Category Archives: Human gut

July 8, 2020

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Good morning! Today’s digest includes a broad selection of interesting research. Particular highlights include a study in rats that found microbiota transplantation attenuated neuroinflammation, a human study on the dramatic microbiome effects of dietary glycans, and a new technique for using drones to collect dolphin microbiome samples.

Pregnancy and early life

History of breastfeeding but not mode of delivery shapes the gut microbiome in childhood, Camille C. Cioffi et al., PLOS ONE

Preprint: Gut microbiota and fecal short-chain fatty acids are not associated with bone mass in healthy Chinese children: a cross-sectional study, Fengyan Chen et al., Research Square

Impact of Long-Term and Low-Dose Antibiotic Prophylaxis on Gut Microbiota in Children, Yuko Akagawa et al., The Journal of Urology

Human gut microbiome

Microbiome and health implications for ethnic minorities after enforced lifestyle changes, David M. Keohane et al., Nature Medicine

Preprint: Metaproteomics reveals potential signatures of disease-specific alterations in the gut microbial proteolytic events in inflammatory bowel disease, Zhixiang Yan et al., Research Square

High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans, Richard Creswell et al., Genome Medicine

Preprint: High-throughput cultivation of stable, diverse, fecal-derived microbial communities to model the intestinal microbiota, Andres Aranda-Diaz et al., bioRxiv

Preprint: pH-dependent spontaneous hydrolysis rather than gut bacterial metabolism reduces levels of the ADHD treatment, Methylphenidate, Julia Aresti et al., bioRxiv

Animal experiments

The gut microbiota attenuate neuroinflammation in manganese exposure by inhibiting cerebral NLRP3 inflammasome, Wang and Yang et al., Biomedicine & Pharmacotherapy

Magnetic fields modulate metabolism and gut microbiome in correlation with Pgc‐1α expression: Follow‐up to an in vitro magnetic mitohormetic study, Yee Kit Tai et al., The FASEB Journal

Preprint: Multi-omics analysis of aspirin treatment response in mice provide molecular insights and targets linked to liver fibrosis regression, Adil Bhat et al., bioRxiv

Animal microbiome

Limited influence of the microbiome on the transcriptional profile of female Aedes aegypti mosquitoes, Josephine Hyde et al., Scientific Reports

The gut bacterial microbiota of sea turtles differs between geographically distinct populations, T. Franciscus Scheelings et al., Endangered Species Research

Bioinformatics

Sparse reduced-rank regression for integrating omics data, Hilafu, Safo and Haine, BMC Bioinformatics

Techniques

An ecological framework to understand the efficacy of fecal microbiota transplantation, Yandong Xiao et al., Nature Communications

The use of Unmanned Aerial Vehicles (UAVs) to sample the blow microbiome of small cetaceans, Cinzia Centelleghe et al., PLOS ONE

July 7, 2020

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Today’s digest features the mighty sourdough microbiome, AGNOSTOS (a computational workflow for genes annotation using clustering and remote homology detection, contextualizing them with genomic and environmental information), and a new episode of the Bioinformatics Chat podcast about reproducible pipelines and NGLess (a user-friendly domain-specific programming language for NGS data processing), and more. Happy reading/listening!

General microbiome

Microbiome definition re-visited: old concepts and new challenges – Gabriele Berg – Microbiome

Positive interactions are common among culturable bacteria – Jared Kehe – bioRxiv

Gut microbiome

An emerging role of Prevotella histicola on estrogen-deficiency induced bone loss through the gut microbiota-bone axis – Zhongxiang Wang – bioRxiv

Identifying novel high-impact rare disease-causing mutations, genes and pathways in exomes of Ashkenazi Jewish inflammatory bowel disease patients – Yiming Wu – medRxiv

Early prediction of liver disease using conventional risk factors and gut microbiome-augmented gradient boosting – Yang Liu – medRxiv

GWAS of stool frequency reveals genes, pathways, and cell types relevant to human gastrointestinal motility and irritable bowel syndrome – Ferdinando Bonfiglio – medRxiv

Relationships of gut microbiota, short-chain fatty acids, inflammation, and the gut barrier in Parkinson’s disease – Velma Aho – medRxiv

Lung microbiome

Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung – Adrian Kordes – Nature Communications

Genitourinary microbiome

Architecture and function of human uromodulin filaments in urinary tract infections – Gregor L. Weiss – Science

The structure and diversity of strain level variation in vaginal bacteria – Brett A. Tortelli – bioRxiv

Synchronous genitourinary lichen sclerosus signals a distinct urinary microbiome profile in men with urethral stricture disease – Andrew J. Cohen – World Journal of Urology

Human urine 1H NMR metabolomics reveals alterations of the protein and carbohydrate metabolism when comparing habitual Average Danish diet vs. healthy New Nordic diet – Alessia Trimigno – Nutrition

Animal experiments

Lactobacillus rhamnosus probiotic prevents airway function deterioration and promotes gut microbiome resilience in a murine asthma model – Irina Spacova – Gut Microbes

Food microbiome

*The Sourdough Microbiome – Justine Dees – ASM

Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function – Brittany A. Niccum – mSystems

Bioinformatics

*Light into the darkness: Unifying the known and unknown coding sequence space in microbiome analyses – Chiara Vanni – bioRxiv

Welcome to the dark side of genomes and metagenomes – a blog post about the above mentioned study – Antonio Fernandez-Guerra

GraphBin: refined binning of metagenomic contigs using assembly graphs – Vijini Mallawaarachchi – Bioinformatics

Podcast

*Reproducible pipelines and NGLess with Luis Pedro Coelho – Roman Cheplyaka – The Bioinformatics Chat

July 3rd, 2020

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General microbiome

Microbiome definition re-visited: old concepts and new challenges – Berg et al. Microbiome

Large-scale metabolic interaction network of the mouse and human gut microbiota. – Lim et al. Scientific Data

Early life microbiome

Very early-life exposure to microbiota-induced TNF drives the maturation of neonatal pre-cDC1 – Kohler et al. Gut.

Human gut microbiome

Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes – Reitmeier et al. Cell Host & Microbe

Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study – Clooney et al. Gut

Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level – Kenny et al. Cell Host & Microbe

Amending microbiota by targeting intestinal inflammation with TNF blockade attenuates development of colorectal cancer – Yang et al. Nature Cancer

Animal microbiome

A Systematic Analysis of Mosquito-Microbiome Biosynthetic Gene Clusters Reveals Antimalarial Siderophores that Reduce Mosquito Reproduction Capacity – Ganley et al. Cell Chemical Biology

Extremophile microbiome

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys – Hou et al. BMC Microbiome

Phages and viruses

Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron – Porter et al. Nature Microbiology

Bioinformatics

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data – Kieser et al. BMC Bioinformatics

Techniques

High-Throughput Stool Metaproteomics: Method and Application to Human Specimens – Gonzalez et al. mSystems

Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture – Villa et al. mSystems

July 1, 2020

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Greetings Everyone,
I want to began the month of July on a note that diversity is the basis for life. I can’t think of anything better to teach us about diversity, co-existence, and evolution than the fascinating Microbiome.
The microbiome affects us right from our birth till the end affecting our mental as well as physical health. The microbiome exhibits all sorts of differences in shape, size, color, metabolic functions in order to sustain life.
Much to learn from these tiny beings!!!!
Today’s Digest comprises of some interesting studies about effect of microbiome on chemotherapy and studies on tumor microbiome. It also includes articles exploring genetics of gut microbiome and the role of microbiome in inflammatory bowel disease. Additionally has a news article about taking microbiome therapies to clinical trials.
Hope you enjoy reading today’s digest!!
“Life on earth is such a good story you cannot afford to miss the beginning… Beneath our superficial differences we are all of us walking communities of bacteria. The world shimmers, a pointillist landscape made of tiny living beings”. – Lynn Margulis

General microbiome
Human Microbiota and Effectiveness of Cancer Chemotherapy – Shvets et al – Experimental Oncology

Immunity to commensal skin fungi promotes psoriasiform skin inflammation – Hurabielle et al – PNAS

Human Tumor microbiome
*Perspective: Probing the tumor micro(b)environment – Atreya et al – Science

Human Eye microbiome
Review: Current Knowledge on the Human Eye Microbiome: A Systematic Review of Available Amplicon and Metagenomic Sequencing Data – Delbeke et al – Acta Ophthalmologica

Human nearly-sterile sites (blood, organs, brain)
Blood Bacterial Profiles Associated with HIV Infection and Immune Recovery – Serranno-Villar et al – The Journal of Infectious Diseases

Human gut microbiome
*Genetics of human gut microbiome composition – Kurilshikov et al – bioRxiv

Review: The microbiome in inflammatory bowel diseases: from pathogenesis to therapy – Liu et al – Protein&Cell

Built environment
Vertical Stratification in Urban Green Space Aerobiomes – Robinson et al – bioRxiv

Food microbiology
Food and mood: how do diet and nutrition affect mental wellbeing? – Firth et al – BMJ

Bioinformatics
DRAM for distilling microbial metabolism to automate the curation of microbiome function – Shaffer et al – bioRxiv

Techniques
MetaRibo-Seq measures translation in microbiomes – Fremin et al – Nature Communications

Microbes on the market
Enterome Secures €46M to Take Microbiome Therapies to Clinical Trials – Helen Albert – Labiotech.eu

Human Microbiome Therapeutics Market Research: Global Status & Forecast by Geography, Type & Application (2016-2026)

June 30, 2020

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Hallo und Guten Morgen from Germany! I hope you are well and have the time and energy to enjoy some microbiome related reading hours. I included a number of interesting reviews, related to mental and general health, soil microbiome and amphibian skin microbiome.
There is also a nice variety of new microbe research, including the influence of temperature changes on the microbiome of lizards and the microbiome’s association with heat tolerance, seasonal cycles of microbial communities in the Baltic Sea and the influence of hydrocarbons pollutants on the human skin microbiome.
Enjoy the reading!

SARS-CoV-2/COVID-19

Preprint: Role of Anti-SARS-CoV-2 antibodies in different cohorts: Can they provide clues for appropriate patient triaging? – Manohar B Mutnal – bioRxiv

General microbiome

Review: Impact of Human Microbiome on Health – Sujata Das – Microbial Diversity, Interventions and Scope

Review: Inflammation in Mental Disorders: Is the Microbiota the Missing Link? – Sophie Ouabbou – Neuroscience Bulletin

Human skin microbiome

Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants – Marcus H. Y. Leung – Microbiome

Human gut microbiome

Review: Current Limitations for the Assessment of the Role of the Gut Microbiome for Attention Deficit Hyperactivity Disorder (ADHD) – Andreas Hiergeist – Frontiers in Psychiatry

Animal microbiome

*Lizard gut microbiome changes with temperature and is associated with heat tolerance – Andrew H. Moeller – Applied and Environmental Microbiology

Review: The Amphibian Skin Microbiome and Its Protective Role Against Chytridiomycosis – Eria A. Rebollar – Herpetologica

Bacterial diversity associated with the abdomens of naturally Plasmodium-infected and non-infected Nyssorhynchus darlingi – Tatiane Marques Porangaba Oliveira – BMC Microbiology

Plant, root, and soil microbiome

Review: Deliberate introduction of invisible invaders: A critical appraisal of the impact of microbial inoculants on soil microbial communities – Panji Cahya Mawarda – Soil Biology and Biochemistry

Plant microbiota modified by plant domestication – Esperanza Martínez-Romero – Systematic and Applied Microbiology

Water and extremophile microbiome

A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes – Sheila Podell – Microbiome

Functional Associations and Resilience in Microbial Communities – Maria-Luisa Avila-Jimenez – Microorganisms

*Autumn to spring microbial community in the northern Baltic Sea: temporal variability in bacterial, viral and nanoflagellate abundance during the cold-water season – Laura Kaikkonen – Polar Biology

Food microbiology

Reservoirs of antimicrobial resistance genes in retail raw milk – Jinxin Liu – Microbiome

Bioinformatics

Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology – Pengshuo Yang – NAR Genomics and Bioinformatics

Review: From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes – Clémence Frioux – Computational and Structural Biotechnology Journal

June 23, 2020

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Human gut microbiome

US nativity and dietary acculturation impact the gut microbiome in a diverse US population – Peters et al. – The ISME Journal


GlycA, a novel marker for low grade inflammation, reflects gut microbiome diversity and is more accurate than high sensitive CRP in reflecting metabolomic profile – Mokkala et al. – Metabolomics

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

Black tea benefits short‐chain fatty acid producers but inhibits genus Lactobacillus in the gut of healthy Sprague–Dawley rats – Gao et al. – Journal of the Science of Food and Agriculture

Animal microbiome (for animals in the wild)

A role for gut microbiota in host niche differentiation – Greene et al. – The ISME Journal


Host-microbiota interaction helps to explain the bottom-up effects of climate change on a small rodent species – Li – The ISME Journal

Plant, root, and soil microbiome

Recovery of fen peatland microbiomes and predicted functional profiles after rewetting – Emsens – The IMSE Journal
Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments – Zhang et. al – Microbiome

Antibiotic resistance

Chlorine disinfection promotes the exchange of antibiotic resistance genes across bacterial genera by natural transformation – Jin et al. – The ISME Journal

Phages and viruses

Narnaviruses: novel players in fungal–bacterial symbioses – Espino-Vazquez – The ISME Journal

June 22, 2020

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General microbiome
Impact of feeding and stirring regimes on the internal stratification of microbial communities in the fermenter of anaerobic digestion plants – Robert Heyera – Bioresource Technology

Human microbiome
REVIEW: Role of the Microbiome in Allergic Disease Development – Andrea C. Aguilera, – Pediatric Allergy and Immunology

Optimization and standardization of the culturomics technique for human microbiome exploration – Ami Diakite – Scientific Reports

Human skin microbiome
The microbiome of diabetic foot ulcers: a comparison of swab and tissue biopsy wound sampling techniques using 16S rRNA gene sequencing – J. Travis – BMC Microbiology

Human gut microbiome
Interpersonal Gut Microbiome Variation Drives Susceptibility and Resistance to Cholera Infection – Salma Alavi – Cell

EDITORIAL: Gut microbes effects on host metabolic alterations in health and disease – Suzana D. Savkovic – Gut Microbes

Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study – Mohammad Tahseen Al Bataineh – Scientific Reports

Alterations in the Gut Microbiome in the Progression of Cirrhosis to Hepatocellular Carcinoma – Yelena Lapidot – mSystems

Human respiratory microbiome
Taxonomic diversity of sputum microbiome in lung cancer patients and its relationship with chromosomal aberrations in blood lymphocytes – V. G. Druzhinin – Scientific Reports

Pregnancy and early life
Human milk microbiota development during lactation and its relation to maternal geographic location and gestational hypertensive status – Yi Wan – Gut Microbes

Maternal Microbiota, Cortisol Concentration, and Post-PartumWeight Recovery Are Dependent on Mode of Delivery – Marta Selma-Royo – Nutrients

Human ancient microbiome
Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia – Anna Philips – BMC Genomics

Animal experiments
Zebrafish microbiome studies make waves – Keaton Stagaman – Lab Animal

Animal microbiome
An Insight into Diversity and Functionalities of Gut Microbiota in Insects – Shengchen Wang – Current Microbiology

Plant, root, and soil microbiome
Microbial assimilation dynamics differs but total mineralization from added root and shoot residues is similar in agricultural Alfisols – Yingde Xu – Soil Biology and Biochemistry

Effects of increasing concentrations of unamended and gypsum modified bauxite residues on soil microbial community functions and structure – A mesocosm study – Camille Fourrier – Ecotoxicology and Environmental Safety

Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables – Peter Kusstatscher – FEMS Microbiology Ecology

Variations of rhizospheric soil microbial communities in response to continuous Andrographis paniculata cropping practices – Junren Li – Botanical Studies

Seed Metabolism and Pathogen Resistance Enhancement in Pisum sativum During Colonization of Arbuscular Mycorrhizal Fungi: An Integrative Metabolomics-Proteomics Approach – Nima Ranjbar Sistani – Frontiers in Plant Science

Water microbiome
Differential Responses of a Coastal Prokaryotic Community to Phytoplanktonic Organic Matter Derived from Cellular Components and Exudates – Hiroaki Takebe – Microbes and Environments

Built environment
MINI-REVIEW: Microorganisms populating the water-related indoor biome – Monika Novak Babič – Applied Microbiology and Biotechnology

Pre-print
Shotgun metagenomics reveals signicant gut microbiome features in different grades of acute pancreatitis – Shanshan Yu – Research Square

Characteristics of Esophagus Flora in Patients with Esophageal Squamous Cell Carcinoma in Central China – Shuixiang He – Research Square

Can root-associated fungi mediate the impact of abiotic conditions on the growth of a High Arctic herb? – Magdalena Wutkowska – bioRxiv

Microbes on the market
Finch Therapeutics Announces Positive Topline Results from Randomized Controlled Trial of CP101, an Oral Microbiome Drug, for the Prevention of Recurrent C. difficile Infection – Finch Therapeutics

Microbes in the news
Gut reaction: How the gut microbiome may influence the severity of COVID-19 – Shirin Moossavi – The Conversation

June 21, 2020

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Hello from the Sonoran Desert! In today’s digest, you’ll find two very interesting reviews! Stagaman and collaborators come back on years of Zebra-fish gut microbiome research and explore the insights gleaned from this awesome model animal. On the other hand, François and Pybus review our understanding of avian viromes in both wild and domesticated bird populations, highlighting the current limitations and pitfalls in this research area.

But today’s digest also contains very interesting research papers! Gulino and collaborators are exploring viromes in New York city wastewater systems. This paper is particularly interesting as bacteriophages are typically left out from urban environments microbiomes studies, despite their abundance and importance in ecosystems.

Finally, today’s non-microbiology pick is a review that comes back on how information theory, developped by Claude Shannon in the late 40s, have been used in computational biology. This paper is particularly interesting for readers wanting to learn more about the basics of information theory and how it is applied today in bioinformatics.

Have a great Sunday!

Pregnancy and early life

Review: The microbiome in pediatric oncology – Rotz et al. – Cancer

Human respiratory microbiome

Metagenomic analysis of the lung microbiome in pulmonary tuberculosis – a pilot study – Hu et al. – Emerging Microbes & infections

Human vaginal microbiome

Taxonomic and Functional Differences in Cervical Microbiome Associated with Cervical Cancer Development –Nkufi Tange et al. – Scientific reports

Human gut microbiome

Preprint: The gut microbiome regulates memory function – Noble et al. – BioRxiV

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

review: Zebrafish microbiome studies make waves – Stagaman et al. – Lab Animal

Built environment (subways, indoor surfaces)

Revealing antimicrobial resistance in stormwater with MinION – Bialasek et al. – Chemosphere

Phages and viruses

Review: Towards an understanding of the avian virome –François et al. – Journal of general Virology

Initial Mapping of the New York City Wastewater Virome –Gulino et al. – mSystems

Bioinformatics

Higher order Markov models for metagenomic sequence classification – Burks et al. –Bioinformatics

Preprint: Combinatorial Algorithms for Strain Level Metagenomic Microbial Detection and Quantification –Zhu et al. –BioRxiV

Preprint: Ultra-rapid metagenotyping of the human gut microbiome – Shi et al. – BioRxiV

My non-microbiology pick

Review: Information Theory in Computational Biology: Where We Stand Today – Chanda et al. – Entropy

June 20th, 2020

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Glad midsommar!

Happy midsummer to everyone from Sweden. Today’s digest is heavy on the preprints with a couple of thought-provoking editorials from the journal Nature. You will notice a lot of articles related to COVID-19. There is an interesting study that proposes the use of dogs and their sensory powers to detect CoV infections. More importantly, a preprint discusses the use of a tyrosine kinase as a potential drug and another preprint discusses the results of a massive FDA-approved drug repurposing screen for COVID. Also in the digest is an article where the researchers have shown that the gut microbiome produces neurotransmitters and another article that explains how Streptomyces spores hitchhike. Another article, although not related to our general theme, is super interesting as well. A group of scientists have proposed that the first egg of the dinosaurs was probably soft-shelled and not like the hard eggs we imagined all this time!

I am sorry for doing a lousy job today at providing a proper context and some informative introduction to today’s digest as it is the most awaited Midsommar holiday and the barbecue is calling! I hope everyone is enjoying the summer. Make sure to follow social distancing guidelines!

COVID-19

Preprint: Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19 – Nirmitee Sanjay Mulgaonkar, et al.

Preprint: Variant analysis of SARS-CoV-2 strains in Middle Eastern countries – Khalid M Bindayna and Shane Crinion

Preprint: Polymorphism and selection pressure of SARS-CoV-2 vaccine and diagnostic antigens: implications for immune evasion and serologic diagnostic performance – Eric Dumonteil and Claudia Herrera

Preprint: Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2 Infected Syrian Hamsters – Rebecca Brocato, et al.

Preprint: High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States – Ryan P McNamara, et al.

Preprint: Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window – Duarte Gouveia, et al.

Preprint: A single dose of recombinant VSV-∆G-spike vaccine provides protection against SARS-CoV-2 challenge – Yfat Yahalom-Ronen, et al.

Preprint: Antiviral treatment of SARS-CoV-2-infected hamsters reveals a weak effect of favipiravir and a complete lack of effect for hydroxychloroquine – Suzanne JF Kaptein, et al.

Preprint: Drug repurposing screens reveal FDA approved drugs active against SARS-Cov-2 – Mark Dittmar, et al.

Preprint: Dog Savior: Immediate Scent-Detection of SARS-COV-2 by Trained Dogs – Omar Vesga, et al.

Preprint: Evaluation of the performance of SARS-CoV-2 serological tools and their positioning in COVID-19 diagnostic strategies. – Aurélie Velay, et al.

General Microbiome

Preprint: Exploring the Stony Coral Tissue Loss Disease Bacterial Pathobiome – Deborah Iwanowicz, et al.

Preprint: Hi-C deconvolution of a textile-dye degrader microbiome reveals novel taxonomic landscapes and link phenotypic potential to individual genomes – Ayixon Sanchez-Reyes, et al.

A metabolic pathway for bile acid dehydroxylation by the gut microbiome – Masanori Funabashi, et al. – Nature

A neurotransmitter produced by gut bacteria modulates host sensory behaviour – Michael P. O’Donnell, et al. – Nature

Proteome

Preprint: Novel functional insights from the Plasmodium falciparum sporozoite-specific proteome by probabilistic integration of 26 studies – Lisette Meerstein-Kessel, et al.

Bacteria

Preprint: Conjugal DNA transfer in the maternally inherited symbiont of tsetse flies Sodalis glossinidius – Christopher G Kendra, et al.

Preprint: Systematic analysis of REBASE identifies numerous Type I restriction-modification systems that contain duplicated, variable hsdS specificity genes that randomly switch methyltransferase specificity by recombination. – John M. Atack, et al.

Preprint: The role of LmeA, a mycobacterial periplasmic protein, in stabilizing the mannosyltransferase MptA and its product lipomannan under stress – Kathryn C Rahlwes, et al.

Preprint: Microbial piggy-back: how Streptomyces spores are transported by motile soil bacteria – Alise R. Muok, et al.

Viruses

Preprint: Herbivore-induced activation of viral phosphatase disarms plant antiviral immunities for pathogen transmission – Pingzhi Zhao, et al.

Preprint: Quantifying the acquisition and retention of lumpy skin disease virus by haematophagus insects and the implications for transmission and control – Beatriz Sanz-Bernardo, et al.

Preprint: Identification of a critical horseshoe-shaped region in the nsp5 (Mpro, 3CLpro) protease interdomain loop (IDL) of coronavirus mouse hepatitis virus (MHV) – Benjamin C. Nick, et al.

Preprint: A sweep of earth’s virome reveals host-guided viral protein structural mimicry; with implications for human disease – Gorka Lasso, et al.

Others

The first dinosaur egg was soft – Mark A. Norell, et al. – Nature

Junior researchers hit by coronavirus-triggered hiring freezes – Chris Woolston – Nature

Peer review should be an honest, but collegial, conversation – Nature

June 17, 2020

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Hello and welcome to Wednesday’s Digest! Today’s selection includes two separate but complementary papers from Cell Host & Microbe. The first, from Brett Finlay’s lab, investigates what drives the loss of Immunoglobulin A recognition by beneficial bacteria in the gut of undernourished children. The second, from Jeffrey Gordon’s lab, examines the impact of prebiotic and microbial interventions on oral vaccination responses in a mouse model of childhood undernutrition. These papers both highlight the important relationship between nutrition, the microbiota, and host mucosal immunity.

There are also a few fungi-focused papers today as well as some interesting animal microbiome research. Tan et al. compare the microbiome of pigs and their farmers and Andrade-Oliveira et al. found that antimicrobial resistance genes from a feline oral commensal can be transferred to a human-associated staphylococci. I also want to call attention to the techniques section, especially a paper by Song and Xie in which they used CRISPR/Cas9 to deplete host contamination in 16S rRNA gene amplicon samples.

Happy reading, y’all!

Pregnancy and Early-life
Analysis of Immune, Microbiota and Metabolome Maturation in Infants in a Clinical Trial of Lactobacillus Paracasei CBA L74-fermented Formula. Roggero, P. et al. Nature Communications.

Ecological Succession in the Vaginal Microbiota During Pregnancy and Birth. Rasmussen, M.A. et al. The ISME Journal.

Neonatal Diet Alters Fecal Microbiota and Metabolome Profiles at Different Ages in Infants Fed Breast Milk or Formula. Brink, L.R. et al. American Journal of Clinical Nutrition.

Human Milk Fungi: Environmental Determinants and Inter-Kingdom Associations With Milk Bacteria in the CHILD Cohort Study. Moossavi, S. et al. BMC Microbiology.

Profiles of Human Milk Oligosaccharides and Their Relations to the Milk Microbiota of Breastfeeding Mothers in Dubai. Ayoub, C. et al. Nutrients.

Human Milk Microbiota Development During Lactation and Its Relation to Maternal Geographic Location and Gestational Hypertensive Status. Wan, Y. et al. Gut Microbes.

Skin Microbiome
Skin Microbiota Analysis-Inspired Development of Novel Anti-Infectives. Liu, Y. et al. Microbiome.

Review: Skin Microbiome Analysis for Forensic Human Identification: What Do We Know So Far? Tozzo, P. et al. Microorganisms.

Review: Protecting the Outside: Biological Tools to Manipulate the Skin Microbiota. O’Sullivan, J.N. et al. FEMS Microbiology and Ecology.

Vaginal Microbiome
Recovery of Vaginal Microbiota After Standard Treatment for Bacterial Vaginosis Infection: An Observational Study. Lehtoranta, L. et al. Microorganisms.

Alterations in Vaginal Microbiota and Associated Metabolome in Women With Recurrent Implantation Failure. Fu, M. et al. mBio.

Gut Microbiome
Alterations of the Gut Microbiota in Patients With COVID-19 or H1N1 Influenza. Gu, S. et al. Clinical Infectious Diseases.

Alterations in the Gut Microbiome and Suppression of Histone Deacetylases by Resveratrol Are Associated with Attenuation of Colonic Inflammation and Protection Against Colorectal Cancer. Alrafas, H.R. et al. Journal of Clinical Medicine.

Long-term Dietary Intervention Reveals Resilience of the Gut Microbiota Despite Changes in Diet and Weight. Fragiadakis, G.K. et al. American Journal of Clinical Nutrition.

Oral Microbiome
Intraoral Microbial Metabolism and Association With Host Taste Perception. Gardner, A. et al. Journal of Dental Research.

Animal Experiments
Combined Prebiotic and Microbial Intervention Improves Oral Cholera Vaccination Responses in a Mouse Model of Childhood Undernutrition. Di Luccia, B. et al. Cell Host & Microbe.

Commensal Bacteria Modulate Immunoglobulin A Binding in Response to Host Nutrition. Huus, K.E. et al. Cell Host & Microbe.

The interplay between the gut microbiota and NLRP3 activation affects the severity of acute pancreatitis in mice. Xueyang, L. et al. Gut Microbes.

Structural and functional changes of gut microbiota in ovariectomized rats and their correlations with altered bone mass. Ma, S. et al. Aging (Albany NY).

Animal Microbiome
Comparative assessment of faecal microbial composition and metabonome of swine, farmers and human control. Tan, S.C. et al. Scientific Reports.

Staphylococcus nepalensis, a Commensal of the Oral Microbiota of Domestic Cats, Is a Reservoir of Transferrable Antimicrobial Resistance. Andrade-Oliveira, A.L. et al. Microbiology.

Increasing the Hindgut Carbohydrate/Protein Ratio by Cecal Infusion of Corn Starch or Casein Hydrolysate Drives Gut Microbiota-Related Bile Acid Metabolism To Stimulate Colonic Barrier Function. Pi, Y. mSystems.

The Microbial Biogeography of the Gastrointestinal Tract of Preterm and Term Lambs. Chong, C.Y.L. et al. Scientific Reports.

Microbial Ecology of Atlantic Salmon (Salmo Salar) Hatcheries: Impacts of the Built Environment on Fish Mucosal Microbiota. Minich, J.J. et al. Applied and Environmental Microbiology.

Dysbiosis in the Gut Microbiota of Soil Fauna Explains the Toxicity of Tire Tread Particles. Ding, J. et al. Environmental Science and Technology.

Insect Microbiome
Dietary Adaptation of Microbiota in Drosophila Requires NF-κB-Dependent Control of the Translational Regulator 4E-BP. Vandehoef, C. et al. Cell Reports.

Responses of soil and earthworm gut bacterial communities to heavy metal contamination. Liu, P. et al. Environmental Pollution.

Effect of Life Stage and Pesticide Exposure on the Gut Microbiota of Aedes Albopictus and Culex Pipiens L. Juma, E.O. et al. Scientific Reports.

Caterpillar Gut and Host Plant Phylloplane Mycobiomes Differ: A New Perspective on Fungal Involvement in Insect Guts. Višňovská, D. et al. FEMS Microbiology Ecology.

Plant, Root, and Soil Microbiome
The Response of Soil and Phyllosphere Microbial Communities to Repeated Application of the Fungicide Iprodione: Accelerated Biodegradation or Toxicity? Katsoula, A. et al. FEMS Microbiology Ecology.

Host Genotype Explains Rhizospheric Microbial Community Composition: The Case of Wild Cotton Metapopulations (Gossypium Hirsutum L.) in Mexico. Hernández-Terán, A. et al. FEMS Microbiology Ecology.

Review: Microbiome Approaches Provide the Key to Biologically Control Postharvest Pathogens and Storability of Fruits and Vegetables. Kusstatscher, P. et al FEMS Microbiology and Ecology.

Review: The Plant Microbiome: From Ecology to Reductionism and Beyond. Fitzpatrick, C.R. et al. Annual Review of Microbiology.

Water Microbiome
Persistence of Wastewater Antibiotic Resistant Bacteria and Their Genes in Human Fecal Material. Scaccia, N. et al. FEMS Microbiolgy Ecology.

Review: Microorganisms Populating the Water-Related Indoor Biome. Babič, M.N. et al. Applied Microbiology and Biotechnology.

Phage
Introducing Lu-1, a Novel Lactobacillus Jensenii Phage Abundant in the Urogenital Tract. Miller-Ensminger, T. et al. PLoS ONE.

Review: Bacteriophage-mediated Manipulation of the Gut Microbiome – Promises and Presents Limitations. Rasmussen, T.S. et al. FEMS Microbiology Reviews.

Bioinformatics
gutMEGA: A Database of the Human Gut MEtaGenome Atlas. Zhang, Q. et al. Briefings in Bioinformatics.

Techniques
Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing. Song, L. and Xie, K. Microbiome.

Optimization and Standardization of the Culturomics Technique for Human Microbiome Exploration. Diakite, A. et al. Scientific Reports

Direct detection of mRNA expression in microbial cells by fluorescence in situ hybridization using RNase H-assisted rolling circle amplification. Takahashi, H. et al. Scientific Reports.