April 25th, 2021

Today’s digest shows some great papers, with two highlights. The first being the value of a ketogenic diet on treating drug-resistant epilepsy in children, suggesting gut microbial dysbiosis is responsible for the drug resistance. the second is a thorough analysis of both the developing microbiota in goats using metagenomics and metatranscriptomics by Pan et al. Enjoy!

Gut microbiome

(Preprint) Gut microbiota diversity and C-Reactive Protein are predictors of disease severity in COVID-19 patients – Moreira-Rosário et al. Bioxriv.

HPV infection and bacterial microbiota in the semen from healthy men. – Tuomimen et al. BMC Infectious Diseases.

(Review) Gastrointestinal dysfunction in Parkinson’s disease: molecular pathology and implications of gut microbiome, probiotics, and fecal microbiota transplantation – Metta et al. Journal of Neurology.

Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets – Gong et al. Microbial pathogenesis.

Vaginal microbiome

Oral administration of Lactobacillus crispatus M247 to papillomavirus-infected women: results of a preliminary, uncontrolled, open trial – Di Pierro et al. Minerva Obstrestics and Gynecology.

Animal experiments

(Preview) Bugs R Us: Restoring sociability with microbiota in autism. – Bellone and Lüscher. Cell reports medicine.

Anti-aging effects of a functional food via the action of gut microbiota and metabolites in aging mice – Zhang et al. Aging.

Animal microbiome

Dynamics of rumen gene expression,microbiome colonization, and their interplay in goats – Pan et al. BMC Genomics.

Evolution of rumen and oral microbiota incalves is influenced by age and time of weaning – Amin et al. Animal Microbiome

Plant, root and soil microbiome

(Review) Impacts of wildfire on soil microbiome in Boreal environments – Köster et al. Current opinion in Environmental Science & Health.

April 24th, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a wide range of topics to explore! I particularly recommend taking the time to read at the fascinating review listed below exploring horizontal gene transfer in environmental microbial communities. They describe how advances in the computational analysis of metagenomic data has allowed us to dive deeper in understanding these processes in microbiomes.

Among the list of very interesting research papers in this digest, you’ll find a fascinating study exploring the symbiotic microbial communities associated with deeper corals. Although extensive litterature has been published on coral microbiomes from shallow waters, this papers is the first to examine microbial communities associated with the deep photosymbiotic corals, living at more than 150 m of depth!

Today’s non-microbiology pick is a really interesting paper from Faldelmola and collaborators reporting on the development by the Pan-African H3Africa Bioinformatics Network of two data portals for African genomic medicine and African microbiomes datasets. The paper explore how they lead a very successful 6-days hackathon allowing to efficiently develop these two important scientific ressources, but also how they build a collaborative community of African researchers and experts.

Have a great Weekend!


General microbiome

Review: Examining horizontal gene transfer in microbial communities – Brito – Nature reviews microbiology

Preprint: Evidence for a billion-years arms race between viruses, virophages and eukaryotes – Barreat and Katzourakis – BioRxiV

Unifying community detection across scales from genomes to landscapes – Hudon et al. – Oikos

Human gut microbiome

Preprint: Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut – Watson et al. – BioRxiV


Animal experiments

Diversity and characteristics of raw milk microbiota from Korean dairy farms using metagenomic and culturomic analysis – Ryu et al. – Food control

Animal microbiome

Preprint: Reclassification of seven honey bee symbiont strains as Bombella apis – Smith et al. – BioRxiV

Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth) – Rouzé et al. – ISME Journal

Metagenomic shotgun sequencing reveals host species as an important driver of virome composition in mosquitoes – Thongsripong et al. – Scientific reports

Water and extremophile microbiome

Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents – McAllister et al. – ISME Journal

Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones – Sun et al. – ISME Journal

Morphological complexity affects the diversity of marine microbiomes – Lemay et al. – ISME Journal

Preprint: Abundance and Microbial Diversity from Surface to Deep Water Layers Over the Rio Grande Rise, South Atlantic – Ferreira et al. – BioRxiV


Bioinformatics

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC – Parrello et al. – Plos One

A roadmap for metagenomic enzyme discovery – Robinson et al. – Natural Product Reports

Techniques

Preprint: Synergistic effect of short- and long-read sequencing on functional meta-omics – Galata et al. – BioRxiV


My non-microbiology picks

H3ABioNet genomic medicine and microbiome data portals hackathon proceedings – Fadlelmola et al. – Database

April 23, 2021

Good morning from New Jersey! Lots of papers to share today, particularly regarding animal microbiota and new bioinformatics tools.

General microbiome

Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer, Alice Tzeng et al., Genome Medicine

Pregnancy and early life

The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition, Xuanji Li et al., Cell Host & Microbe

Multi-site human microbiome

Review: Microbiome-immune interactions in tuberculosis, Giorgia Mori et al., PLOS Pathogens

Human gut microbiome

Dynamic Changes in Microbiome Composition Following Mare’s Milk Intake for Prevention of Collateral Antibiotic Effect, Almagul Kushugulova et al., Frontiers in Cellular and Infection Microbiology

Review: The aging gut microbiome and its impact on host immunity, Bosco and Noti, Genes & Immunity

Animal experiments

Ingestion of Bifidobacterium longum changes miRNA levels in the brains of mice, DeVries and Horstman et al., PLOS ONE

Heat-inactivated Lactobacillus plantarum nF1 promotes intestinal health in Loperamide-induced constipation rats, Seon-Ah Park et al., PLOS ONE

The pregnane X receptor drives sexually dimorphic hepatic changes in lipid and xenobiotic metabolism in response to gut microbiota in mice, Sharon Ann Barretto et al., Microbiome

One dog’s waste is another dog’s wealth: A pilot study of fecal microbiota transplantation in dogs with acute hemorrhagic diarrhea syndrome, Arnon Gal et al., PLOS ONE

Animal microbiome

Diversity and functional landscapes in the microbiota of animals in the wild, Levin, Raab, Pinto, and Rothschild et al., Science

Microbiome reduction and endosymbiont gain from a switch in sea urchin life history, Tyler J. Carrier et al., PNAS

Diet and gut microbiome enterotype are associated at the population level in African buffalo, Claire E. Couch et al., Nature Communications

Coral microbiome changes over the day–night cycle, Alicia M. Caughman et al., Coral Reefs

An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota, Mao and Chuang et al., PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Preprint: Genome-centric analyses of seasonal phyllosphere microbiome activities in perennial crops, Adina Howe et al., bioRxiv

Influence of Plant Host and Organ, Management Strategy, and Spore Traits on Microbiome Composition, Kristi Gdanetz et al., Phytobiomes Journal

Built environment

Categorisation of culturable bioaerosols in a fruit juice manufacturing facility, Shirleen M. Theisinger et al., PLOS ONE

Bioinformatics

Preprint: Deconstructing taxa x taxa x environment interactions in the microbiota: A theoretical examination, Senay Yitbarek et al., bioRxiv

Preprint: Extended taxonomic profiling of diverse environments with mOTUs 2.6, Hans-Joachim Ruscheweyh et al., bioRxiv

Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome, Donovan H. Parks et al., Frontiers in Microbiology

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC, Bruce Parrello et al., PLOS ONE

April 21, 2021

General microbiome

Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection – Mu et al. – Microbiome

Pregnancy and early life

A Microbiota-Directed Food Intervention for Undernourished Children – Chen et al. – The New England Journal of Medicine

Bacterial-fungal interactions in the neonatal gut influence asthma outcomes later in life – Boutin et al. – eLife

Human vaginal microbiome

[REVIEW]The effect of different contraceptive methods on the vaginal microbiome – Bastianelli et al. – Expert Review of Clinical Pharmacology

Human gut microbiome and virome

The Gut Microbiome in Progressive Multiple Sclerosis – Cox et al. – Annals of Neurology

Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity – Zuo et al. – Microbiome

[REVIEW]The Gut Microbiome: a New Frontier in Musculoskeletal Research – Li et al. – Current Osteoporosis Reports

[REVIEW]Inflammation‐driven brain and gut barrier dysfunction in stress and mood disorders – Doney et al. – European Journal of Neuroscience

The gut microbiota is associated with clinical response to statin treatment in patients with coronary artery disease – Wang et al. – Atherosclerosis

[REVIEW]Dietary restrictions modulate the gut microbiota: Implications for health and disease – Schmidt and Lorentz – Nutrition Research

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

Altering the microbiome inhibits tumorigenesis in a mouse model of oviductal high-grade serous carcinoma – Chen et al. – Cancer Research

Screening of probiotic candidates in a simulated piglet small intestine in vitro model – Hansen et al. – FEMS Microbiology Letters

Animal microbiome (for animals in the wild)

Microbiome reduction and endosymbiont gain from a switch in sea urchin life history – Carrier et al. – PNAS

[PREPRINT]Evidence that faecal carriage of resistant Escherichia coli by 16-week-old dogs in the United Kingdom is associated with raw feeding and that E. coli from these dogs are shared with humans and cause opportunistic infections – Mounsey et al. – bioRxiv

Diversity structure of the microbial communities in the guts of four neotropical termite species – Vikram et al. – PeerJ

Alteration of gut microbiota with a broad‐spectrum antibiotic does not impair maternal care in the European earwig – van Meyel et al. – Journal of Evolutionary Biology

Food microbiology

The effects of vegetable pickling conditions on the dynamics of microbiota and metabolites – Sawada et al. – PeerJ

Techniques

[PREPRINT]Development of Microbiome Biomarkers for IgA: a Joint Modeling Approach – Sengupta et al. – bioRxiv

April 16, 2021

In today’s digest read about the presence/absence of ACBP orthologues in human gut metagenomes and how the gut microbiome links nutrition with cardiometabolic health, LEGO-based microscope, SIAMCAT for statistical inference of associations between microbial communities and host phenotypes, bacteriophage plaques size tool, and more. Check out a list of awesome webinars and courses. Happy Friday!

OPEN #NSURP2021 CALL for mentors and mentees: The National Summer Undergraduate Research Project – A community-driven initiative to create rewarding remote summer research opportunities for BIPOC and Latinx undergraduate students in the microbial sciences.

Microbiome in the news

*Microbiome research in general and business newspapers: How many microbiome articles are published and which study designs make the news the most? – Andreu Prados-Bo and Gonzalo Casino – PlosOne

General

Prokaryotic taxonomy and nomenclature in the age of big sequence data – Philip Hugenholtz – The ISME Journal

The metabolic network of the last bacterial common ancestor – Joana C. Xavier – Communications Biology

Techniques

*Designing a high-resolution, LEGO-based microscope for an educational setting – Bart Eduard Vos – bioRxiv

Genome-Based Targeted Sequencing as a Reproducible Microbial Community Profiling Assay – Jacquelynn Benjamino – mSphere

Gut microbiome

*Microbial ACBP/DBI-like genes are rare in the human gut microbiome and show no links with obesity – Andrew Maltez Thomas – Applied and Environmental Microbiology

The long-term genetic stability and individual specificity of the human gut microbiome – Lianmin Chen – Cell

Review: Emulating the gut–liver axis: Dissecting the microbiome’s effect on drug metabolism using multiorgan-on-chip models – Mara Lucchetti – Current Opinion in Endocrine and Metabolic Research

Urinary microbiome

The human urobiome – Linda Brubaker – Mammalian Genome

Urinary microbiota of women with recurrent urinary tract infection: collection and culture methods – Baylie R. Hochstedler – International Urogynecology Journal

Vaginal microbiome

Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil – Marcelle Oliveira de Almeida – PeerJ

Comparative Genome Analyses of Lactobacillus crispatus Isolates from Different Ecological Niches Reveal an Adaptation of This Species to the Human Vaginal Environment – Leonardo Mancabelli – Applied and Environmental Microbiology

Probiotics

Review: Lacticaseibacillus rhamnosus GR-1, a.k.a. Lactobacillus rhamnosus GR-1: Past and Future Perspectives – Mariya I.Petrova – Trends in Microbiology

Probiotic Lactobacillus sp. Strains Inhibit Growth, Adhesion, Biofilm Formation, and Gene Expression of Bacterial Vaginosis-Inducing Gardnerella vaginalis – Zhixiang Qian – Microorganisms

Oral microbiome

Dental biofilm microbiota dysbiosis is associated with the risk of acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation – Vitor Heidrich – medRxiv

Soil microbiome

Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps) – Carla Perez-Mon – Microbial Genomics

Phages and viruses

*Plaque Size Tool: an automated plaque analysis tool for simplifying and standardising bacteriophage plaque morphology measurements – Ellina Trofimova and Paul R Jaschke – bioRxiv

The gut virome of healthy children during the first year of life is diverse and dynamic – Blanca Taboada – PlosOne

Bioinformatics

Taxonomic analysis of metagenomic data with kASA – Silvio Weging – Nucleic Acids Research

*Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox – Jakob Wirbel – Genome Biology

Review: Integrating pan-genome with metagenome for microbial community profiling – Chaofang Zhong – Computational and Structural Biotechnology Journal

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing – Caitlin M. Singleton – Nature Communications

Evaluation of the effects of library preparation procedure and sample characteristics on the accuracy of metagenomic profiles – Christopher Gaulke – bioRxiv

Democratising deep learning for microscopy with ZeroCostDL4Mic – Lucas von Chamier – Nature Communications

Webinars

Offered talks on Plasmids and Mobile Elements for 2021 – Plasmids around the globe – International Society for Plasmid Biology and Other Mobile Genetic Elements

Spring 2021 Microbiome Informatics webinars – OSU Center of Microbiome Science

EMBARK Spring Webinars – AMR focused webinars – EMBARK project

BISMiS Live – Microbial taxonomy: where are we now and where are we going? Iain Sutcliffe – Bergey’s Intl. Society for Microbial Systematics; registration here

Berkeley Lab Live Science – Exploring Earth – Berkeley Lab – April 23

Conferences

ISAPP 2021 Virtual Annual Meeting – International Scientific Association for Probiotics and Prebiotics – June 1–2

Courses

Open Online R Stream – Wolfgang Viechtbauer

RaukR: Advanced R for Bioinformatics Summer School – NBIS/SciLifeLab – June 14-24

April 14, 2021

General microbiome

[REVIEW]The microbiome and human cancer – Sepich-Poore et al. – Science

[PERSPECTIVE]A framework for microbiome science in public health – Wilkinson et al. – Nature Medicine

A framework for microbiome science in public health –

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae – Shaw et al. – Science Advances

Human gut microbiome

[REVIEW]Immune System, Microbiota, and Microbial Metabolites: The Unresolved Triad in Colorectal Cancer Microenvironment – Hanus et al. – Front. Immunol.

[REVIEW]Microbiome and colorectal cancer: A review of the past, present, and future – Johns & Petrelli – Surgical Oncology

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

Microbiota-derived short chain fatty acids modulate microglia and promote Aβ plaque deposition – Colombo et al. – eLife

Intestinal microbiota drives cholestasis-induced specific hepatic gene expression patterns – Juanola et al.

Animal microbiome (for animals in the wild)

When your host shuts down: larval diapause impacts host-microbiome interactions in Nasonia vitripennis – Dittmer & Brucker – Microbiome

Plant, root, and soil microbiome

Gut microbiota-derived inosine from dietary barley leaf supplementation attenuates colitis through PPARγ signaling activation – Li et al. – Microbiome

Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils – Bao et al. – Microbiome

Rhizosphere community selection reveals bacteria associated with reduced root disease – Yin et al. – Microbiome

Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps) – Perez-Mon – Microbioal Genomics

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

[PREPRINT]The Polar Night Shift: Annual Dynamics and Drivers of Microbial Community Structure in the Arctic Ocean – Wietz et al. – bioRxiv

Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities – Fortunato et al. – Environmental Microbiology

Plasmids

[PREPRINT]Plasmid fitness costs are caused by specific genetic conflicts – Hall et al. – bioRxiv

Bioinformatics

[PREPRINT]Comprehensive benchmarking of tools to identify phages in metagenomic shotgun sequencing data – Ho, Millard & van Schaik – bioRxiv

April 10, 2021

Have a nice weekend! Today, in this (late) Digest: articles about gut microbiome and COVID19 and neurological disorders, as well as other studies with skin, respiratory and vaginal microbiomes. We have also: wine microbiome, rumen eukaryotome, hydrocarbon degraders, some bioinformatic pipelines and more!

Human and General Microbiome

Faecalibacterium prausnitzii increases following fecal microbiota transplantation in recurrent Clostridioides difficile infection – Olle Björkqvist – PLoS ONE

Comprehensive profiling of the gut microbiota in patients with chronic obstructive pulmonary disease of varying severity – Yu-Chi Chiu –  PLoS ONE

Nutrition and the microbiota post-COVID-19 – G. G. F. Alberca – The Saudi Journal of Gastroenterology

Book Chapter: From “Leaky Gut” to Impaired Glia-Neuron Communication in Depression – Leszek Rudzki – Major Depressive Disorder

Skin microbiome of patients with interdigital tinea pedis: Corynebacterium striatum is more abundant in the patients – Mayumi Miyamoto – The Journal of Dermatology 

Selected Clostridia Strains from The Human Microbiota and their Metabolite, Butyrate, Improve Experimental Autoimmune Encephalomyelitis – Laura Calvo-Barreiro – Neurotherapeutics

Gut Microbiota Composition and Epigenetic Molecular Changes Connected to the Pathogenesis of Alzheimer’s Disease – Priyanka Nagu – Journal of Molecular Neuroscience 

Global climate change, diet, and the complex relationship between human host and microbiome: Towards an integrated picture – Francesco Catania – BioEssays

Global research trends in the microbiome related to irritable bowel syndrome: A bibliometric and visualized study – Sa’ed H Zyoud – World Journal of Gastroenterology

Coronavirus disease-2019 and the intestinal tract: An overview – Gabriela Gama Freire Alberca – World Journal of Gastroenterology

Comparison of Argentinean microbiota with other geographical populations reveals different taxonomic and functional signatures associated with obesity – Susana A. Pesoa – Scientific Reports 

Six-month follow-up of gut microbiota richness in patients with COVID-19 – Yanfei Chen – Gut (BMJ)

The combined therapy of fecal microbiota transplantation and laxatives for functional constipation in adults: A systematic review and meta-analysis of randomized controlled trials – Fang, Sijia MM – Medicine

Vaginal metabolic profiles during pregnancy: Changes between first and second trimester – Luca Laghi – PLoS ONE

Microbiome profiling of uncinate tissue and nasal polyps in patients with chronic rhinosinusitis using swab and tissue biopsy – Sung-Woo Cho – PLoS ONE

Patient attitudes towards faecal sampling for gut microbiome studies and clinical care reveal positive engagement and room for improvement – Laura A. Bolte – PLoS ONE

Microbes in the Media

Microbiome research in general and business newspapers: How many microbiome articles are published and which study designs make the news the most? – Andreu Prados-Bo – PLoS ONE

Food Microbiome

Minireview: The ecology of wine fermentation: a model for the study of complex microbial ecosystems – CG Conacher – Applied Microbiology and Biotechnology

Animal Microbiome

The rumen eukaryotome is a source of novel antimicrobial peptides with therapeutic potential – Lucy A. Onime – BMC Microbiology

The skin microbiota in equine pastern dermatitis: a case-control study of horses in Switzerland – Sarah Kaiser‐Thom – Veterinary Dermatology

Association between aging-dependent gut microbiome dysbiosis and dry eye severity in C57BL/6 male mouse model: a pilot study – Chang Ho Yoon – BMC Microbiology

Environmental Microbiome

Black Yeast Genomes Assembled from Plastic Fabric Metagenomes Reveal an Abundance of Hydrocarbon Degradation Genes – Osman Radwan – Microbiology Resource Annoucements

Effects of supplemental feeding on the fecal bacterial communities of Rocky Mountain elk in the Greater Yellowstone Ecosystem – Claire E. Couch – PLoS ONE

Bioinformatics

A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota – Yafei Chang – Briefings in Bioinformatics

DisBalance: a platform to automatically build balance-based disease prediction models and discover microbial biomarkers from microbiome data – Fenglong Yang – Briefings in Bioinformatics

Review: Metagenomic Data Assembly – The Way of Decoding Unknown Microorganisms – Alla L. Lapidus – Frontiers in Microbiology

Built Environments

Analyzing indoor mycobiomes through a large-scale citizen science study in Norway – Sarah Kaiser‐Thom – Veterinary Dermatology

Forensic Microbiomes

Review: Microbiomes in forensic botany: a review – Sarah Ishak – Forensic Science, Medicine and Pathology 

Other papers

Untargeted Stable Isotope Probing of the Gut Microbiota Metabolome Using 13 C-Labeled Dietary Fibers – Pan Deng – Journal of Proteome Research

Metaproteomic sample preparation methods bias the recovery of host and microbial proteins according to taxa and cellular compartment – Patrick G.Gavin – Journal of Proteomics

April 07, 2021

General microbiome

Primate phageomes are structured by superhost phylogeny and environment – Gogarten et al. – PNAS

Fungal‐induced glycolysis in macrophages promotes colon cancer by enhancing innate lymphoid cell secretion of IL‐22 – Zhu et al. – The EMBO Journal

A method for detection of SARS-CoV-2 RNA in healthy human stool: a validation study – Coryell et al. – The Lancet Microbe

The Ocular Microbiome and Microbiota and their Effects on Ocular Surface Pathophysiology and Disorders – Aragona et al. – Survey of Ophthalmology

Human oral microbiome

Multi-dimensional study of the oral microbiome, metabolite, and immunologic environment in peanut allergy – Ho et al. – Journal of Allergy and Clinical Immunology

Human skin microbiome

Temporal Variation in Staphylococcus aureus Protein A Genotypes from Nose and Skin in Atopic Dermatitis Patients – van Mierlo et al. – Dermatology

Sex‐Based Differences in Fecal Short‐Chain Fatty Acid and Gut Microbiota in Irritable Bowel Syndrome Patients – Sun et al. – Journal of Digestive Diseases

Human gut microbiome

[REVIEW]Ecological and evolutionary responses to antibiotic treatment in the human gut microbiota – Pennycook & Scanlan – FEMS Microbiology Reviews

Animal microbiome (for animals in the wild)

The Fecal and Serum Metabolomics of Giant Pandas Based on Untargeted Metabolomics – Yang et al. – Zoological Scienc

Microbes in space

Astrobiology of life on Earth – Hallsworth et al. – Environmental Microbiology
Mars’ surface is not universally biocidal – Hallsworth – Environmental Microbiology

Bioinformatics

Draft Genome Sequences and Antimicrobial Profiles of Three Staphylococcus epidermidis Strains from Neonatal Blood Samples – Afeke et al. – Microbiology Resource Announcements

CoCoNet: An Efficient Deep Learning Tool for Viral Metagenome Binning – Arisdakessian et al. – Bioinformatics

Techniques

Rank normalization empowers a t-test for microbiome differential abundance analysis while controlling for false discoveries – Davis, Huang & Wang – Briefings in Bioinformatics

Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing – Tourancheau et al. – Nature Methods

April 6, 2021

Human gut microbiome

Thousands of previously unknown phages discovered in whole-community human gut metagenomes – Benler et al. – Microbiome

*Elevated rates of horizontal gene transfer in the industrialized human microbiome – Groussin et al. – Cell

Animal microbiome

Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes – Keenum et al. – Microbiome

Swine growth promotion with antibiotics or alternatives can increase antibiotic resistance gene mobility potential – Muurinen et al. – Scientific Reports

Methods

Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data – Stamboulian et al. – Microbiome

High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains – Zünd et al. – Microbiome

A comprehensive metagenomics framework to characterize organisms relevant for planetary protection – Danko et al. – Microbiome

April 3, 2021

Have a nice weekend! Today we want to highlight a new podcast about Microbiome and Health, available in Spotify. We also have today a set of studies, covering aspects of the urinary microbiome, drug-microbiome dynamics, and cancer microbiota.

Microbes in the Media

Biomes Podcast with Dr. Ruairi Robertson (Available in Spotify)

Human and General Microbiome

Microbiome and Metabolome Analyses Reveal Novel Interplay Between the Skin Microbiota and Plasma Metabolites in Psoriasis – Dongmei Chen – Frontiers in Microbiology

Microreview: Organ-on-chip to investigate host-pathogens interactions – Thomas Feaugas – Cellular Microbiology

Investigating colonization patterns of the infant gut microbiome during the introduction of solid food and weaning from breastmilk: A cohort study protocol – Sara Dizzell – PLoS One

Urinary Microbiota; Which Non-Invasive Urine Collection Method Should We Use? – Muhammed Selcuk Ozer – IJCP

A specific association between laxative misuse and suicidal behaviours in patients with anorexia nervosa and bulimia nervosa – Aiste Lengvenyte – Eating and Weight Disorders – Studies on Anorexia, Bulimia and Obesity

Bile Microbiota in Liver Transplantation: Proof of Concept Using Gene Amplification in a Heterogeneous Clinical Scenario – Francesco D’Amico – Frontiers in Surgery

The Unique Impact of COVID-19 on Human Gut Microbiome Research – Ella Burchill – Frontiers in Medicine

Modeling of Urinary Microbiota Associated With Cystitis – Marina Ceprnja – Frontiers in Cellular and Infection Microbiology

Identification of Microbiome Etiology Associated With Drug Resistance in Pleural Empyema – Zhaoyan Chen – Frontiers in Cellular and Infection Microbiology

Analysis of Gut Microbiome Using Explainable Machine Learning Predicts Risk of Diarrhea Associated With Tyrosine Kinase Inhibitor Neratinib: A Pilot Study – Chi Wah Wong – Frontiers in Oncology 

Antitumor efficacy of a neoantigen cancer vaccine delivered by electroporation is influenced by microbiota composition – Lucia Lione – OncoImmunology 

Associations between dysbiosis-inducing drugs, overall survival and tumor response in patients treated with immune checkpoint inhibitors – Louis Gaucher – Therapeutic Advances in Medical Oncology

The Hygiene Hypothesis – Learning From but Not Living in the Past – Petra I. Pfefferle – Frontiers in Immunology

Strength Exercise Confers Protection in Central Nervous System Autoimmunity by Altering the Gut Microbiota – Hao Chen – Frontiers in Immunology

Beneficial Microbes and Compounds

Enrichment of Food With Tannin Extracts Promotes Healthy Changes in the Human Gut Microbiota – Silvia Molino – Frontiers in Microbiology

Bifidobacterium Lactis Probio-M8 regulates gut microbiota to alleviate Alzheimer’s disease in the APP/PS1 mouse model – Jianing Cao – European Journal of Nutrition 

Animal Microbiome

Re-Analysis of 16S rRNA Gene Sequence Data Sets Uncovers Disparate Laboratory-Specific Microbiomes Associated with the Yellow Fever Mosquito (Aedes aegypti) – Jonas Frankel-Bricker – Microbial Ecology 

FOXO regulates the expression of antimicrobial peptides and promotes phagocytosis of hemocytes in shrimp antibacterial immunity – Cang Li – PLoS Pathogens

Environmental Microbiome

Microbial characteristics response to the soil quality of newly created farmland on the Loess Plateau – Chen Xu – Environmental Science and Pollution Research

Bioinformatics

Human microbiome privacy risks associated with summary statistics – Jae-Chang Cho – PLoS One

ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data – Achal Dhariwal – NAR Genomics and Bioinformatics