Category Archives: General Microbiome

January 27, 2021

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General microbiome

[REVIEW]The complexities of the diet-microbiome relationship: advances and perspectives – Leeming et al. – Genome Medicine

Human skin microbiome

A mixed community of skin microbiome representatives influences cutaneous processes more than individual members – Loomis et al. – Microbiome

Analysis of the Composition and Functions of the Microbiome in Diabetic Foot Osteomyelitis Based on 16S rRNA and Metagenome Sequencing Technology – Zou et al. – Diabetes

Human gut microbiome

Gut microbiota condition the therapeutic efficacy of trastuzumab in HER2-positive breast cancer – Di Modica et al. – Cancer Research

[REVIEW]Role of the gut microbiota in type 2 diabetes and related diseases – Yang et al. – Metabolism

Animal microbiome (for animals in the wild)

Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas – Baniel et al. – Microbiome

Taxonomic and functional adaption of the gastrointestinal microbiome of goats kept at high altitude (4800 m) under intensive or extensive rearing conditions – Zhang et al. – FEMS Microbiology Ecology

Shifts in bacterial communities and antibiotic resistance genes in surface water and gut microbiota of guppies (Poecilia reticulata) in the upper Rio Uberabinha, Brazil – Jia et al. – Ecotoxicology and Environmental Safety

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

Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing – Okazaki et al. – Microbiome

Microbiota entrapped in recently-formed ice: Paradana Ice Cave, Slovenia – Mulec et al. – Scientific Reports

Sea‐ice microbial communities in the Central Arctic Ocean: Limited responses to short‐term pCO2 perturbations – Torstensson et al. – Limnology and Oceanography

Built environment (subways, indoor surfaces)

Bacterial community assemblages in classroom floor dust of 50 public schools in a large city: characterization using 16S rRNA sequences and associations with environmental factors – Park et al. – Microbiome

[REVIEW]Plastics and the microbiome: impacts and solutions – Lear et al. – Environmental Microbiome

Bioinformatics

[REVIEW]Understanding the host-microbe interactions using metabolic modeling – Jansma & El Aidy – Microbiome

January 26, 2021

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Review articles on hygiene hypothesis and COVID, role of microbiome in cancer, different studies on efficacy of probiotics in inflammatory and metabolic diseases, and many more…

General microbiome

The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome – B. Brett Finlay – PNAS

Exploring the Role of Gut Microbiome in Colon Cancer – Indranil Chattopadhyay – Applied Biochemistry and Biotechnology

Cancer trigger or remedy: two faces of the human microbiome – Anna Grenda – Applied Microbiology and Biotechnology

Human microbiome

Microbiota, Epigenetics and Trained Immunity: Convergent Drivers and Mediators of the Asthma Trajectory from Pregnancy to Childhood – Susan V Lynch – American Journal of Respiratory and Critical Care Medicine

Gut Microbial Signature of Hepatocellular Cancer in Men with Cirrhosis – Somaya Albhaisi – Liver Transplantation

An Evaluation of the Fecal Microbiome in Lynch Syndrome – Adalberto Gonzalez – Journal of Gastrointestinal Cancer

Gut microbiota condition the therapeutic efficacy of trastuzumab in HER2-positive breast cancer – Martina Di Modica – Cancer Research

Recent, mid-, and late-adulthood antibiotic use are associated with subsequent risk of diverticulitis – Long H.Nguyen – Gastroenterology

Animal microbiome

Gestational gut microbial remodeling is impaired in a rat model of preeclampsia superimposed on chronic hypertension – Jeanne A Ishimwe – Physiological Genomics

Diet, habitat environment and lifestyle conversion affect the gut microbiomes of giant pandas – Leijin – Science of the Total Environment

Functional Foods

Probiotic Lactobacillus casei Shirota prevents acute liver injury by reshaping the gut microbiota to alleviate excessive inflammation and metabolic disorders – Ren Yan – Microbial Biotechnology

Functional characterization and immunomodulatory properties of Lactobacillus helveticus strains isolated from Italian hard cheeses – Miriam Zago – PlosOne

The Acid-Dependent and Independent Effects of Lactobacillus acidophilus CL1285, Lacticaseibacillus casei LBC80R, and Lacticaseibacillus rhamnosus CLR2 on Clostridioides difficile R20291 – Sathursha Gunaratnam – Probiotics and Antimicrobial Proteins

Polyphosphate, Derived from Lactobacillus brevis, Modulates the Intestinal Microbiome and Attenuates Acute Pancreatitis – Shuhei Takauji – Digestive Diseases and Sciences

Human Intestinal Barrier: Effects of Stressors, Diet, Prebiotics, and Probiotics – Michael Camilleri – Clinical and Translational Gastroenterology

Plant, root and soil microbiome

Insights into the plant responses to drought and decoding the potential of root associated microbiome for inducing drought tolerance – Piyush Mathur – Physiologia Plantarum

Water microbiome

A genomic view of the microbiome of coral reef demosponges – S. J. Robbins – ISME Journal

Microbes in news

Gut Bacteria Offer Insight into Molecules Protective Against Asthma and COVID-19 – Biospace

January 19, 2021

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Today’s digest includes a full list of the collection of articles looking at the prenatal microbiota that was recently published in Microbiome as well as some excellent articles from Cell Host & Microbe. 

General Microbiome

A microbial metabolite remodels the gut-liver axis following bariatric surgery – Chaudhari et al. Cell Host & Microbe. 

[REVIEW] The microbiota in pneumonia: From protection to predisposition. Thibeault et al. Science Translational Medicine. 

Prenatal Microbiome

BMC Microbiome has published a collection of articles looking at the prenatal microbiome including perspectives, and commentaries from a range of experts.  

A philosophical perspective on the prenatal in utero microbiome debate – Walter and Hornef. Microbiome. 

Batch effects account for the main findings of an in utero human intestinal bacterial colonization study – Goffau et al. Microbiome

Group therapy on in utero colonization: seeking common truths and a way forward. Silverstein and Mysorekar. Microbiome. 

Lessons learned from the prenatal microbiome controversy. Blaser et al. Microbiome. 

Microbiome or no microbiome: are we looking at the prenatal environment through the right lens? – Fricke and Ravel. Microbiome. 

Corroborating evidence refutes batch effect as explanation for fetal bacteria – Rackeiyte et al. Microbiome

Gut microbiome

Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. Tanes et al. Cell Host & Microbe

Biogeography of the Relationship between the Child Gut Microbiome and Innate Immune System – Amenyogbe et al. mSystems

Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy – He et al. mSystems

Traditional Human Populations and Nonhuman Primates Show Parallel Gut Microbiome Adaptations to Analogous Ecological Conditions – Sharma et al. mSystems

Animal microbiome

Heritable Gut Microbiome Associated with Salmonella enterica Serovar Pullorum Infection in Chickens –  Ding et al. mSystems 

Probiotics

Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice – Lee et al. Nature Microbiology. 

January 15, 2021

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Today’s digest features a collection of reviews, opinion pieces, discussion on prenatal microbiome, pipeline to extract metabolic models from whole metagenome sequencing data (metaGEM), novel type of colistin resistance genes, mechanisms that shape microbial pangenomes, and more. Check out a list of free web-based microbial seminars. Happy reading/listening!

General microbiome

*Mechanisms That Shape Microbial Pangenomes – Maria Rosa Domingo-Sananes
and James O. McInerney – Trends in Microbiology

Evolution to alternative levels of stable diversity leaves areas of niche space unexplored – Ilan Naftali Rubin – bioRxiv

Prenatal microbiome

*The prenatal in utero microbiome controversy: Microbiome or no microbiome: are we looking at the prenatal environment through the right lens? – W. Florian Fricke and Jacques Ravel – BMC Microbiome

Urinary microbiome

The Urinary Microbiome in Postmenopausal Women with Recurrent Urinary Tract Infections – Monique H. Vaughan – bioRxiv

Alterations in Urobiome in Patients With Bladder Cancer and Implications for Clinical Outcome: A Single-Institution Study – Jiarong Zeng – Frontiers in Cellular and Infection Microbiology

Bare Versus Hair: Do Pubic Hair Grooming Preferences Dictate the Urogenital Microbiome? – Geynisman-Tan J – Female Pelvic Medicine & Reconstructive Surgery

Vaginal microbiome

Amylases in the Human Vagina – Kenetta L. Nunn – mSphere

Gut microbiome

Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes – Moamen M. Elmassry – PlosOne

Microbiome and ischemic stroke: A systematic review – Yee Teng Lee – PlosOne

Antimicrobial resistance

*A novel type of colistin resistance genes selected from random sequence space – Michael Knopp – Plos Genetics

Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance – Kara K. Tsang – Microbial Genomics

A framework for identifying the recent origins of mobile antibiotic resistance genes – Stefan Ebmeyer – Communications Biology

Minimal biophysical model of combined antibiotic action – Bor Kavčič – Plos Computational Biology

Mobilization of antibiotic resistance genes differ by resistance mechanism – Tue Kjaergaard Nielsen – bioRxiv

Carbapenem and Colistin Resistance in Enterobacter: Determinants and Clones – Zhiyong Zong – Trends in Microbiology

Animal microbiome

Fermented traditional Chinese medicine alters the intestinal microbiota composition of broiler chickens – Peng Huang – Research in Veterinary Science

Plant/root/soil microbiome

Coordination between microbiota and root endodermis supports plant mineral nutrient homeostasis – Isai Salas-González – Science

Food microbiome

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community – Sonja Blasche – Nature Microbiology

Generation of lactose and protease positive probiotic Lacticaseibacillus rhamnosus GG by conjugation with Lactococcus lactis NCDO 712 – Nazar Hussain – Applied and Environmental Microbiology

Phages and Viruses

Engineered Phage Endolysin Eliminates Gardnerella Biofilm without Damaging Beneficial Bacteria in Bacterial Vaginosis Ex Vivo – Christine Landlinger – Pathogens

Bioinformatics

*metaGEM: reconstruction of genome scale metabolic models directly from metagenomes – Francisco Zorrilla – bioRxiv

Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species – Thomas Sakoparnig – eLife

CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data – Anna Abramova – Bioinformatics

Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it – Huy N Nguyen – Bioinformatics

Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge – Runzhi Zhang – Biology Direct

RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation – Wenjun Li – Nucleic Acids Research

Techniques

A co-culture microplate for real-time measurement of microbial interactions – Charles Jo – bioRxiv

Webinars

Mind, Mood & Microbes Expert Q&A: From Mechanisms to Clinical Applications – Jane Foster, Mauro Costa-Mattioli, John Cryan, Eldin Jašarević, Aletta D. Kraneveld, Filip Scheperjans, Elaine Hsiao – 21 January

SGBUG (Singapore Bacterial Ultra Group) seminar: Silencing bacterial genes with CRISPR-dCas9: from basic insights to high-throughput screens – David Bikard – 21 January

LoopSeq Solo Webinar: High Resolution Metagenomic Sequencing using DADA2 and LoopSeq Long-Read Sequencing – Benjamin Callahan – 21 January

FEMS Yeast Research Webinar on Genomic Insights into Yeast Diversity and Evolution – FEMS – 28 January

SSB Seminar: Double Trouble: Inappropriate Image Duplications in Biomedical Publications – Elisabeth Bik – 29 January

Geomicrobiology Network Seminar Series – The Mineralogical Society of Great Britain and Ireland

Winter 2021 WESTalks – Weekly seminars related to Water and the Environment with speakers from around the globe – IC-IMPACTS Student Engagement Committee (SEC) and the University of British Columbia’s Future Waters

MicroSeminars 2021 – Free Web-based Microbiology Seminar Series

Conferences &c

1st Microbiome PT Summit – The Portuguese Microbiome Community – 4 February

The 2021 UK Cellular Microbiology Network meeting – The Francis Crick Institute – 1-2 March

The Biology and Physics of Bacterial Chromosomes meeting – 4 March

Symposium Celebrating 100th Birthday and Research Accomplishments of Dr. Evelyn M. Witkin – Waksman Institute of Microbiology – 13 April

Podcast

TWiM 233: Antivirals made by bacteria – Hosts: Vincent Racaniello, Elio Schaechter, Michele Swanson, and Michael Schmidt – This week in microbiology podcast

January 14, 2021

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Greetings from Pittsburgh!

Today’s digest contains lots of microbial ecology articles focused on everything from the impacts of sleep on dental biofilm to the response of soil microbiota to high petroleum pollution. Also included are two articles focused on insect-plant interactions, with the first focusing on gall induction in insects and the second on the intestinal microbiota of the pine defoliator C. chuxiongica.

General microbiome

Novel cyanotoxin-producing Synechococcus in tropical lakes – Yew-Hoong et al. – Water Research

Multi-site human microbiome

Impacts of sleep on the characteristics of dental biofilm – Sotozono et al. – Scientific Reports

Animal experiments

Dysbiosis of rat vagina is efficiently rescued by the vaginal microbiota transplantation or probiotic combination: Vaginal microbiota transplantation rescues dysbiosis in rat vagina – Chen et al. – International Journal of Antimicrobial Agents

Are bacterial symbionts associated with gall induction in insects? – Hammer et al. – Arthropod-Plant Interactions

The diversity and function of intestinal microorganisms in four geographic Cephalcia chuxiongica (a pine defoliator) populations – Yu et al. – Journal of Applied Entomology

Animal microbiome

Linking bacterial communities associated with the environment and the ecosystem engineer Orchestia gammarellus at contrasting salt marsh elevations – Hernández et al. – Microbial Ecology

Plant, root, and soil microbiome

Response of bacterial and fungal communities to high petroleum pollution in different soils – Galitskaya et al. – Scientific Reports

Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing – Hu et al. – AMB Express

First reported quantitative microbiota in different livestock manures used as organic fertilizers in the Northeast of Thailand – Wongsaroj et al. – Scientific Reports

Water and extremophile microbiome

Coastal bacterial community response to glacier melting in the Western Antarctic Peninsula – Alcamán-Arias et al. – Microorganisms

Microbial necromass formation, enzyme activities and community structure in two alpine elevation gradients with different bedrock types – Bhople et al. – Geoderma

Exploring the taxonomical and functional profile of As Burgas hot spring focusing on thermostable β-galactosidases – DeCastro et al. – Scientific Reports

The effect of an adsorbent matrix on recovery of microorganisms from hydrocarbon-contaminated groundwater – Taylor et al. – Microorganisms

Built environment

Electrochemical performance and response of bacterial community during phenanthrene degradation in single-chamber air-cathode microbial fuel cells – Hua et al. – Environmental Science and Pollution Research

Food microbiology

Combination of Flos Sophorae and chili pepper as a nitrite alternative improves the antioxidant, microbial communities and quality traits in Chinese sausages – Tang et al. – Food Research International

January 12, 2021

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Good morning, today we have a quite divers selection of studies. Of special note are the results of the PREDICT 1 study, published in Nature Medicine (Asnicar et al.). Furthermore, we cover among others virome in pregnant women, gut microbiome and PD, some animal microbiome studies, water microbiome, and bioinformatic tools.

General microbiome

[Meeting Report]Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020 – LaPelusa et al. – Microbiome

Identifying background microbiomes in an evidence recovery laboratory: A preliminary study – Neckovic et al. – Science & Justice

Human vaginal microbiome/virome

Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis – Zhang et al. – Virology Journal

Human gut microbiome

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals – Asnicar et al. – Nature Medicine

Gut Microbiota Dysbiosis Is Associated with Elevated Bile Acids in Parkinson’s Disease – Li et al. – Metabolites

Animal microbiome

The Combined Effects of Magnesium Oxide and Inulin on Intestinal Microbiota and Cecal Short-Chain Fatty Acids – Omori et al. – Nutrients

Effect of host breeds on gut microbiome and serum metabolome in meat rabbits – Ye et al. – BMC Veterinary Research

Differential response of digesta- and mucosa-associated intestinal microbiota to dietary insect meal during the seawater phase of Atlantic salmon – Li et al. – Animal Microbiome

Plant, root, and soil microbiome

Diversity and composition of the Panax ginseng rhizosphere microbiome in various cultivation modesand ages – Tong et al. – BMC Microbiology

Water microbiome

Eukaryotic community diversity and pathogenic eukaryotes in a full-scale drinking water treatment plant determined by 18S rRNA and metagenomic sequencing – Li et al. – Environmental Science and Pollution Research

Microbial community structure in aquifers associated with arsenic: analysis of 16S rRNA and arsenite oxidase genes – Sonthiphand et al. – PeerJ

Fungi Present in Antarctic Deep-Sea Sediments Assessed Using DNA Metabarcoding – Ogaki et al. – Environmental Microbiology

Built environment

Comparative analysis of impact of human occupancy on indoor microbiomes – Cao et al. – Frontiers of Environmental Science & Engineering

Bioinformatics

Re-purposing software for functional characterization of the microbiome – Gardiner et al. – Microbiome

[PREPRINT]Mining underutilized whole-genome sequencing projects to improve 16S rRNA databases – Nolan et al. – bioRxiv

Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function – Jing et al. – BMC Genomics

Techniques

Exploring protocol bias in airway microbiome studies: one versus two PCR steps and 16S rRNA gene region V3 V4 versus V4 – Drengenes et al. – BMC Genomics

Quantitative image analysis of microbial communities with BiofilmQ – Hartmann et al. – Nature Microbiology

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

Do the bugs in our guts make us sick, sad and obese? – Sismondo – Toronto Star

New microbiome research finds associations between microbes, diet, and metabolic health – Krawiec – Nutritional outlook

January 06, 2021

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Good morning, today we selected papers about the cancer microbiome atlas, detection of blood parasites, antibiotics and gut microbiome, metabolome and a new binning approach for metagenomic data using auto-encoders.

General microbiome

The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants – Dohlaman et al. – Cell Host & Microbe

Human nearly-sterile sites (blood, organs, brain)

Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing – Flaherty et al. – Microbiome

Human gut microbiome

Long-Term Impact of Suppressive Antibiotic Therapy on Intestinal Microbiota – Escudero-Sanchez et al. – genes

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

Metagenomics dataset used to characterize microbiome in water and sediments of the lake Solenoe (Novosibirsk region, Russia) – Bryanskaya et al. – Data in Brief

*Metabolome

Changes in the Serum Metabolome of Patients Treated With Broad-Spectrum Antibiotics – Kaskiw et al. – Pathogens and Immunity

Walnut Consumption, Plasma Metabolomics, and Risk of Type 2 Diabetes and Cardiovascular Disease – Guasch-Ferre et al. – The Journal of Nutrition

Bioinformatics

Improved metagenome binning and assembly using deep variational autoencoders – Nissen et al. – Nature Biotechnology

December 31, 2020

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General microbiome

Review: Brain-gut axis: From the conditioned reflex to the microbiota-gut-brain communication system – Klara Gyires – Integrative Physiology

Human skin microbiome

Microbiological profile of diabetic foot ulcers in Kuwait – Asma Alhubail – PLOS ONE

Human respiratory microbiome

The airways microbiome of individuals with asthma treated with high and low doses of inhaled corticosteroids – Matthew J Martin – PLOS ONE

Human gut microbiome

The beneficial or detrimental fluoride to gut microbiota depends on its dosages – Guijie Chen – Ecotoxicology and Environmental Safety

Review: Synthetic Gut Microbiome: Advances and Challenges – Humphrey A. Mabwi – Computational and Structural Biotechnology Journal

Review: Microbiota-Gut-Brain Axis as a Regulator of Reward Process – Rubén García-Cabrerizo – Journal of Neurochemistry

Review: Modulatory effects of gut microbiome in cancer immunotherapy: A novel paradigm for blockade of immune checkpoint inhibitors – Sama Rezasoltani – Cancer Medicine

Animal experiments

Effects of heat-killed Enterococcus faecalis T-110 supplementation on gut immunity, gut flora, and intestinal infection in naturally aged hamsters – Takio Inatomi – PLOS ONE

Nasal Tissue Extraction Is Essential for Characterization of the Murine Upper Respiratory Tract Microbiota – L Patrick Schenck – mSphere

Animal microbiome

Review: Gut microbiota of animals living in polluted environments are a potential resource of anticancer molecules – Morhanavallee Soopramanien – Journal of Applied Microbiology

Plant, root, and soil microbiome

Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats  – Martino Adamo – PLOS ONE

Changes in microbial communities at different soil depths through the first rainy season following severe wildfire in North China artificial Pinus tabulaeformis forest – Qianqian Qin – Journal of Environment Management

Shifts in a Phenanthrene-Degrading Microbial Community are Driven by Carbohydrate Metabolism Selection in a Ryegrass Rhizosphere – Longfei Jiang – ACS

Forest gaps mediate the structure and function of the soil microbial community in a Castanopsis kawakamii forest – Xuelin Wang – Ecological Indicators

Review: Herbicide bioremediation: from strains to bacterial communities – Marcos Pileggi – Heliyon

Spatial scale structure soil bacterial communities across an Arctic landscape – Lucie A Malard – Applied and Environmental Microbiology

Metagenomic Analysis of Rhizosphere Bacteria in Desert Plant Calotropis procera – Ahmed M Ramadan

Water and extremophile microbiome

Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte – Ana Rita Moura Polónia – Antonie van Leeuwenhoek

Preprint: Novel integrative elements and genomic plasticity in ocean ecosystems – Thomas Hackl – bioRxiv

Food microbiology

The diversity of microbial communities in Chinese milk fan and their effects on volatile organic compound profiles – Chen Chen – Journal of Dairy Science

Characterizing Relationship of Microbial Community in Xiaoqu and Volatiles of Light-aroma-type Xiaoqu Baijiu – Zhe Wang – Food Science and Technology Research

Virus and phages

Acquisition, prevalence and clearance of type-specific human papillomavirus infections in young sexually active Indian women: A community-based multicentric cohort study – Richard Muwonge – PLOS ONE

Techniques

Informed sequential pooling approach to detect SARS-CoV-2 infection – Renato Millioni – PLOS ONE

Thesis: Statistical Methods for Longitudinal Data Analysis and Reproducible Feature Selection in – Lingjing Jiang – UC San Diego Electronic Theses and Dissertations

MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences – Yue Xing – Frontiers in Microbiology

Microbes and evolution

Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history – Eva Brons – PLOS BIOLOGY

The role of Ulva fasciata in the evolution of the microbial community and antibiotic resistance genes in maricultural sediments – Yuqin Luo – Marine Pollution Bulletin

Preprint: The Diversity and Evolution of Microbial Dissimilatory Phosphite Oxidation – Sophia D Ewens – bioRxiv

Microbes in the news

Synthetic Biologics Inc. (SYN) Soars 5.43% on December 25 – equities.com

The Brain, Gut and Consciousness: Microbiology of Our Mind – Inquiries Journal

Non-microbiology pick

Preprint: National Institutes of Health Institute and Center Award Rates and Funding Disparities – Michael S Lauer – bioRxiv

Communicating risk in human-wildlife interactions: How stories and images move minds – Sarah K Guenther – PLOS ONE

December 23, 2020

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Good morning from Northern Germany! It is almost Xmas. Today’s microbiome digest is rather long and comprises some interesting findings about c-section and the gut microbiome in early life, human breast milk, chronic pain, antimicrobial resistance, imbalance of the gut microbiome in relation to Parkinon’s disease and COVID19, diet, honey bees (two pre-prints), roundup, and last but not least some bioinformatic papers. Additionally, we select some interesting reviews. Of specific interest is a study about showing reveals poor correlations in microbial taxonomic abundance between humans and mice after gnotobiotic transfer.

General microbiome

Sequence variant analysis reveals poor correlations in microbial taxonomic abundance between humans and mice after gnotobiotic transfer – Fouladi et al. – The ISME Journal

Application of ecological and evolutionary theory to microbiome community dynamics across systems – McDonald, Marchesi & Koskella – Proceedings of the Royal Society B

[BOOK CHAPTER]Salivary and Urinary Metabolome in Pediatric Obesity and Metabolic Syndrome – Troisi et al. – Obesity and Diabetes

Human early life microbiome

Cesarean delivery is associated with decreased beneficial gut microbes and increased pathobionts and butyrate excretion: a longitudinal study over the first year of life. – Mueller et al – BJOG

Human oral microbiome

[OPINION]Future directions for studying resilience of the oral ecosystem – Zemouri et al. – British Dental Journal

Human milk microbiome

Maternal diet alters human milk oligosaccharide composition with implications for the milk metagenome – Seferovic et al. – Scientific Reports

Mapping the Human Milk Microbiome: Impetus for a Long-Awaited Renaissance in Maternal and Infant Nutrition Research? – McGuire & McGuire – The Journal of Nutrition

[PREVIEW]Breast Milk Modulates Transgenerational Immune Inheritance – Zimmermann & Macpherson – Cell

An Immunologic Mode of Multigenerational Transmission Governs a Gut Treg Setpoint – Ramanan et al. – Cell

Human respiratory/lung microbiome

[REVIEW]The Lung Microbiome and Pneumonia – Pettigrew, Tanner & Harris

[REVIEW]Microbiome: A Supportive or a Leading Actor in Lung Cancer? – Martins, Mendes & Schmitt – Pathobiology

Human skin microbiome

[REVIEW]Skin and Gut Microbiome in Psoriasis: Gaining Insight Into the Pathophysiology of It and Finding Novel Therapeutic Strategies – Chen et al. – Frontiers in Microbiology

Human gut microbiome

An association between chronic widespread pain and the gut microbiome – Freidin et al. – Rheumatology

The Gut Microbiome as a Reservoir for Antimicrobial Resistance – Anthony et al. – The Journal of Infectious Diseases

[REVIEW]Dietary modification of gut microbial metabolism protects the kidney – Carney – Nature Reviews Nephrology

Gut Microbiome Imbalance and Neuroinflammation: Impact of COVID‐19 on Parkinson’s Disease – Follmer – Movement Disorders

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

[REVIEW]Gut Microbiota Status in COVID-19: An Unrecognized Player? – Zeppa et al. – Front. Cell. Infect. Microbiol.

Animal microbiome

[PREPRINT]Honeybee gut microbiota modulates host behaviors and neurological processes – Zhang et al. – bioaRxiv

[PREPRINT]Honeybee genetics shape the strain-level structure of gut microbiota in social transmission – Wu et al. – bioRxiv

Description of the microbiota in epidermal mucus and skin of sharks (Ginglymostoma cirratum and Negaprion brevirostris) and one stingray (Hypanus americanus) – Caballero et al. – PeerJ

Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species – Microbiome – Suppa et al. – Microbiome

Plant, root, and soil microbiome

Influence of vintage, geographic location and cultivar on the structure of microbial communities associated with the grapevine rhizosphere in vineyards of San Juan Province, Argentina – Aguilar et al. – PLOS One

[REVIEW]Restoring degraded microbiome function with self-assembled communities – Gutierrez et al. – FEMS Microbiology Ecology

Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves – Regalado et al. – The ISME Journal

Bioinformatics/Data analysis

A joint modeling approach for longitudinal microbiome data improves ability to detect microbiome associations with disease – PLOS Computation Biology – Luna, Mansbach & Shaw

Predicting Nash equilibria for microbial metabolic interactions – Cai, Tan & Chan – Bioinformatics

microeco: An R package for data mining in microbial community ecology – Liu et al. – FEMS Microbiology Ecology

[REVIEW]Multi-omics data integration considerations and study design for biological systems and disease – Graw et al. – Molecular Omics

Techniques

[PREPRINT]Improved microbial community characterization of 16S rRNA via metagenome hybridization capture enrichment – Beaudry et al. – bioRxiv

December 18, 2020

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Greetings from cold and snowy Pittsburgh!

As I type this, my housemate (who is an essential healthcare worker) should be getting the first dose of her COVID-19 vaccine! Although I’m not sure what the distribution of COVID-19 vaccines is expected to look like, today’s digest includes an article mapping routine measles vaccination coverage in low- and middle- income countries. I’ve also highlighted a few interesting environmental microbiology preprints, including one on the role of ecosystem engineers in shaping arid soil bacterial communities.

Happy holidays and happy reading!

Events and jobs

Danone North America Gut Microbiome, Yogurt and Probiotics Fellowship Grant – Applications for the 2020-2021 grant are currently open and are due on February 24, 2021.

General microbiome

Mapping routine measles vaccination in low- and middle-income countries – Local Burden of Disease Vaccine Coverage Collaborators – Nature

The functional proteome landscape of Escherichia coli – Mateus et al. – Nature

Preprint: Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae – Shaw et al. – bioRxiv


Plant, root, and soil microbiome

Preprint: The role of ecosystem engineers in shaping the diversity and function of arid soil bacterial communities – Baubin et al. – bioRxiv

Preprint: Environmental interactions with amoebae as drivers of bacterial-fungal endosymbiosis and pathogenicity – Itabangi et al. – bioRxiv