Category Archives: Animal microbiome

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 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 08, 2020

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Today, we present a broad spectrum of new studies covering among others the mycobiome of human milk, gut microbes and their association with brain development and cognitive function, and a catalogue of previously unseen microbial genomes. Of particular interest is a study that integrates different sources of data to model a personalized gut microbiome. Last but not least we selected a pre-print on the design and characterization of multiepitopes vaccine for SARS-CoV.

General microbiome

Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer – Costa et al. – Microbiome

REVIEW: Conceptualizing the vertebrate sterolbiome – Ridlon – Applied and Environmental Microbiology

Human milk mycobiome

Human milk fungi: environmental determinants and inter-kingdom associations with milk bacteria in the CHILD Cohort Study – Moossavi et al. – BMC Microbiology

Human skin microbiome

Skin microbiota analysis-inspired development of novel anti-infectives – Liu et al. – Microbiome

Human vaginal microbiome

PREPRINT: Vaginal microbiota of adolescents and their mothers: A preliminary study of vertical transmission and persistence – Bassis – bioRxiv

Human gut microbiome

Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome – Thiele et al. – Mol Syst Biol

REVIEW: The gut microbiota profile of adults with kidney disease and kidney stones: a systematic review of the literature – Stanford et al. – BMC Nephrology

PREPRINT: Gut microbes and their genes are associated with brain development and cognitive function in healthy children – Bonham et al. – bioRxiv

Animal microbiome (for animals in the wild)

Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttata – van Veelen et al. – Animal Microbiome

PREPRINT: Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity – Youngblut – bioRxiv

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

Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms – Zhong et al. – Microbiome

The role of metal contamination in shaping microbial communities in heavily polluted marine sediments – Di Cesare et al. – Environmental Pollution

Techniques

Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing – Song & Xie – Microbiome

SARS-CoV-2

PREPRINT: In silico design and characterization of multiepitopes vaccine for SARS-CoV from its Spike proteins – Kathwate – bioRxiv

June 5, 2020

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Today’s digest features a review on genetic variability within species in microbiomes, a study on Lactobacilli in the human nose, a new episode of Microbiology Lab Pod with the latest science news on functional metagenomics, a novel resistance gene called GAR, and more. Happy reading/listening!

General microbiome

*Diversity within species: interpreting strains in microbiomes – Thea Van Rossum – Nature Reviews

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes – Bin Ma – Microbiome

Oral and nasal microbiome

Local oral and nasal microbiome diversity in age-related macular degeneration – Jacob Rullo – Scientific Reports

*Lactobacilli Have a Niche in the Human Nose – Ilke De Boeck – Cell Reports

Gut microbiome

Resistant maltodextrin intake reduces virulent metabolites in the gut environment: randomized control study in a Japanese cohort – Yuichiro Nishimoto – MedRxiv

Pregnancy and early life

One year cross-sectional study in adult and neonatal intensive care units reveals the bacterial and antimicrobial resistance genes profiles in patients and hospital surfaces – Ana Paula Christoff – PlosOne

Animal microbiome

Cecal microbiome composition and metabolic function in probiotic treated broilers – Denise R. Rodrigues – PlosOne

Characterization of native Escherichia coli populations from bovine vagina of healthy heifers and cows with postpartum uterine disease – Candelaria Gonzalez Moreno – PlosOne

Animal experiments

Structural and Functional Changes of Gut Microbiota in Ovariectomized Rats and Their Correlations With Altered Bone Mass – Sicong Ma – Aging

Plant, root, and soil microbiome

Dissecting the effect of continuous cropping of potato on soil bacterial communities as revealed by high-throughput sequencing – Jing Zhao – Plos One

Water microbiome

Increasing flow rate reduces biofouling and colonization by filamentous bacteria in drippers fed with reclaimed wastewater – Kevin Lequette – bioRxiv

Phages and viruses

Integration of phage and yeast display platforms: A reliable and cost effective approach for binning of peptides as displayed on-phage – Priyanka Pandya – PlosOne

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes – Kira Moon – Microbiome

Bioinformatics

Estimating Microbial Interaction Network: Zero-inflated Latent Ising Model Based Approach– Jie Zhou – bioRxiv

Assessment of statistical methods from single cell, bulk RNA-seq and metagenomics applied to microbiome data – Matteo Calgaro – bioRxiv

Metabolomics

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power– Jasmin Hafner – Synthetic Biology

Inferring Active Metabolic Pathways from Proteomics and Essentiality Data – Ariadna Montero-Blay – Cell Reports

Podcast

*May 2020 Pod: Discovering novel resistance genes and how bacteria become virulent – Bengtsson-Palme Lab and Marlies Böhm – Microbiology Lab Pod

June 4, 2020

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General microbiome

Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer – Costa et al. – Microbiome

Human microbiome

Review – Host–microbiota interactions in immune-mediated diseases. Ruff et al. – Nature Reviews Microbiology

Human gut microbiome

Gut microbial diversity, inflammation, and oxidative stress are associated with tacrolimus dosing requirements early after heart transplantation – Jennings et al. PLOS One

Review – Interaction between drugs and the gut microbiome – Weersma et al. – Gut

Mucosal Microbiota and Metabolome along the Intestinal Tract Reveal a Location-Specific Relationship – Yuan et al. mSystems

Animal microbiome

The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance – Barelli et al. mSystems.

Plant, root and soil microbiome

Diversity of isoprene-degrading bacteria in phyllosphere and soil communities from a high isoprene-emitting environment: a Malaysian oil palm plantation – Carrion et al. Microbiome

Probiotics

Probiotics for the prevention of antibiotic-associated adverse events in children—A scoping review to inform development of a core outcome set – Lukasik et al. –  PLOS One

Phages and viruses

Predicting host taxonomic information from viral genomes: A comparison of feature representations – Young et al. PLOS Comp Biology. 

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes – Moon et al. Microbiome.

Bioinformatics

The hidden layers of microbial community structure: extracting the concealed diversity dimensions from our sequencing data – Fasolo et al. – FEMS Microbiology Letters

Compositional Lotka-Volterra describes microbial dynamics in the simplex – Joseph et al. PLOS Computational Biology.

Techniques

Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing – Blattman et al. – Nature Microbiology.

June 3, 2020

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Today’s post covers articles on role of microbiome in sepsis, early life microbiota related to cystic fibrosis and respiratory syncitial virus disease, promise and challenge with cancer microbiome, effect of probiotics on intestinal homeostasis after chemotherapy and many more!

General microbiome

Predictive biology: modelling, understanding and harnessing microbial complexity – Allison J. Lopatkin – Nature Reviews Microbiology

The Gut Microbiome’s Role in the Development, Maintenance, and Outcomes of Sepsis – Max W Adelman – Critical Care

The Promise and Challenge of Cancer Microbiome Research – Sumeed Syed Manzoor – Genome Biology

Antidiabetic Effects of Flavan-3-ols and Their Microbial Metabolites – Estefanía Márquez Campos – Nutrients

Human microbiome

Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome – Roie Levy – PNAS

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale – Soumaya Zlitni – Genome Medicine

Comparative Assessment of Faecal Microbial Composition and Metabonome of Swine, Farmers and Human Control – Shiang Chiet Tan – Scientific Reports

Matching Between Donors and Ulcerative Colitis Patients Is Important for Long-Term Maintenance After Fecal Microbiota Transplantation – Koki Okahara – Journal of Clinical Medicine

Preganancy and early life

Alterations in Vaginal Microbiota and Associated Metabolome in Women With Recurrent Implantation Failure – Min Fu – mBio

Development of the Gut Microbiota in Early Life: The Impact of Cystic Fibrosis and Antibiotic Treatment – Maartje Kristensen – Journal of Cystic Fibrosis

Altered Gut Microbiota in Infants Is Associated With Respiratory Syncytial Virus Disease Severity – Jeffrey N Harding – BMC Microbiology

Ecological Succession in the Vaginal Microbiota During Pregnancy and Birth – M A Rasmussen – Isme Journal

Animal experiments

Host genotype and exercise exhibit species-level selection for members of the gut bacterial communities in the mouse digestive system – R. A. Dowden – Scientific Reports

Repetitive, Mild Traumatic Brain Injury Results in a Progressive White Matter Pathology, Cognitive Deterioration, and a Transient Gut Microbiota Dysbiosis – Mariana Angoa-Pérez – Scientific Reports

Association of Gut Microbiota Composition and Function With an Aged Rat Model of Senile Osteoporosis Using 16S rRNA and Metagenomic Sequencing Analysis – Sicong Ma – Aging

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 – Yu Pi – mSystems

Plant, root and soil microbiome

Using Soil Bacterial Communities to Predict Physico-Chemical Variables and Soil Quality – Syrie M Hermans – Microbiome

Analysis of bacterial and archaeal communities associated with Fogo volcanic soils of different ages – Corinne Biderre-Petit – Fems Microbial Ecology

Water microbiome

Functional potential and assembly of microbes from sediments in a lake bay and adjoining river ecosystem for polycyclic aromatic hydrocarbon biodegradation – Zaisheng Yan – Environmental Microbiology

Functional foods

Effect of Probiotics on the Maintenance of Intestinal Homeostasis After Chemotherapy: Systematic Review and Meta-Analysis of Pre-Clinical Studies – W G Lima – Beneficial Microbes

Non microbiology picks

Racial Disparities in Knowledge, Attitudes and Practices Related to COVID-19 in the USA– Wilson M Alobuia – Journal of Public Health

Ozone Treatment for Elimination of Bacteria and SARS-CoV-2 for Medical Environments – Craig Westover – BioRxiv

May 27, 2020

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Good morning everybody. It was a bit calm during the last days. Today’s Microbiome Digest tries to give a nice summary of a broad range of latest microbiome related research. Enjoy it!

General microbiome

A microbiological survey of handwashing sinks in the hospital built environment reveals differences in patient room and healthcare personnel sinks – Franco et al – Scientific Reports

Multi-site human microbiome

REVIEW: Interaction between microbiota and immunity in health and disease – Zheng, Liwinski and Elinav – Cell Research

REVIEW: A Comprehensive Review on Natural Bioactive Compounds and Probiotics as Potential Therapeutics in Food Allergy Treatment – Pratap et al. – Front. Immunol.

Editorial: The intestinal microbiota in health and disease – Day, Keenan and Tannock – Journal of the Royal Society of New Zealand

Human oral microbiome

Longitudinal Study of Oral Microbiome Variation in Twins – Freire et al. – Scientific Reports

Human skin microbiome

Skin Microbiome in Atopic Dermatitis – Edslev, Agner and Andersen – Acta Dermato-venereologica

Human gut microbiome and virome

Preprint: Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation – Sims et al. – medRxiv

The intestinal virome in children with cystic fibrosis differs from healthy controls – Coffey et al. – PLOS One

The human gut microbiota and depression: widely reviewed, yet poorly understood – Simpson, Schwartz and Simmons – Journal of Affective Disorders

The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients? – Magne et al. – Nutrients

Book Chapter: Who Inhabits Our Gut? Introducing the Human Gut Microbiota – Flint – Why Gut Microbes Matter

Book Chapter: Variability and Stability of the Human Gut Microbiome – Flint – Why Gut Microbes Matter

Book Chapter: How to Analyse Microbial Communities? – Flint – Why Gut Microbes Matter

Book Chapter: Treating the Gut Microbiome as a System – Flint – Why Gut Microbes Matter

Metabolomics

REVIEW: Application of metabolomics to the study of irritable bowel syndrome – Bennet et al. – Neurogastroenterology & Motility

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

Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse – van de Wouw et al. – Microbiology

Preprint: Physical activity shapes the intestinal microbiome and immunity of healthy mice but has no protective effects against colitis in MUC2-/- mice – Estaki et al. – bioRxiv

Synergetic responses of intestinal microbiota and epithelium to dietary inulin supplementation in pigs – He et al. – European Journal of Nutrition

Animal microbiome (for animals in the wild)

No correlation between microbiota composition and blood parameters in nesting flatback turtles (Natator depressus) – Scheelings et al. – Scientific Reports

Linking perturbations to temporal changes in diversity, stability, and compositions of neonatal calf gut microbiota: prediction of diarrhea – Ma et al. – The ISME Journal

Plant, root, and soil microbiome

The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts – Zolti et al. – Microbiology

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

16S rRNA Gene Diversity in the Salt Crust of Salar de Uyuni, Bolivia, the World’s Largest Salt Flat – Pecher et al. – Microbiol Resour Announc

Built environment (subways, indoor surfaces)

Fungal diversity and its contribution to the biodeterioration of mural paintings in two 1700-year-old tombs of China – Ma et al. – International Biodeterioration & Biodegradation

Characterizing Microbial Signatures on Sculptures and Paintings of Similar Provenance – Torralba et al. – Microbial Ecology

Food microbiology

Proteomic and Metabolomic Correlates of Healthy Dietary Patterns: The Framingham Heart Study – Walker et al. – Nutrients

Bioinformatics/Resources

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining – Mungan et al. – Nucleic Acid Research

Draft Genome Sequence of a Novel Species of Halococcus (Strain IIIV-5B), an Endophytic Archaeon Isolated from the Leaf Tissue of Avicennia germinans – Zayas-Rivera et al. – Microbiol Resour Announc

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 – Asnicar et al. – Nature Communications

May 22, 2020

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We’ve got a decently sized digest today with a lot of environmental microbe papers, including descriptions of novel species. There is also the Cell paper (highlighted) from Peter Turnbaugh’s group on ketogenic diets and the gut microbiome, which has been getting a lot of press. For new bioinformatic and other techniques, we have a new R package to predict functional profiles in Tax4Fun2, an assessment of phylogenetic rooting methods for bacteria, and a description of fiber intervention used in undergraduate classes for active learning.

 Have a great weekend!

Events

Today is the last day of the Virtual Microbiome Summit.

Pregnancy and early life

Women’s multisite microbial modulation during pregnancy – Luiz G. Sparvoli – Microbial Pathogenesis

Multi-site human microbiome

Review: Bi-Directional Interactions Between Microbiota and Ionizing Radiation in Head and Neck and Pelvic Radiotherapy-Clinical Relevance – Nidhya Teresa Joseph – International Journal of Radiation Biology

Human oral microbiome

Defining the oral microbiome by whole-genome sequencing and resistome analysis: the complexity of the healthy picture – Elisabetta Caselli – BMC Microbiology

Human gut microbiome

Ketogenic diets alter the gut microbiome resulting in decreased intestinal Th17 cells – Qi Yan Ang – Cell

Preprint: Host genetic and environmental factors shape the human gut resistome – Caroline I. Le Roy – bioRxiv

MinION Sequencing of colorectal cancer tumour microbiomes—A comparison with amplicon-based and RNA-Sequencing – William S. Taylor – PLOS One (Originally posted to the Digest as a pre-print, now published)

Animal experiments

Broilers divergently selected for digestibility differ for their digestive microbial ecosystems – Marion Borey – PLOS One

Dietary Isomalto/Malto‐Polysaccharides Increase Fecal Bulk and Microbial Fermentation in Mice – Rima H. Mistry – Molecular Nutrition and Food Research

Longitudinal Effects of Dietary Oxidized Lipids on the Gut Microbiome and Mycobiome in Pigs – Folagbayi Arowolo – FASEB Journal

Animal microbiome

Single-cell amplicon sequencing reveals community structures and transmission trends of protist-associated bacteria in a termite host – Michael E. Stephens – PLOS One

Plant, root, and soil microbiome

Xylella fastidiosa subsp. pauca and olive produced lipids moderate the switch adhesive versus non-adhesive state and viceversa – Valeria Scala – PLOS One

Mitochondrial genome sequence of Phytophthora sansomeana and comparative analysis of Phytophthora mitochondrial genomes – Guohong Cai – PLOS One

nirS-type denitrifying bacterial communities in relation to soil physicochemical conditions and soil depths of two montane riparian meadows in North China. – Xiaoli Han – Environmental Science and Pollution Research

Tissue-Specific Dynamics in the Endophytic Bacterial Communities in Arctic Pioneer Plant Oxyria digyna – Cindy Given – Frontiers in Plant Science

Effects of Cultured Root and Soil Microbial Communities on the Disease of Nicotiana tabacum Caused by Phytophthora nicotianae – Tianbo Liu – Frontiers in Microbiology

Novel putative rhizobial species with different symbiovars nodulate Lotus creticus and their differential preference to distinctive soil properties – M Rejili – FEMS Microbiology Letters

Water, air, and extremophile microbiome

The microbiome of alpine snow algae shows a specific inter-kingdom connectivity and algae-bacteria interactions with supportive capacities – Lisa Krug – ISME Journal

Variation of near surface atmosphere microbial communities at an urban and a suburban site in Philadelphia, PA, USA – JD Stewart – Science of the Total Environment

Pilot-scale petroleum refinery wastewaters treatment systems: performance and microbial communities’ analysis – Fatma Karray – Process Safety and Environmental Protection

Adverse effects of levofloxacin and oxytetracycline on aquatic microbial communities – Zhigao Zhou – Science of the Total Environment

Application of microbial network analysis to discriminate environmental heterogeneity in Fildes Peninsula, Antarctica – Qian Liu – Marine Pollution Bulletin

Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium – HS Tee – ISME Journal

Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site – Christen L. Grettenberger – BMC Microbiology

Halocatena pleomorpha gen. nov. sp. nov., an extremely halophilic archaeon of family Halobacteriaceae isolated from saltpan soil – Ashish Verma – IJSEM

Unveiling Cultivable and Uncultivable Halophilic Bacteria Inhabiting Marakkanam Saltpan, India and Their Potential for Biotechnological Applications – Jojy John – Geomicrobiology Journal

Flavobacterium profundi sp. nov., isolated from a deep-sea seamount – Qian Wang – IJSEM

Food microbiology

Molecular epidemiology, genetic diversity and antimicrobial resistance of Staphylococcus aureus isolated from chicken and pig carcasses, and carcass handlers – Onyinye J. Okorie-Kanu – PLOS One

Traditional milk transformation schemes in Côte d’Ivoire and their impact on the prevalence of Streptococcus bovis complex bacteria in dairy products – Aimé R Sanhoun – PLOS One

Comparison of Microbial Communities and Amino Acid Metabolites in Different Traditional Fermentation Starters Used during the Fermentation of Hong Qu Glutinous Rice Wine – Zhang-Cheng Liang – Food Research International

Preprint: Monitoring the microbiome for food safety and quality using deep shotgun sequencing – Kristen L. Beck – bioRxiv

Viruses

Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)? – Ping Liu – PLOS Pathogens

Vector competence of Aedes aegypti from New Caledonia for the four recent circulating dengue virus serotypes – Olivia O’Connor – PLOS Neglected Tropical Diseases

Bioinformatics

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences – Franziska Wemheuer – Environmental Microbiome

Techniques

Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families – Taylor Wade – PLOS One

Science education techniques: Fiber Force: A Fiber Diet Intervention in an Advanced Course-Based Undergraduate Research Experience (CURE) Course – Julia Massimelli Sewall – Journal of Microbiology & Biology Education

Science and art

This photographer creates prints with algae.

Non-microbiology picks:

Herd of fuzzy green “glacier mice” baffles scientists.