiotic Mixture Containing Lactobacillus helveticus, Bifidobacterium longum and Lactiplantibacillus plantarum Affects Brain Responses Toward an Emotional Task in Healthy Subjects: A Randomized Clinical Trial – Julia Rode – Frontiers in Nutrition

Vaginal microbiome

Identification and characterization of novel endolysins targeting Gardnerella vaginalis biofilms to treat bacterial vaginosis – Sara Arroyo-Moreno – npj Biofilms and Microbiomes

Gut microbiome

*Review: Deciphering mechanisms and implications of bacterial translocation in human health and disease – Shen Jin – Current Opinion in Microbiology

Two Competing Guilds as a Core Microbiome Signature for Chronic Diseases – Guojun Wu – bioRxiv

Neonatal Immune Challenge influences the Microbiota and Behaviour in a Sexually Dimorphic Manner – A. Cuskelly – Brain, Behavior, and Immunity

Review: Diet- and microbiota-related metabolite, 5-aminovaleric acid betaine (5-AVAB), in health and disease – Retu Haikonen – Trends in Endocrinology & Metabolism

Gut mycobiome

Review: “Molding” immunity—modulation of mucosal and systemic immunity by the intestinal mycobiome in health and disease – Mackenzie W. Gutierrez – Nature Mucosal Immunology

Animal experiments

Evolution of the murine gut resistome following broad-spectrum antibiotic treatment – Laura de Nies – Nature Communications & Behind the paper here.

Plant, root/soil microbiome

*Sugars dominate the seagrass rhizosphere – E. Maggie Sogin – Nature Ecology & Evolution


A snapshot of the global drinking water virome: Diversity and metabolic potential vary with residual disinfectant use – Bridget Hegarty – Water Research


Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification – Charlotte C. van de Velde – ISME Communications


A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments – Shaojun Pan – Nature Communications

HiFine: integrating Hi-c-based and shotgun-based methods to reFine binning of metagenomic contigs – Yuxuan Du and Fengzhu Sun – Bioinformatics

happi: a Hierarchical Approach to Pangenomics Inference – Pauline Trinh – bioRxiv

Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome – Rebecca H. Smit – bioRxiv

TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles – Varuni Sarwal – bioRxiv

April 30, 2022

Human Microbiome

Three-dimensional imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa – Octavio Mondragón-Palomino – PNAS

Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans – Samuel M Lancaster – Cell Host & Microbe

Comprehensive human amniotic fluid metagenomics supports the sterile womb hypothesis – HanChen Wang – Scientific Reports

Disordered development of gut microbiome interferes with the establishment of the gut ecosystem during early childhood with atopic dermatitis – Min-Jung Lee – Gut Microbes

A starch- and sucrose-reduced dietary intervention in irritable bowel syndrome patients produced a shift in gut microbiota composition along with changes in phylum, genus, and amplicon sequence variant abundances, without affecting the micro-RNA levels – Clara Nilholm – United European Gastroenterology Journal

Alterations in intestinal microbiota in ultramarathon runners – Mika Sato – Scientific Reports

Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity – Sabine Hazan – BMJ Open Gastroenterology

Gut microbiota alterations in critically ill older patients: a multicenter study – Mesa Victoria – BMC Geriatrics

Bone marrow transplantation induces changes in the gut microbiota that chronically increase the cytokine response pattern of splenocytes – Saeed Katiraei – Scientific Reports

Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome – Adam L Edwinson – Nature Microbiology

Review: Communication between the gut microbiota and peripheral nervous system in health and chronic disease – Tyler M Cook – Gut Microbe

Systematic Review: Adverse events in fecal microbiota transplantation: a systematic review and meta-analysis – Eliot A Rapoport – Annals of Gastroenterology

Review: Eco-evolutionary impact of ultraviolet radiation (UVR) exposure on microorganisms, with a special focus on our skin microbiome – Sandhya Rai – Microbiological Research

Beneficial Microbes and Compounds

Review: The huge clinical potential of microbiota in the treatment of pancreatic cancer: The next frontier – Zhilin Zhang – Biochimica et Biophysica Acta. Reviews on Cancer

Oral Administration of Lactobacillus paracasei N1115 on Neonatal Mice Prevents the Intestinal Inflammation in Adulthood – Yiping Xun – Letters in Applied Microbiology

Animal Model Microbiome

ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs – Hui Yang – Nature

External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells – Chi-Chan Lee – EMBO Reports

Non-Model Animal Microbiome

Host-Associated Bacterial Communities Vary Between Daphnia galeata Genotypes but Not by Host Genetic Distance – Amruta Rajarajan – Microbial Ecology

Faecal Microbiota Divergence in Allopatric Populations of Podarcis lilfordi and P. pityusensis, Two Lizard Species Endemic to the Balearic Islands – Iris Alemany – Microbial Ecology

Gut microbiota of ring-tailed lemurs (Lemur catta) vary across natural and captive populations and correlate with environmental microbiota – Sally L Bornbusch – Animal Microbiome

Mechanisms of fungal community assembly in wild stoneflies moderated by host characteristics and local environment – Yu-Xi Zhu – NPJ Biofilms and Microbiomes

Changes to the gut microbiota of a wild juvenile passerine in a multidimensional urban mosaic – Öncü Maraci – Scientific Reports

Comparative study on gut microbiota in three Anura frogs from a mountain stream – Zhuo Chen – Ecology and Evolution

Plant Microbiome

Insights into the microbiome assembly during different growth stages and storage of strawberry plants – Expedito Olimi – Environmental Microbiome

More Microbes, Genes, and Proteins

Hypothesis: Does Lactobacillus reuteri influence ergothioneine levels in the human body? – Irwin K Cheah – FEBS Letters

Type VI secretion systems of pathogenic and commensal bacteria mediate niche occupancy in the gut – Antonio Serapio-Palacios – Cell Reports

Review: Utilization of glycosaminoglycans by the human gut microbiota: participating bacteria and their enzymatic machineries – Parkash Singh Rawat – Gut Microbes


DEPP: Deep Learning Enables Extending Species Trees using Single Genes – Yueyu Jiang – Systematic Biology

A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments – Shaojun Pan – Nature Communications

Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype – Cameron Martino – mSystems

Review: Could Artificial Intelligence/Machine Learning and Inclusion of Diet-Gut Microbiome Interactions Improve Disease Risk Prediction? Case Study: Coronary Artery Disease – Baiba Vilne – Frontiers in Microbiology

Review: Microbial dark matter: from discovery to applications – Yuguo Zha – Genomics, Proteomics & Bioinformatics

April 8, 2022

Good morning! Today’s microbiome digest is brought to you by mild insomnia induced by a mid-afternoon coffee. It includes two food related studies, one on pathogenic E. coli found in ready-to-eat foods and the other focused on a antifungal lipopeptide produced by B. velezensis isolated from honey, and an an article focused on a new approach for processing frozen lung and lavage samples for use in microbiome studies. Also included are several articles focused on the gut microbiome, and several preprints focused on soil microbiome studies. Finally, I want to highlight a piece that details the positive outcomes associated with the National Summer Undergraduate Research Project (NSURP). Registration for this year’s program is still open until April 15th, and the organizers are looking for both mentors, mentees, and donors!

Pregnancy and early life

Group B Streptococcus colonization at delivery is associated with maternal peripartum infection – Brigtsen et al. – PLOS ONE

Human gut microbiome

Mycobacterium avium subsp. paratuberculosis and microbiome profile of patients in a referral gastrointestinal diseases centre in the Sudan – Elmagzoub et al. – PLOS ONE

Animal experiments

Vertical transmission of attaching and invasive E. coli from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life – Brand et al. – PLOS ONE

Sex differences in the fecal microbiome and hippocampal glial morphology following diet and antibiotic treatment – Saxena et al. – PLOS ONE

Animal microbiome

Preprint: Anthropogenic disturbance impacts gut microbiome homeostasis in a Malagasy primate – Wasimuddin et al. – bioRxiv

Plant, root, and soil microbiome

Preprint: Microclimate is a strong predictor of the native and invasive plant-associated soil microbiota on San Cristóbal Island, Galápagos archipelago – Schoenborn et al. bioRxiv

Preprint: The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types – Vitamaki et al. – bioRxiv

Preprint: Tracing carbon metabolism with stable isotope metabolomics reveals the legacy of diverse carbon sources in soil – Wilhelm et al. – bioRxiv

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Preprint: Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments – Kohtz et al. – bioRxiv

Food microbiology

Processed ready-to-eat (RTE) foods sold in Yenagoa Nigeria were colonized by diarrheagenic Escherichia coli which constitute a probable hazard to human health – Beshiru et al. – PLOS ONE

Purification and characterization of antifungal lipopeptide produced by Bacillus velezensis isolated from raw honey – Ziong et al. – PLOS ONE


An optimized approach for processing of frozen lung and lavage samples for microbiome studies – Wiscovitch-Russo et al. – PLOS ONE

Science, publishing, and career

***National Summer Undergraduate Research Project (NSURP): A Virtual Research Experience to Deliver REAL (Retention, Equity, Access, and Life-Changing) Outcomes for Underrepresented Minorities in STEM – Johnson & Knox – JMBE

March 23, 2022

General microbiome

Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance – Yu et al. – Nature Microbiology

Human skin microbiome

Skin microbiota diversity among genetically unrelated individuals of Indian origin – Pothbhare et al. – PeerJ

Human gut microbiome

[REVIEW]Gut microbiota and allergic diseases in children – Akagawa & Kaneko – Allergology International

[REVIEW]Gut microbiome: New biomarkers in early screening of colorectal cancer – Zhou et al. – Journal of Clinical Laboratory Analysis

Can gut microbiota throughout the first 10 years of life predict executive functioning in childhood? – Eckermann et al. – Developmental Psychobiology

[PREPRINT]Meta-analysis of the autism gut microbiome identifies factors influencing study discrepancies and machine learning classification – Chavira, Wang & Mills – bioRxiv

Changes of Intestinal Microflora in Colorectal Cancer Patients after Surgical Resection and Chemotherapy – Huang et al. – Computational and Mathematical Methods in Medicine

Animal microbiome

Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation – Dallas & Warne – Microbial Ecology

Changes in gut microbiota composition with age and correlations with gut inflammation in rats – Meng et al. – PLOS One

[REVIEW]Translational multi-omics microbiome research for strategies to improve cattle production and health – Wang & Guan – Emerging Topics in Lefe Sciences

Multi-omics reveals host metabolism associated with the gut microbiota composition in mice with dietary ε-polylysine – Zhang et al. – Food & Function

Soil causes gut microbiota to flourish and total serum IgE levels to decrease in mice – Zhou et al. – Environmental Microbiology

Microbiome-metabolomics deciphers the effects of Cistanche deserticola polysaccharides on agedconstipated rats – Liu et al. – Food & Function

Plant, root, and soil microbiome

[PREPRINT]Plant Virus Database: a resource for exploring the diversity of plant viruses and their interactions with hosts – Wu et al. – bioRxiv

Waste microbiome

[PREPRINT]Identification of Microbial Flora and Isolation of Functional Strains Related to the Degradation of Domestic Waste – Huang, Liu & Zong – bioRxiv

Food microbiology

Comprehensive characterization of the bacterial community structure and metabolite composition of food waste fermentation products via microbiome and metabolome analyses – Li et al. – PLOS One


MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations – Gregory et al. – Microbiome

HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities – Kalmar et al. – PLOS Genetics


[PREPRINT]Vaginal microbiome-host interactions modeled in a human vagina-on-a-chip – Mahajan et al. – bioRxiv

Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)

Florence tomb by Michelangelo restored with aid of bacteria – The Guardian

March 7, 2022

hard to do science

Originally tweeted by Peter Fabian (@PeterFabianLab) on March 4, 2022.

General microbiome

Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves – Philippe Piccardi – bioRxiv

Could a Focus on the “Why” of Taxonomy Help Taxonomy Better Respond to the Needs of Science and Society? – Leighton Pritchard – Preprints

Vaginal microbiome

Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation – Seth M. Bloom – Nature Microbiology

Citizen-science map of the vaginal microbiome – Sarah Lebeer – Research Square

Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data – Michael T France – Genome Biology

Urinary microbiome

Review: The gut, vaginal, and urine microbiome in overactive bladder: a systematic review – Christina Sze – International Urogynecology Journal

Gut microbiome

Identification of antimicrobial peptides from the human gut microbiome using deep learning – Yue Ma – Nature Biotechnology

Microbiome risk profiles as biomarkers for inflammatory and metabolic disorders – Amira Metwaly – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Temporal variations shape the gut microbiome ecology of the moth Brithys crini – Jesús Marín-Miret – Environmental Microbiology


Systematically assessing microbiome–disease associations identifies drivers of inconsistency in metagenomic research – Braden T. Tierney – PlosBiology

MultiBaC: An R package to remove batch effects in multi-omic experiments – Manuel Ugidos – Bioinformatics

HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps – Yuxuan Du & Fengzhu Sun – Genome Biology

TOMORROW MVIF #7 and the latest microbiome science!

Hey #microbiome people! 🦠
In MARCH there is #MVIF #7!

You can register for free here:

⭐️Keynote Speaker: prof Willem De Vos ⭐️

📅Check out day and time in your city here:

See you there! 😎

Originally tweeted by Microbiome Virtual International Forum (@MicrobiomeVIF) on February 17, 2022.

March 3, 2022

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


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

February 28, 2022

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


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


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

February 16, 2022

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.

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

February 9, 2022

Today’s digest includes a Nature Medicine news feature on the role of preprints in the COVID-19 pandemic. Also included are an article about unsupervised clustering methods for microbiome data, the response of anammox consortia to nutrient starvation, and a handful of interesting preprints.

Animal experiments

Preprint: Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig – Gaio et al. – bioRxiv

Plant, root, and soil microbiome

Preprint: Ecological insights into soil health according to the life-history traits and environment-wide associations of bacteria in agricultural soils – Wilhelm et al. – bioRxiv

Water and extremophile microbiome

Response and resilience of anammox consortia to nutrient starvation – Wang et al. – Microbiome


Preprint: Model-free prediction of microbiome compositions – Asher & Bashan – bioRxiv

Preprint: Predicting the re-distribution of antibiotic molecules caused by inter-species interactions in microbial communities – Reding – bioRxiv

Performance determinants of unsupervised clustering methods for microbiome data – Shi et al. – Microbiome

Science, publishing, and career

Rise of the preprint: how rapid data sharing during COVID-19 has changed science forever – Watson – Nature Medicine