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 18, 2020

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Greetings from Pittsburgh!

Today’s digest is unintentionally themed around change. Included is an article on the metabolic versatility of Salmonella enterica and another on the genetic diversification of Escherichia coli. If you’re more interested in the big picture, there is also an article about the evolution of ecological niches in plant-associated microbes as well as an article about the impacts of global change on soil microbial diversity and functionality.

Here’s to hoping that we are just as resilient as the microbes we study!

Events and jobs

A special plug for the National Summer Undergraduate Research Project (NSURP). NSURP is a community-driven initiative to create rewarding remote summer research opportunities for BIPOC undergraduate students in the microbial sciences. They are actively recruiting mentors and students for this summer, with the hope to match pairs by June 22nd.

General microbiome

Salmonella finds a way: Metabolic versatility of Salmonella enterica serovar Typhimurium in diverse host environments – Taylor and Winter – PLOS Pathogens

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli – Touchon et al. – PLOS Genetics

Human skin microbiome

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

Animal experiments

MAPK-dependent hormonal signaling plasticity contributes to overcoming Bacillus thuringiensis toxin action in an insect host – Guo et al. – Nature Communications

Investigation of the effects of probiotic, Bacillus subtilis on stress reactions in laying hens using infrared thermography – Soroko and Zaborski – PLOS ONE

Gut carriage of antimicrobial resistance genes in women exposed to small-scale poultry farms in rural Uganda: A feasibility study – Weil et al. – PLOS ONE

Animal microbiome

Anti-microbial activity of whole blood and plasma collected from Anna’s Hummingbirds (Calypte anna) against three different microbes – DeRogatis et al. – PLOS ONE

Bacteriophages specific to Shiga toxin-producing Escherichia coli exist in goat feces and associated environments on an organic produce farm in Northern California, USA – Lennon et al. – PLOS ONE

Plant, root, and soil microbiome

Survival of Escherichia coli O157 in autoclaved and natural sandy soil mesocosms – Baker et al. – PLOS ONE

Geometry and evolution of the ecological niche in plant-associated microbes – Chaloner et al. – Nature Communications

Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality – Zhou et al. – Nature Communications

Food microbiology

Neighboring plants divergently modulate effects of loss-of-function in maize mycorrhizal phosphate uptake on host physiology and root fungal microbiota – Fabiańska et al. – PLOS ONE

Phages and viruses

Comparative analysis of viruses in four bee species collected from agricultural, urban, and natural landscapes – Olgun et al. – PLOS ONE

Bioinformatics

bigPint: A Bioconductor visualization package that makes big data pint-sized – Rutter and Cook – PLOS Computational Biology

Techniques

Subduing the influence of PCR inhibitors on amplifying aged, degraded, and low copy number DNA: PCR enhancer cocktail-p and rescue PCR – Kemp et al. – PLOS ONE

Click-to-Capture: A method for enriching viable Staphylococcus aureus using bio-orthogonal labeling of surface proteins – Shalizi et al. – PLOS ONE

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.

June 16, 2020

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Sorry for the late afternoon digest. We are in the midst of trying to get our lab back up and running! There are several interesting papers today, including a commentary on the holobiont model and the usefulness of integrating microbiome and GWAS data, the development of a “Microbiome-Derived Metabolism Screen” for personalized medicine published in Cell, and a paper investigating phylosymbiosis in the skin microbiome of fish. My non-microbiology pick is a urine sampling method to assess diet, which could be very useful to gut microbiome scientists.

General microbiome

Commentary: Re-evaluating the relationship between missing heritability and the microbiome – Gavin M. Douglas – Microbiome

Book chapter: Pharmacomicrobiomics – Weihua Huang – Pharmacogenomics in Precision Medicine

Human gut microbiome

Review: Altered Composition of Gut Microbiota in Depression: A Systematic Review – Zahra Amirkhanzadeh Barandouzi – Frontiers in Psychiatry

Review: Tryptophan Metabolites Along the Microbiota-Gut-Brain Axis: An Interkingdom Communication System Influencing the Gut in Health and Disease – Annalisa Bosi – International Journal of Tryptophan Research

Personalized Mapping of Drug Metabolism by the Human Gut Microbiome – Bahar Javdan – Cell

Bacteroides thetaiotaomicron-derived outer membrane vesicles promote regulatory dendritic cell responses in health but not in inflammatory bowel disease – Lydia Durant – Microbiome

Animal microbiome

The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge – Michael P. Doane – Microbiome

Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands – Ethan R Wyrsch – Microbial Genomics

Intestinal Microbiota Analyses of Litopenaeus vannamei During a Case of Atypical Massive Mortality in Northwestern Mexico – Alejandro López-Cortés – Current Microbiology

Identification of hepatitis C virus in the common bed bug–a potential, but uncommon route for HCV infection? – Jiaxin Ling – Emerging Microbes & Infections

Eggshell and environmental bacteria contribute to the intestinal microbiota of growing chickens – Joel J. Maki – Journal of Animal Science and Biotechnology

Topography of the respiratory tract bacterial microbiota in cattle – Christopher McMullen – Microbiome

Plant, root, and soil microbiome

Exploring slope spatial heterogeneity by nitrogen transfer and arbuscular mycorrhizal community – Yanyan Yu – Journal of Soils and Sediments

Disentangling drivers of soil microbial potential enzyme activity across rain regimes: An approach based on the functional trait framework – Gabin Piton – Soil Biology and Biochemistry

Microbial communities in petroleum-contaminated seasonally frozen soil and their response to temperature changes – Xusheng Wang – Chemosphere

Review: The Plant Microbiome: From Ecology to Reductionism and Beyond – Connor R. Fitzpatrick – Annual Review of Microbiology

Biogeographic patterns of microbial co-occurrence ecological networks in six American forests – Qichao Tu – Soil Biology and Biochemistry

Water, air, and extremophile microbiome

Microbial communities of container aquatic habitats shift in response to Culex restuans larvae – Ephantus J. Muturi – FEMS Microbiology Ecology

Climate mediates continental scale patterns of stream microbial functional diversity – Félix Picazo – Microbiome

Bacterial diversity of a high-altitude permafrost thaw pond located on Ojos del Salado (Dry Andes, Altiplano-Atacama region) – Júlia Margit Aszalós – Astrobiology  

Effects of active volcanism on bacterial communities in the highest-altitude crater lake of Ojos del Salado (Dry Andes, Altiplano-Atacama Region) – Júlia Margit Aszalós – Astrobiology  

Methanogenesis in the Lake Elton saline aquatic system – Anna Kallistova – Extremophiles

Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities? – Winifred Johnson – FEMS Microbiology Ecology

Food microbiology

Lactic acid accumulation under heat stress related to accelerated glycolysis and mitochondrial dysfunction inhibits the mycelial growth of Pleurotus ostreatus – Zhiyu Yan – Applied Microbiology and Biotechnology

Evaluation and comparison of the microbial communities and volatile profiles in homemade suansun from Guangdong and Yunnan provinces in China – Qianqian Guan – Journal of the Science of Food and Agriculture


Non-Microbiology Pick

Developing community-based urine sampling methods to deploy biomarker technology for the assessment of dietary exposure – Amanda J. Lloyd – Public Health Nutrition

June 15, 2020

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We’ve got a belated post for you today (sorry all!) with a good balance of recent research on plant, animal and free-living microbiomes. Rather than highlight specific pieces of literature, I would encourage any who are interested in the microbiome from an evolutionary perspective to check out the recording of the ERC funded IDEM group’s recent discussion of the Holobiont Concept, featuring some preeminent proponents and critics of this model.

Seminar Recordings

ERC IDEM Group Holobiont Discussion – Dr. Scott Gilbert (7:17), Dr. Joan Roughgarden (1:05:03), Dr. Ford Doolittle (2:04:42)

General microbiome

Intestinal fermentation in vitro models to study food- induced gut microbiota shift: an updated review – Nissen et al. – FEMS Microbiology Letters

Human gut microbiome

Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions – Baldini et al. – BMC Biology

High Oscillospira abundance indicates constipation and low BMI in the Guangdong Gut Microbiome Project – Chen et al. – Scientific Reports

Animal microbiome

Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house mice – Belheouane et al. – The ISME Journal

Competitive traits of coral symbionts may alter the structure and function of the microbiome – McIlroy et al. – The ISME Journal

Evolutionary development and co‐phylogeny of primate‐associated bifidobacteria – Lugli et al. – Environmental Microbiology

Plant, root, and soil microbiome

Microbial functional traits in phyllosphere are more sensitive to anthropogenic disturbance than in soil – Xiang et al. – Environmental Pollution

Water and extremophile microbiome

Eutrophication as a driver of microbial community structure in lake sediments – Han et al. – Environmental Microbiology

Techniques

MetaFS: Performance assessment of biomarker discovery in metaproteomics – Tang et al. – Briefings in Bioinformatics

Microbes on the market

(Radio) Using our Microbiome to Change the Way We Live – KPCW https://www.kpcw.org/post/using-our-microbiome-change-way-we-live#stream/0

June 13, 2020

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Somewhat of a brief digest for today, but to make up for that, the long-awaited results of the PREDICT I study were published in Nature Medicine!

Human gut microbiome

Human postprandial responses to food and potential for precision nutrition – Berry et al. – Nature Medicine

Insect microbiome

Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity – Bovo et al. – Scientific Reports

Plant, root, and soil microbiome

Low Turnover of Soil Bacterial rRNA at Low Temperatures – Schostag et al. – Frontiers in Microbiology

Water and extremophile microbiome

Preprint: Diatom Modulation of Microbial Consortia Through Use of Two Unique Secondary Metabolites – Shibl et al. – bioRxiv

Complementary sampling methods for coral histology, metabolomics, and microbiome – Greene et al. – Methods in Ecology and Evolution

Phages and viruses

Preprint: Phage infection mediates inhibition of bystander bacteria – Chatterjee et al. – bioRxiv

Depth-related variability in viral communities in highly stratified sulfidic mine tailings – Gao et al. – Microbiome

Bioinformatics

GAD: A Python Script for Dividing Genome Annotation Files into Feature-Based Files – Yasser et al. – Interdisciplinary Sciences: Computational Life Sciences

June 12, 2020

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Buenos dias and greetings from Spain!

Today we can announce a Virtual Skin Microbiome Symposium held by New York Society of Cosmetic Chemists (NYSCC), that will start on June 15 to June 22, 2020, will include five on-demand sessions, a live panel Q&A and the Suppliers’ Day Digital Pop-Up & Solutions Center.

COVID-19

Epidemiological models are important tools for guiding COVID-19 interventions – Robin N. Thompson – BMC Medicine

Diagnosis of COVID-19 in children: the story evolves – R. Harwood and I. Sinha – BMC Medicine

Africa’s response to COVID-19 – Chikwe Ihekweazu and Emmanuel Agogo – BMC Medicine

Evaluation of the potential incidence of COVID-19 and effectiveness of containment measures in Spain: a data-driven approach – Alberto Aleta and Yamir Moreno – BMC Medicine

Pre-print – Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype – Shubham Gaurav – bioRxiv

General microbiome

Feasibility of collection and analysis of microbiome data in a longitudinal randomized trial of community gardening – Mireia Gascon – Future microbiology

Targeted microbiome depletion – A Du Toit – Nature Reviews Microbiology

Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host D Gouveia et al. – Biofilms and Microbiomes

Microbiome factors in HPV-driven carcinogenesis and cancers D Lin et al. – Plos Pathogens

Human respiratory microbiome

Clinical diagnostic application of metagenomic next-generation sequencing in children with severe nonresponding pneumonia – Heping Wang – PLOS ONE

Human vaginal microbiome

Exploring potential of vaginal Lactobacillus isolates from South African women for enhancing treatment for bacterial vaginosis – Anna-Ursula Happel – PLOS ONE

Human nearly-sterile sites

Parapseudoflavitalea muciniphila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a human peritoneal tumour and reclassification of Pseudobacter ginsenosidimutans as Pseudoflavitalea ginsenosidimutans comb. nov. – Paul A. Lawson et al. – Microbiology society

Draft Genome Sequence of Escherichia coli UMB1353, Isolated from the Female Urinary Tract – T Crawford et al. – Microbiology Resource Announcements

Human gut microbiome

Pre-print – The effect of short-course antibiotics on the resistance pro le of colonizing gut bacteria in the ICU: a prospective cohort study – C Munck et al. – Research Square

Pre-print – Dietary sphinganine is selectively assimilated by members of the gut microbiome – Min-Ting Lee et al. – bioRxiv

Pre-print – Nutritional combinatorial impact on the gut microbiota and plasma short-chain fatty acids levels in the prevention of mammary cancer in Her2/neu estrogen receptor-negative transgenic mice – Manvi Sharma et al. – bioRxiv

Animal experiments

Evaluation of the bacterial ocular surface microbiome in ophthalmologically normal dogs prior to and following treatment with topical neomycin-polymyxin-bacitracin – Callie M Rogers et al. – PLOS ONE

Short-chain fructo-oligosaccharides supplementation to suckling piglets: Assessment of pre- and post-weaning performance and gut health – Miriam Ayuso – PLOS ONE

Polysaccharides isolated from Cordyceps Sinensis contribute to the progression of NASH by modifying the gut microbiota in mice fed a high-fat diet – Lei Chen et al. – PLOS ONE

Effect of dietary gossypol supplement on fermentation characteristics and bacterial diversity in the rumen of sheep – CaiDie Wang – PLOS ONE

Polysaccharides isolated from Cordyceps Sinensis contribute to the progression of NASH by modifying the gut microbiota in mice fed a high-fat diet – Lei Chen – PLOS ONE

β-glucan administration improves growth performance and gut health in New Zealand White and APRI rabbits with different breed responses – Mahmoud M Abo Ghanima – PLOS ONE

Comparative study of gut microbiota in Tibetan wild asses (Equus kiang) and domestic donkeys (Equus asinus) on the Qinghai-Tibet plateau – H Liu, X Zhao – PeerJ

Pre-print – Differential genes and microbiota revealed by serum metabolomics of obese rats after intervention by Rhizoma Coptidis – K Luo et al. – Research Square

Pre-print – Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria – Leeann Klassen et al. – bioRxiv

Animal microbiome

Characterizing the microbiome of ectoparasitic louse flies feeding on migratory raptors – Rebecca A McCabe et al. – PLOS ONE

Characterization of the microbiota of commercially-traded finfish fillets – HR Shehata et al. – Food Research International

A bug’s life-delving into the challenges of helminth microbiome studies – F Formenti et al. – PLoS Neglected Tropical Diseases

Fish skin and gut microbiomes show contrasting signatures of host species and habitat – FÉ Sylvain et al. – Applied and Environmental

Plant, root, and soil microbiome

Isolation, Screening and Identification of Free-Living Diazotrophic Bacteria from Salinated Arid Soils – SA Begmatova et al. – Microbiology

Eukaryotic Microbial Communities in Japanese Arable AndisolsInvestigated by Amplicon Sequencing of 18S rRNA – GenesKazumori Mise et al. – American Society for microbiology

Combined effects of green manure returning and addition of sewage sludge compost on plant growth and microorganism communities in gold tailings. – YJ Ai et al. – Environmental Science and Pollution

Taxonomic shifts in arbuscular mycorrhizal fungal communities with shade and soil nitrogen across conventionally managed and organic coffee agroecosystems. – L Aldrich-Wolfe et al. – Mycorrhiza

Metagenomics Framework for the study of Soil Microbial Communities Based 16s rRNA Gene profiling approach – A Basu et al. – International Journal of Biotechnology

Soil microbial communities in the rhizosphere of Robinia pseudoacacia L. after being exposed to elevated atmospheric CO2 and cadmium for 4 years – X Jia et al. – Applied Soil Ecology

Soil aggregates by design: Manufactured aggregates with defined microbial composition for interrogating microbial activities in soil microhabitats – HJ Harvey et al – Soil Biology and Biochemistry

Would fertilization history render the soil microbial communities and their activities more resistant to rainfall fluctuations? J Kátai et al. – biorxiv

Pre-print – Meta-transcriptomic detection of diverse and divergent RNA viruses in green and chlorarachniophyte algae – Justine Charon et al. – bioRxiv

Water and extremophile microbiome

Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area – Shuping Wang et al. – PLOS ONE

Spatial dynamics of eukaryotic microbial communities in the German Bight – PAA Sprong et al. – Journal of Sea Research

Temporal distribution of microbial community in an industrial wastewater treatment system following crash and during recovery periods – H Barak et al. – Chemosphere

Pre-print – Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbiome structure and key drivers – Chenjing Jiang et al. – bioRxiv

Pre-print – Ozone nanobubble treatment effectively reduced pathogenic Gram positive and negative bacteria in freshwater and safe for tilapia – Chayuda Jhunkeaw et al. – bioRxiv

Pre-print – Impact of trimethoprim on the river microbiome and antimicrobial resistance. James Delaney et al. – bioRxiv

Bioinformatics

gutMEGA: a database of the human gut MEtaGenome Atlas – Q Zhang et al. – Briefings in Bioinformatics