Category Archives: Animal microbiome

January 28, 2021

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Happy almost Friday from the US’s west coast, everybody! I recently finished reading “Braiding Sweetgrass: Indigenous Wisdom, Scientific Knowledge, and the Teachings of Plants” by Robin Wall Kimmerer and plants have been on my mind so today’s Digest is heavy on the plant microbiome research. Two plant papers I found especially fascinating applied different experimental designs to study the same issue: one looks at how the mono-cropping of maize negatively impacts soil microbial communities and the other found that sugarcane/peanut intercropping enriches for beneficial microbes that promote nitrogen and phosphate release from the soil. There are also several papers looking at the relationship between microbes and the host immune system and an eLife paper in which the popular shelter-in-place hobby of making sourdough and our beloved microbiome field collide. Happy reading!

Pregnancy and Early Life
Fecal Microbiota Nutrient Utilization Potential Suggests Mucins as Drivers for Initial Gut Colonization of Mother-Child Shared Bacteria. – Nilsen, M. et al., Applied and Environmental Microbiology.

Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States. – Casaburi, G. et al., Scientific Reports.

Human Gut Microbiome
Gut bacteria-derived 5-hydroxyindole is a potent stimulant of intestinal motility via its action on L-type calcium channels. – Waclawiková, B. et al., PLoS Biology.

Animal Experiments
Gut CD4+ T cell phenotypes are a continuum molded by microbes, not by TH archetypes. – Kiner, E. et al., Nature Immunology.

Regulation of Gut Microbiota Disrupts the Glucocorticoid Receptor Pathway and Inflammation-related Pathways in the Mouse Hippocampus. – Rao, X. et al., Experimental Neurobiology.

Decreased Ecological Resistance of the Gut Microbiota in Response to Clindamycin Challenge in Mice Colonized with the Fungus Candida albicans. – Markey, L. et al., mSphere.

Gut Commensal Segmented Filamentous Bacteria Fine-Tune T Follicular Regulatory Cells to Modify the Severity of Systemic Autoimmune Arthritis. – Bates, N.A. et al., Journal of Immunology.

Microbial metabolism of L-tyrosine protects against allergic airway inflammation. – Wypych, T.P. et al., Nature Immunology.

Animal Microbiome
Host development overwhelms environmental dispersal in governing the ecological succession of zebrafish gut microbiota. – Xiao, F. et al., npj Biofilms and Microbiomes.

Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria. – Klassen, L. et al., Microbiome.

Plant, Root, and Soil Microbiome
Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition. – Tláskal, V. et al., mSystems.

Natural Bacterial Assemblages in Arabidopsis thaliana Tissues Become More Distinguishable and Diverse during Host Development. – Beilsmith, K. et al., mBio.

Colonization of naïve roots from Populus tremula x alba involves successive waves of fungi and bacteria with different trophic abilities. – Fracchia, F. et al., Applied and Environmental Microbiology.

The role of host promiscuity in the invasion process of a seaweed holobiont. – Bonthond, G. et al., The ISME Journal.

Sugarcane/peanut intercropping system improves the soil quality and increases the abundance of beneficial microbes. – Tang, X. et al., Journal of Basic Microbiology.

Variation of rhizosphere microbial community in continuous mono-maize seed production. – Zhao, Y. et al., Scientific Reports.

Food Microbiology
The diversity and function of sourdough starter microbiomes. – Landis, E.A. et al., eLife.

Probiotics
Optimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract. – Westfall, S. et al., Scientific Reports.

Metagenomics
How reliably do metagenome-assembled genomes (MAGs) represent natural populations? Insights from comparing MAGs against isolate genomes derived from the same fecal sample. – Meziti, A. et al., Applied and Environmental Microbiology.

Techniques
Precision modification of the human gut microbiota targeting surface-associated proteins. – Marcos-Fernández, R. et al., Scientific Reports.

High-throughput cultivation and identification of bacteria from the plant root microbiota. – Zhang, J. et al., Nature Protocols.

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 24, 2021

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Hyvää Päivää from Helsinki, Finland ! Today’s digest contains quite a lot of different topics. If you are interested in  early-life microbiome, I recommend taking a look at the paper from Mortensen and collaborators. To understand the role of the maternal vaginal microbiome’s in seeding their child and the importance of the delivery mode in early-life microbiome acquisition, they studied 665 mother–child dyads and modeled the transfer of the vaginal microbiota from mother to infants.

In today’s digest, you’ll also find a really interesting preprint from Abiriga and collaborators, looking at the microbiome of a groundwater aquifer contaminated by a municipal landfill while undergoing intrinsic bioremediation. This preprint is particularly notable because studies looking at the microbiome of contaminated aquifers are particularly rare, despite groundwater contaminations from landfills being a very common issue.

Today’s non-microbiology pick takes a look at the difficulty of detecting scientificly fraudulent images produced by Generative Adversarial Networks (GANs). They demonstrate that this deep-learning method can generate realistic western blot images that are indistinguishable from real western blots. In conclusion, the authors argues that additional information should be required to ensure that the western blots published in scientific publication are not generated images. 

Have a great Sunday!

Human respiratory microbiome

Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism – Sulaiman et al. – European respiratory journal

Human skin microbiome

Preprint: Comparative investigation of the Diabetic foot ulcer microbiome – Saeb et al. – BioRxiv

Human vaginal microbiome

Preprint: Vaginal bacterial load in the second trimester is associated with early preterm birth recurrence: a nested case-control – Goodfellow et al. – MedRxiv

Modeling transfer of vaginal microbiota from mother to infant in early life – Mortensen et al. – eLife

Human gut microbiome

Review: Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations – Lamichhane et al. – Metabolites

Animal microbiome

Individual fate and gut microbiome composition in the European wild rabbit (Oryctolagus cuniculus) – Funosas et al. – Scientific reports

Plant, root, and soil microbiome

Microbiome structure and functional potential in permafrost soils of the Western Canadian Arctic – Varsadiya et al. – FEMS Microbial ecology

Book chapter: Microbial Diversity of Phyllosphere – Dhankhar et al. – Phytomicrobiome Interactions and Sustainable Agriculture

Review: Novel and Emerging Capabilities that Can Provide a Holistic Understanding of the Plant Root Microbiome – Singer et al. – Phytomes journal

Water and extremophile microbiome

Book chapter: Potential of Extremophiles for Bioremediation – Kaushik et al. – Microbial Rejuvenation of Polluted Environment. Microorganisms for Sustainability, vol 25. Springer, Singapore.

Built environment

Microbial Diversity Analysis of Sediment from Yeosu New Harbor of South Korea Using 16S rRNA Gene Amplicon Sequencing – Lee et al. – Microbiology ressource announcements

Preprint: Characterisation of the bacterial microbiota of a landfill-contaminated confined aquifer undergoing intrinsic remediation – Abiriga et al. – BioRxiv

Phages and viruses

Reduced metagenomic sequencing (RMS) approach to determine the gut-associated phageome in mother-child – Manohar et al. – Human Microbiome Journal

Review: Enteric Viruses and Inflammatory Bowel Disease – Tarris et al. – Viruses

Bioinformatics

book chapter: Advances in Omics and Bioinformatics Tools for Phyllosphere Studies – Bansal – Phytomicrobiome Interactions and Sustainable Agriculture

MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning – Dhungel et al. – BMC Bioinformatics

My non-microbiology picks

Preprint: Emerging Concern of Scientific Fraud: Deep Learning and Image Manipulation – Qi et al. – BioRxiv

January 22, 2021

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Good morning from New Jersey! A wide range of microbiome research to share with you today. Highlights include fecal microbiota transplantation in horses with colitis and a review on the foggy relationship between microbes and plastics. There are also a couple papers on metabolic modeling and an examination of how much black soldier flies like human food waste (hint: a lot).

Jobs

New postdoctoral positions were just announced at the University of Minnesota for “research at the interface of microbiome + human genomics” in the lab of Dr. Ran Blekhman (disclosure: my Ph.D. advisor).

Human skin microbiome

Potential role of the skin and gut microbiota in premenarchal vulvar lichen sclerosus: A pilot case-control study, Chattopadhyay and Arnold et al., PLOS ONE

Human gut microbiome

Degradation of complex arabinoxylans by human colonic Bacteroidetes, Gabriel V. Pereira et al., Nature Communications

Review – The complexities of the diet-microbiome relationship: advances and perspectives, Emily R. Leeming et al., Genome Medicine

Review – Understanding the host-microbe interactions using metabolic modeling, Jansma and El Aidy, Microbiome

Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime, Li and Nelson, Microbial Ecology

Animal experiments

Preprint – The Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster, Nana Ankrah et al, bioRxiv

Animal microbiome

Assessment of clinical and microbiota responses to fecal microbial transplantation in adult horses with diarrhea, Caroline A. McKinney et al., PLOS ONE

Climate change alters the haemolymph microbiome of oysters, Elliot Scanes et al., Marine Pollution Bulletin

Functional screening of a Caatinga goat (Capra hircus) rumen metagenomic library reveals a novel GH3 β-xylosidase, Betulia de Morais Souto et al., PLOS ONE

Built environment

Impact of Processed Food (Canteen and Oil Wastes) on the Development of Black Soldier Fly (Hermetia illucens) Larvae and Their Gut Microbiome Functions, Thomas Klammsteiner et al., Frontiers in Microbiology

Review – Plastics and the microbiome: impacts and solutions, G. Lear et al., Environmental Microbiome

Bioinformatics

Real-time resolution of short-read assembly graph using ONT long reads, Son Hoang Nguyen et al., PLOS Computational Biology

Covariance matrix filtering with bootstrapped hierarchies, Bongiorno and Challet, PLOS ONE

January 21, 2021

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Today’s post include review article on gut-liver axis, research articles on diet-microbiota interaction in Chinese adults, association between microbiome and type1 diabetes, and new metagenomic profiling method using phylogenetic markers.

General microbiome

Bacterial and eukaryotic extracellular vesicles and non-alcoholic fatty liver disease: new players in the gut-liver axis? – Alexandre Villard – American Joural of Physiology Gastrointestinal and Liver Physiology

Potential Contribution of the Intestinal Microbiome to Phenethylamine-Induced Hyperthermia – Aburahma A. – Brain, Behavior and Evolution

Human microbiome

Long-term diet quality is associated with gut microbiome diversity and composition among urban Chinese adults – Danxia Yu – American Journal of Clinical Nutrition

Long-term dietary intake from infancy to late adolescence is associated with gut microbiota composition in young adulthood – Kolade Oluwagbemigun – American Journal of Clinical Nutrition

The gut microbiota metabolite propionate ameliorates intestinal epithelial barrier dysfunction-mediated Parkinson’s disease via the AKT signaling pathway – Tingting Huang – Neuroreport

Fecal and mucosal microbiota profiling in pediatric inflammatory bowel diseases – Lorenza Putignani – European Journal of Gastroenterology and Hepatology

Associations between diet, the gut microbiome and short chain fatty acids in youth with islet autoimmunity and type 1 diabetes – Jessica E. Harbison – Pediatric Diabetes

Reproducing the scalp microbiota community: co‐colonization of a 3D reconstructed human epidermis with C. acnes and M. restricta – Marisa Melon – International Journal of Cosmetic Science

Hepatic steatosis relates to gastrointestinal microbiota changes in obese girls with polycystic ovary syndrome – Beza Jobira – PlosOne

Animal microbiome

Infection trains the host for microbiota-enhanced resistance to pathogens – Apollo Stacy – Cell

Changes of Gut Microbiota and Its Correlation With Short Chain Fatty Acids and Bioamine in Piglets at the Early Growth Stage – Renli Qi – Frontiers in Veterinary Science

Functional Foods

Prospecting Human Milk Oligosaccharides as a Defense Against Viral Infections – Rebecca E Moore- ACS Infectious Diseases

Techniques

TIPP2: metagenomic taxonomic profiling using phylogenetic markers – Nidhi Shah – Bioinformatics

Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water – Meghan Maguire – PlosOne

Microbes in news

Your Microbiome Isn’t Shaped Just By What You Feed It – Discover

Taurine Enhances the Microbiome’s Resistance to Future Pathogens – Genetic Engineering and Biotech News

January 20, 2021

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Good morning readers! Today we have two very interesting studies published in Nature Genetics. One focuses on host factors influencing human gut microbiome composition, the other shows the influence of ABO histo-blood groups on gut microbiome.

Human gut microbiome

Large-scale association analyses identify host factors influencing human gut microbiome composition – Kurilshikov et al. – Nature Genetics

Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome – Rühlemann et al. – Nature Genetics

Fecal microbiome and metabolome differ in healthy and food-allergic twins – Bao et al. – JCI

Hepatic steatosis relates to gastrointestinal microbiota changes in obese girls with polycystic ovary syndrome – Jobira et al. – PLOS One

Animal microbiome

Microbiota modulates gut immunity and promotes baculovirus infection in Helicoverpa armigera – Yuan et al. – Insect Science

Immunological design of commensal communities to treat intestinal infection and inflammation – Brown et al. – PLOS Pathogens

Ticks Resist Skin Commensals with Immune Factor of Bacterial Origin – Hayes et al. – Cell

Techniques

The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology – Jeong et al. – Scientific Reports

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