January 14, 2021

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 13, 2021

Good morning! Today we have a rather short reading list. One study links gut microbiome and COVID19. A second study shows the impact of the gut microbiome on the peripheral immune response. Additionally, two preprints were selected.

Human gut microbiome

Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19 – Yeoh et al. – Gut

Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma – Behary et al. – Nature Communications

Animal microbiome (for animals in the wild)

[PREPRINT]Alterations in gut microbiota linked to provenance, sex, and chronic wasting disease in white-tailed deer (Odocoileus virginianus) – Minich et al. – bioRxiv

Bioinformatics

[PREPRINT]AncestralClust: Clustering of Divergent Nucleotide Sequences by Ancestral Sequence Reconstruction using Phylogenetic Trees – Pipes & Nielsen – bioRxiv

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

Gut Microbiome and COVID-19 Severity: New Evidence for Link – Molly Walker – MedpageToday

January 12, 2021

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 08, 2021

Human gut microbiome

Altered diversity and composition of gut microbiota in Wilson’s disease – Cai et al. – Scientific Reports

Emotional well-being and gut microbiome profiles by enterotype – Lee et al. – Scientific Reports

The Composition and Concordance of Lactobacillus Populations of Infant Gut and the Corresponding Breast-Milk and Maternal Gut – Zhang et al. – Front. Mircobiol.

Lifestyle modifications result in alterations in the gut microbiota in obese children – Cho – BMC Microbiology

Animal microbiome

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

Modeling dysbiosis of human NASH in mice: Loss of gut microbiome diversity and overgrowth of Erysipelotrichales – Carter et al. – PLOS One

Geography as non-genetic modulation factor of chicken cecal microbiota – Viso et al. – PLOS One

Intestinal microbial communities of rainbow trout (Oncorhynchus mykiss) may be improved by feeding a Hermetia illucens meal/low-fishmeal diet – Rimoldi et al. – Fish Physiology and Biochemistry

Dramatic shifts in intestinal fungal community between wintering Hooded Crane and Domestic Goose – Xiang et al. – Avian Research (BMC)

Bacterial diversity in intestinal mucosa of mice fed with Dendrobium officinale and high-fat diet – Li et al. – 3 Biotech

Shift of Maternal Gut Microbiota of Tibetan Antelope (Pantholops hodgsonii) During the Periparturition Period – Shi et al. – Current Microbiology

Plant, root, and soil microbiome

Bacterial seed endophyte shapes disease resistance in rice – Matsumoto et al. – Nature Plants

Environment

Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya – Muturi et al. – PLOS One

Wastewater treatment alters microbial colonization of microplastics – Kelly et al. – PLOS One

Bioinformatics

MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome – Patumcharoenpol et al. – PLOS Computational Biology

Techniques

Assessment of two DNA extraction kits for profiling poultry respiratory microbiota from multiple sample types – Abundo et al. – PLOS One

Januar 04, 2021

Good morning and happy new year! The first post in 2021 is rather short and covers gut microbiota and cancer, FMT, gut microbiota in calves and microbiome/archeaome of two wild animal species.

Human gut microbiome

Dysbiosis of gut microbiota in patients with esophageal cancer – Deng et al. – Microbial Pathogenesis

[REVIEW]Immunotherapy in Solid Tumors and Gut Microbiota: The Correlation—A Special Reference to Colorectal Cancer – Koulouridi et al. – Cancers

Fecal Microbiota Transplantation Is Highly Effective in Real-World Practice: Initial Results From the FMT National Registry – Kelly et al. – Gastroenterology

Fecal microbiota transplantation for graft-versus-host disease in children and adults: methods, clinical effects, safety – Goloshchapov et al. – Therapeutic archive (Article in Russian)

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

Analysis of the developing gut microbiota in young dairy calves—impact of colostrum microbiota and gut disturbances – Hang, Wredle & Dicksved – Tropical Animal Health and Production

Animal microbiome (for animals in the wild)

Consistent patterns in 16S and 18S microbial diversity from the shells of the common and widespread red-eared slider turtle (Trachemys scripta) – Parks, Kedy & Skalla – PLOS One

Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte – Polonia et al. – Antonie van Leeuwenhoek Journal of Microbiology

December 31, 2020

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 27, 2020

Joyeuses fêtes from Paris, France ! In today’s digest, you will find great papers looking at various animal and plant microbiomes. In particular, I recommend taking some time to look at a preprint from Brealey and collaborators exploring the impact of human antibiotic use on oral microbiome in wild animals. The authors used shotgun metagenomics to determine the abundance and diversity of antimicrobial resistance genes in the oral microbiome of brown bears from Swedish museum specimens. Importantly, they show a significant increase in antimicrobial resistance genes in correlation with modern human antibiotics use, showing an impact even on wildlife of our antibiotic consumption.

Today’s non-microbiology pick takes a look back at the history of bioinformatics through the data analysis and visualization of papers published between 1998 and 2019. In addition of reading this very interesting paper, you can take a look at the data collected through interactive visualizations available at http://bioinfo.dcc.ufmg.br/history !

Have a great Sunday!


Pregnancy and early life

Preprint: Metabolomic signature of the maternal microbiota in the fetus – Pessa-Morikawa et al. – BioRXiv

Human nearly-sterile sites

Preprint: The urinary microbiome in postmenopausal women with recurrent urinary tract infections – Hiersoux Vaughan et al. – BioRXiv

Preprint: Biofilm development on urinary catheters promotes the appearance of viable but non-culturable (VBNC) bacteria – Wilks et al. – BioRXiv


Animal microbiome

Preprint: Wild animal oral microbiomes reflect the history of human antibiotics use – Brealey et al. – BioRXiV

Plant, root, and soil microbiome

Dissimilarity analysis of microbial communities in the rhizosphere and tissues of diseased and healthy cherry trees (Cerasus pseudocerasus) – Ding et al. – Canadian Journal of Plant Pathology

First Recorded Account of Arbuscular Mycorrhizal Fungi in Sand Dunes in South Eastern Australia: Biogeography and Species Richness – Hanlon et al. – Journal of Coastal Research

Diversity and structural differences of bacterial microbial communities in rhizocompartments of desert leguminous plants – Zhou et al. – PLOS ONE

Preprint: Orchard management and landscape context mediate the floral microbiome of pear – Schaeffer et al. – BioRXiv

Water and extremophile microbiome

Interplay of microbial communities with mineral environments incoralline algae – Valdespino-Castillo et al. – Science of the total environment

Acid Mine Drainage as Energizing Microbial Niches for the Formation of Iron Stromatolites: The Tintillo River in Southwest Spain – Chacon-Baca et al. – Astrobiology


Bioinformatics

PStrain: An Iterative Microbial Strains Profiling Algorithm for Shotgun Metagenomic Sequencing Data – Wang et al. – Bioinformatics

MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data – Leung et al. – BMC Genomics


My non-microbiology picks

A Brief History of Bioinformatics Told by Data Visualization – Mariano et al. – Brazilian Symposium on Bioinformatics

 

December 23, 2020

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 17, 2020

Bonjour from Paris, France ! In today’s digest, readers interested in viromes will find a nice selection of papers looking at the viral populations associated to deep lake waters, birds, star fish and human gut! I also recommend anyone interested in this topic to take a look at a preprint from Amgarten and collaborators presenting a new computational tool called “vHULK”, allowing an in-silico bacteriophage host prediction!

Readers may also be interested in taking a look at the announcement of a new web interface allowing the exploration of the Human Microbiome Project (HMP). The ressource, called HMPDACC, provides a unified data repository for the two phases of the HMP, allows to search samples on a multitude of metadata, and provides analysis pipelines and standardized protocols to facilitate community use of HMP dataset.

Finally, today’s non-microbiology digest is a paper taking a look at the avalanche of papers and preprints published this year around the COVID-19 pandemic. Impressively, 84,180 indexed publications were relevant to COVID-19 written by 322,279 unique authors from all scientific subfields (except for Automobile Design & Engineering scientists!)

Have a great Saturday!


General microbiome

Preprint: Trait Evolution in Microbial Communities – Zhao et al. – BioRXiv

Human gut microbiome

The Pre‐treatment Gut Microbiome is Associated with Lack of Response to Methotrexate in New Onset Rheumatoid Arthritis – Artacho et al. – Arthitis and Rheumatology

Chapter: Oral Microbes: A Hidden Yet Powerful Evidence for Futuristic Forensic Investigation – Patel and Ganguly Soni – In: Shrivastava P., et al. (eds) Forensic DNA Typing: Principles, Applications and Advancements. Springer.

Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer Biobank – Wirth et al. – Cancers


Animal microbiome

Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea – Oliveira et al. – mircoorganisms


Phages and viruses

Comparative Metagenomics of Palearctic and Neotropical Avian Cloacal Viromes Reveal Geographic Bias in Virus Discovery – Truchado et al. – microorganisms

Virome Analysis of Near-Bottom Coastal Water of Lake Baikal – Butina et al. – Microbiology ressource announcements

Virome Variation during Sea Star Wasting Disease Progression in Pisaster ochraceus (Asteroidea, Echinodermata) – Hewson et al. – Viruses

Gut eukaryotic virome in colorectal carcinogenesis: Is that a trigger? – Massimino et al. – Computational and structural biotechnology journal

Bioinformatics

Preprint: vHULK, a new tool for bacteriophage host prediction based on annotated genomic features and deep neural networks – Amgarten et al. – BioRXiv

HMPDACC: a Human Microbiome Project Multi-omic data resource – Huot Creasy et al. Nucleic Acids Research

Review: Literature on Applied Machine Learning in Metagenomic Classification: A Scoping Review – Tonkovic et al. – biology


My non-microbiology picks

Preprint: The rapid, massive infection of the scientific literature and authors by COVID-19 – Ioannidis et al. – BioRXiv

December 16, 2020

COVID19

Inferring the effectiveness of government interventions against COVID-19 – Brauner et al. – Science

COVID 19 mortality: Probable role of microbiome to explain disparity – Kumar & Chander – Medical Hyptheses

General microbiome

[PREPRINT] Theory of (antimicrobial) relativity: When competitors determine a species’ drug sensitivity. – Reding – bioRxiv

Human respiratory microbiome

Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients – Mostafa et al. – mBio

Human oral microbiome

Variation in oral microbiome is associated with future risk of lung cancer among never-smokers – Hosgood et al. – Lung cancer

Human gut microbiome

Effect of an 8-week Exercise Training on Gut Microbiota in Physically Inactive Older Women – Zhong et al. – Int J Sports Med

Vitamin D metabolites and the gut microbiome in older men – Thomas et al. – Nature Communications

Animal microbiome

[PREPRINT] Longitudinal profiling of the macaque vaginal microbiome reveals similarities to diverse human vaginal communities: implications for use as a pre-clinical model for bacterial vaginosis – Rhoades et al. – bioRxiv

The earthworm microbiome is resilient to exposure to biocidal metal nanoparticles – Swart et al. – Environmental Pollution

Plant, root, and soil microbiome

Environmental microbiome mapping as a strategy to improve quality and safety in the food industry – Filippis et al. – Current Opinion in Food Science

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

Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum “Campylobacterota” – Shiotani et al. – PLOS One

Techniques

A rapid approach to profiling diverse fungal communities using the MinION™ nanopore sequencer – Mafune et al. – BioTechniques

[PREPRINT] Microbe-seq: high-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome – Zheng et al. – bioRxiv

Microbes in the news

Oral Microbiome Diversity and Species Abundance Linked to Lung Cancer in Nonsmokers