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

December 10, 2020

Good morning from New Jersey! Only a few new research articles to share with you today, but FOUR new reviews on the microbiome’s role in cancers and periodontal disease. And if you’re feeling adventurous, PLOS ONE just published an article on human postmortem decomposition that includes a brief evaluation of the buried corpse microbiome.

Jobs

A new postdoctoral position was just posted at the University of Minnesota for research on new methods of fecal microbiota transplantation.

General microbiome

Review – Unexpected guests in the tumor microenvironment: microbiome in cancer, Abigail Wong-Rolle et al., Protein Cell

Review – Understanding the microbial components of periodontal diseases and periodontal treatment-induced microbiological shifts, Ioannis Fragkioudakis et al., Journal of Medical Microbiology

Human gut microbiome

Identification of a Novel Cobamide Remodeling Enzyme in the Beneficial Human Gut Bacterium Akkermansia muciniphila, Kenny C. Mok et al., mBio

Interpretable Machine Learning Framework Reveals Robust Gut Microbiome Features Associated With Type 2 Diabetes, Wanglong Gou et al., Diabetes Care

Gut microbial ecosystem in Parkinson’s disease: New clinico‐biological insights from multi‐omics, Ai Huey Tan et al., Annals of Neurology

Review – Intervention on Gut Microbiota May Change the Strategy for Management of Colorectal Cancer, Sedigheh Taghinezhad‐S et al., Gastroenterology and Hepatology

Short-Chain Fatty Acid-Producing Gut Microbiota Is Decreased in Parkinson’s Disease but Not in Rapid-Eye-Movement Sleep Behavior Disorder, Hiroshi Nishiwaki et al., mSystems

Animal experiments

Respiratory tissue-associated commensal bacteria offer therapeutic potential against pneumococcal colonization, Soner Yildiz et al., eLife

Effects of Pinus massoniana pollen polysaccharides on intestinal microenvironment and colitis in mice, Niu and Shang et al., Food & Function

A Subset of Roux-en-Y Gastric Bypass Bacterial Consortium Colonizes the Gut of Nonsurgical Rats without Inducing Host-Microbe Metabolic Changes, Zhigang Liu et al., mSystems

Plant, root, and soil microbiome

Preprint – Rapid evolution of bacterial mutualism in the plant rhizosphere, Erqin Li et al., bioRxiv

Review – Coffee Microbiota and Its Potential Use in Sustainable Crop Management, Benoit Duong et al., Frontiers in Sustainable Food Systems

Bioinformatics

Review – Tissue-associated microbial detection in cancer using human sequencing data, Rebecca M. Rodriguez et al., BMC Bioinformatics

Techniques

Preprint – BIOME-Preserve: A Novel Storage and Transport Medium for Preserving Anaerobic Microbiota Samples for Culture Recovery, Embriette R. Hyde et al., bioRxiv

December 08, 2020

General microbiome

The Microbial Conveyor Belt: Connecting the Globe through Dispersion and Dormancy – Mestre & Höfer – Trends in Microbiology

Microbiomes for All – Muth & Caplan – Frontiers in Microbiology

Human oral microbiome

[REVIEW]The Oral Host–Microbial Interactome: An Ecological Chronometer of Health? – Freire, Nelson & Edlund – Trends in Microbiology

Human vaginal microbiome

Impact of vaginal microbiome communities on HIV antiretroviral-based pre-exposure prophylaxis (PrEP) drug metabolism – Cheu et al. – PLOS Pathogens

Human gut microbiome

The Effect of Probiotics Supplementation on Gut Microbiota After Helicobacter pylori Eradication: A Multicenter Randomized Controlled Trial – Tang et al. – Infectious Diseases and Therapy

Therapeutic potential of natural products against atherosclerosis: Targeting on gut microbiota – Zhao et al. – Pharmacological Research

Glycan utilization systems in the human gut microbiota: a gold mine for structural discoveries – Tamura & Brumer – Current Opinion in Structural Biology

Animal microbiome (for animals in the wild)

Distinct gut microbiotas between southern elephant seals and Weddell seals of Antarctica – Kim, Cho & Lee – Journal of Microbiology

Plant, root, and soil microbiome

Soil texture and properties rather than irrigation water type shape the diversity and composition of soil microbial communities – Obayomi et al. – Applied Soil Ecology

Microbes in space

[BOOK CHAPTER]Antarctic Bacteria as Astrobiological Models – Abbott & Pearce – Extremophiles as Astrobiological Models

Bioinformatics

MANTA, an integrative database and analysis platform that relates microbiome and phenotypic data – Chen et al. – PLOS One

[REVIEW]Measuring the microbiome: best practices for developing and benchmarking microbiomics methods – Bokulich et al. – Computational and Structural Biotechnology Journal

[REVIEW]Seeing the forest for the trees: retrieving plant secondary biochemical pathways from metabolome networks – Desmet et al. – Computational and Structural Biotechnology Journal

Evaluation of Single Sample Network Inference Methods for Metabolomics-Based Systems Medicine – Jahagirdar & Saccenti – Journal of Proteome Research

November 30, 2020

Hello from Luebeck! Today we selected among others maternal obesity and neurodevelopment, infant growth, breastfeeding and c-section, dental microbiome, gut microbiome and diseases/cancer, a couple of animal and plant microbiome studies. Of particular interest is a study diet and problem solving in a bird species (Parus major).

General microbiome

[REVIEW]The dynamic wound microbiome – Liu et al. – BMC Medicine

[REVIEW]Microbiome and Cervical Cancer – Castanheira et al. – Pathobiology

Pregnancy and early life

[REVIEW]The impact of maternal obesity on childhood neurodevelopment – Tong & Kalish – Journal of Perinatology

Perinatal environment shapes microbiota colonization and infant growth: impact on host response and intestinal function – Selma-Royo et al. – Microbiome

Breastfeeding restored the gut microbiota in caesarean section infants and lowered the infection risk in early life – Guo et al. BMC Pediatrics

Human oral microbiome

Dental plaque microbiota profiles of children with caries-free and caries-active dentition – Qudeimat et al. – Journal of Dentistry

[REVIEW]Microbiomics: Were we all wrong before? – Kumar – Periodontology 2000

[REVIEW]Metaproteome and metabolome of oral microbial communities – Bostanci et al. – Periodontology 2000

Human gut microbiome

Gutmicrobiota, immunity and pain – Santoni, Miccini & Batelli – Immunology Letters

The Healthy Microbiome (What is the definition of a healthy gut microbiome?) – Shanahan, Ghosh & O’Toole – Gastroenterology

Altered gut bacterial and metabolic signatures and their interaction in gestational diabetes mellitus – Wang et al. – Gut Microbes

Animal microbiome (for animals in the wild)

Diet induces parallel changes to the gut microbiota and problem solving performance in a wild bird – Davidson et al. Scientific Reports

Wild black bears harbor simple gut microbial communities with little difference between the jejunum and colon – Gillman, McKenney & Lafferty – Scientific Reports

Age Patterning in Wild Chimpanzee Gut Microbiota Diversity Reveals Differences from Humans in Early Life – Reese et al. – Current Biology

Plant, root, and soil microbiome

Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream – Piazzon et al. – Microbiome

A comparison of the functional diversity of microbial communities in maize rhizosphere soils in the North West Province of South Africa – Chinenyenwa Fortune Chukwuneme, Ayansina Segun Ayangbenro, Olubukola Oluranti Babalola – Rhizosphere

[REVIEW]Beyond the extremes: Rocks as ultimate refuge for fungi in drylands – Coleine et al. – Mycologia

Bioinformatics

[REVIEW]Emerging computational tools and models for studying gut microbiota composition and function – Park et al. – Current Opinion in Biotechnology

November 27, 2020

Hello from Luebeck!

Today’s digest covers the connection between human diseases and gut microbiome, the gut feeling, secrets about plant growth and vertical stratification in urban spaces. Happy reading and happy black Friday!

General microbiome

Human microbiome and allergy – Montecchiani & Fanos – Pediatric Allergy and Immunology

Early life and childhood

Early Gut Fungal and Bacterial Microbiota and Childhood Growth – Schei et al. – Frontiers in Pediatrics

Oral human microbiome

Characterization of Lactobacilli isolated from carious dentin after selective caries removal and cavity sealing – Damé-Teixeira et al. – Archives of Oral Biology

Human gut microbiome

A Pilot Study: Changes of Intestinal Microbiota of Patients With Non-small Cell Lung Cancer in Response to Osimertinib Therapy – Cong et al. – Frontiers in Microbiology

What connection is there between intestinal microbiota and heart disease? – Poli – European Heart Journal Supplements

The Student-Centered Classroom: The New Gut Feeling – Lyles & Oli – FEMS Microbiology Letters

Animal microbiome

Comparison of the fecal microbiota composition between the blue Sheep (Pseudois nayaur) fed with Lolium perenne and Sorghum sudanense – Wu, Yuan & Pan – Canadian Journal of Microbiology

Plant, root, and soil microbiome

[REVIEW]The plant microbiome: The dark and dirty secrets of plant growth – Tkacz & Poole – Pants People Plant

Water and extremophile microbiome

[PREPRINT]Rapid shift in microbial community structure in a neutral hydrothermal hot spring from Costa Rica – Rojas-Gätjens et al. – bioRxiv

Environment

Vertical Stratification in Urban Green Space Aerobiomes – Robinson et al. – Environmental Health Perspectives

Techniques

Power calculations for detecting differences in efficacy of fecal microbiota donors – Olesen – Contemporary Clinical Trials Communications

November 20, 2020

Today’s digest features a systematic assessment of best practices for the sequencing-based characterization of the human vaginal microbiome, studies on link between the plaque microbiome and peri-implantitis, cutimycin [a Cutibacterium acnes-produced antibiotic that affects niche competition among the human skin microbiota] and antibiotic resistance genes in shower drains, washing machines, and dishwashers. There is a new Micro Binfie Podcast episode about moving from the wet lab into the dry lab to become a bioinformatician. Also, check out a list of interesting (freely available) events. Happy reading/listening!

Oral microbiome

*Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics – Paolo Ghensi – npj Biofilms and Microbiomes

Skin microbiome

*A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles – Jan Claesen – Science Translational Medicine

Review: Staphylococcus epidermidis—Skin friend or foe? – Morgan M. Brown and Alexander R. Horswill – Plos Pathogen

Gut microbiome

Preterm Infants Harbour a Rapidly Changing Mycobiota That Includes Candida Pathobionts – Stephen A. James – Journal of Fungi

Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology – Antonio Molinaro – Nature Communications

Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers – Allyson L. Byrd – Journal of experimental medicine

Workshop report: Toward the development of a human whole stool reference material for metabolomic and metagenomic gut microbiome measurements – Rupasri Mandal – Metabolomics

Minireview: Communal Living: Glycan Utilization by the Human Gut Microbiota – Jonathon A. Briggs – Environmental Microbiology

Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut – Leszek Michalak – Nature Communications

Vaginal microbiome

*Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome – Luisa W. Hugerth – mSphere

Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth – Conor Feehily – npj Biofilms and Microbiomes

Intercepting genomic variability of Gardnerella vaginalis species through comparative genomics analyses: evolutionary and ecological implications – Chiara Tarracchini – Applied and Environmental Microbiology

Engineered phage endolysin eliminates Gardnerella in bacterial vaginosis without damaging the healthy vaginal microbiome – Christine Landlinger – medRxiv

Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid – Katelyn Brandt & Rodolphe Barrangou – BMC Microbiology

Dominance network analysis of the healthy human vaginal microbiome not dominated by Lactobacillus species – Wendy Li and Zhanshan Sam Ma – Computational and Structural Biotechnology Journal

Animal microbiome

The haybiome: Characterising the viable bacterial community profile of four different hays for horses following different pre-feeding regimens – Simon Daniels – Plos One

Review: Value of Probiotics in Canine and Feline Gastroenterology – Silke Salavati Schmitz – Veterinary Clinics of North America: Small Animal Practice

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel – Marco Gerdol – Genome Biology

Technique

Phylotype-Level Characterization of Complex Lactobacilli Communities Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach – Shaktheeshwari Silvaraju – Applied and Environmental Microbiology

Metagenomics

Metagenomic assessment of the global distribution of bacteria and fungi – Mohammad Bahram – Environmental Microbiology

Bioinformatics

On the complexity of haplotyping a microbial community – Samuel M Nicholls – Bioinformatics

Challenges in Benchmarking Metagenomic Profilers – Zheng Sun – bioRxiv

Unifying the global coding sequence space enables the study of genes with unknown function across biomes – Chiara Vanni – bioRxiv

Nucleotide-resolution bacterial pan-genomics with reference graphs – Rachel M Colquhoun – bioRxiv

Efficient storage and analysis of quantitative genomics data with the Dense Depth Data Dump (D4) format and d4tools – Hao Hou – bioRxiv

An Integrated Workflow for Enhanced Taxonomic and Functional Coverage of the Mouse Faecal Metaproteome – Nicolas Nalpas – bioRxiv

The misuse of colour in science communication – Fabio Crameri – Nature Communications

Antimicrobial Resistance

*The Household Resistome: Frequency of β-Lactamases, Class 1 Integrons, and Antibiotic-Resistant Bacteria in the Domestic Environment and Their Reduction during Automated Dishwashing and Laundering – Laura Schages – Applied and Environmental Microbiology

The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm – Shireen M Kotay – bioRxiv

fosM, a new family of fosfomycin resistance gene identified in bacterial species isolated from human microbiota – Sami Khabthani – Antimicrobial Agents and Chemotherapy

Heme is crucial for medium-dependent metronidazole resistance in clinical isolates of C. difficile – Ilse M. Boekhoud – bioRxiv

Events

Black In Immuno WeekBlack in Immuno – 22-28 November 2020
*A collective of scientists to celebrating, amplifying, and promoting the work of Black Immunologists across the globe.

Webinar: Antibiotic Resistance in the Environment – Organizer: Resistomap – Date: Tuesday, 24 November 2020

Webinar: Microbiology Webinars – FEMS – webinar recordings available

Virtual course and symposium: Harnessing Our Inner Ecology To Track and Treat Disease – Institute for Systems Biology – October 15 and 16, 2020
*all course materials/tutorials and talks are available for free on the website

Virtual Conference on Prokaryotic Small Proteins – Organizers: Todd Gray, Kai Papenfort, Gigi Storz and Joe Wade – January 12-14, 2021

Podcast

*Moving from wet to dry with Phil Ashton – Hosts: Andrew Page, Nabil-Fareed Alikhan and Lee Katz – Micro Binfie Podcast

Real-time quantitative proteomics with Devin Schweppe – Host: Jacob Schreiber – The Bioinformatics Chat

Interspecies collaborations with Mindaugas Gapševičius – Host: Aga Pokrywka – Ferment Radio

Microbiome as Organ: Researcher Colin Hill Talks Bacteria and Bacteriophages in Human Body with Colin Hill – Host: Richard Jacobs – The Finding Genius Podcast

What Does Your Microbiome Say About You? with Colin Hill – Host: Andrea Hardy – Let’s Gut Real

Colouring booklet

Microbes, diet and beyond by Microbiome Support EU project; Illustrations by Maria Pock

Boardgame

Drugs vs Bugs, a free and exciting Print’n’Play boardgame developed by Célia Souque

November 17, 2020

Multi-site human microbiome

Microbiome diversity predicts surgical success in patients with rectovaginal fistula – Leach et al. – International Urogynecology Journal

Human oral microbiome

[REVIEW]Oral Microbiota and Cancer Development – Tuominen & Rautava – Pathobiology

Human vaginal/pregnancy microbiome

Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth – Feehily et al. – npj biofilms and microbiomes

Human gut microbiome

[REVIEW]IBDs and the pediatric age: Their peculiarities and the involvement of the microbiota – Cococcioni et al. – Digestive and Liver Disease

Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers – Byrd et al. – JEM

Species-dependent variation of the gut bacterial communities across Trypanosoma cruzi insect vectors – Arias-Giraldo – PLOS One

Gut Microbiota and Cancer Correlates – Malaviya et al. – Probiotic Research in Therapeutics

Short-Chain Fatty Acids and Lipopolysaccharide as Mediators Between Gut Dysbiosis and Amyloid Pathology in Alzheimer’s Disease – Marizzoni et al. – Journal of Alzheimer’s Disease

Built environment (subways, indoor surfaces)
Unravelling the importance of the eukaryotic and bacterial communities and their relationship with Legionella spp. ecology in cooling towers: a complex network – Paranjape et al. – Microbiome

Techniques
Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities – Kleiner et al. – Microbiome

[REVIEW]NMR: Unique Strengths That Enhance Modern Metabolomics Research – Edison et al. – Analytical Chemistry

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

Study offers “indisputable” link between Alzheimer’s and gut microbiome – Lavars – New Atlas

October 27, 2020

Greetings from Pittsburgh, PA!

Today’s digest a contains articles focused on the oral microbiome, koala symbionts, soil microbial communities, and more. For those of you who are a bit too tired to digest cutting-edge research, I suggest using the 10 simple steps outlined in the highlighted editorial to colorize your own data visualizations. Finally, if you just need a break, I suggest bookmarking the article on the whale skin microbiome and revisiting the film Star Trek IV: The Voyage Home.

Happy reading (or movie watching)!

General microbiome

Taxonomic profiling and functional characterization of the healthy human oral bacterial microbiome from the north Indian urban sub-population – Verma et al. – Archives of Microbiology

Pregnancy and early life

Maternal and cord blood vitamin D level and the infant gut microbiota in a birth cohort study – Kassem et al. – Maternal Health, Neonatology and Perinatology

Human gut microbiome

Review: A review on preventive role of ketogenic diet (KD) in CNS disorders from the gut microbiota perspective – Rawat et al. – Reviews in Neurosciences

Animal experiments

Challenges in microbiological identification of aerobic bacteria isolated from the skin of reptiles – Brockmann et al. – PLOS ONE

Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum – Dahlhausen et al. – Peer J

Vertical transmission of zika virus in Aedes albopictus – Lai et al. – PLOS Neglected Tropical Diseases

Cultured-dependent and cultured-independent study of bacteria associated with Thai commercial stingless bee Lepidotrigona terminata – Suphaphimol et al. – Journal of Apicultural Research

Animal microbiome

**Skin microbiome of beluga whales: spatial, temporal, and health-related dynamics – Van Cise et al. – Animal Microbiome

Diversity of bacterial symbionts associated with Myzus persicae (Sulzer) (Hemiptera: Aphididae: Aphidinae) revealed by 16S rRNA Illumina sequencing – Xu et al. – Microbial Ecology

Plant, root, and soil microbiome

Protists and collembolans alter microbial community composition, C dynamics and soil aggregation in simplified consumer–prey systems – Erktan et al. – Biogeosciences

Responses of soil bacteria and fungi after 36 years fertilizer, straw cover, and irrigation management practices in northwest China – Zhang et al. – Soil Use and Management

Water and extremophile microbiome

Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance – Herold et al. – Nature Communications

Islands in the sand: Are all hypolithic microbial communities the same? – Lebre et al. – FEMS Microbiology Ecology

Shifts of sediment bacterial community and respiration along a successional gradient in a typical karst plateau lake wetland (China) – Xia et al. – Journal of Oceanology and Limnology

Salinity controls soil microbial community structure and function in coastal estuarine wetlands – Zhang et al. – Environmental Microbiology

Phages and viruses

Association of host proteins with the broad host range filamentous phage NgoΦ6 of Neisseria gonorrhoeae – Piekarowicz et al. – PLOS ONE

Bioinformatics

**Editorial: Ten simple rules to colorize biological data visualization – Hattab et al. – PLOS Computational Biology

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy – de Koning et al. – GigaScience

Predicting antimicrobial resistance using conserved genes – Nguyen et al. – PLOS Computational Biology

Techniques

Review: Innovations to culturing the uncultured microbial majority – Lewis et al. – Nature Reviews Microbiology

Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods – Wang et al. – PeerJ

Science, publishing, and career

Comment: Crowdsourcing virtual summer research opportunities to support minorities in microbiology – Johnson et al. – Nature Microbiology

October 14, 2020

Good morning from sunny San Francisco, California! Today’s digest shares some fascinating in vivo studies including a paper from Ou et al. examining the role of host antimicrobial proteins α-definsins in bacterial colonization and epithelial cell adherence in the gut and a proof-of-concept paper from Hsu et al. in which the authors orally delivered an engineered phage to the gut of mice that was capable of specifically repressing gene expression in bacteria. Additionally, there are some great plant, root, and soil microbiome papers (Kusstatscher et al. show that treating maize seeds with a plant growth-promoting rhizobacteria improves plant health) and water microbiome papers (León-Zayas et al. published a super collaborative paper looking at microbiome sharing between sediments, seagrasses, and reef fish at multiple sites). Finally, I wanted to highlight a paper by Zelaya et al. outlining a course-based undergraduate research experience for teaching microbiology that focuses on the bean beetle microbiome. Happy reading!

Pregnancy and Early Life
Review: The early life education of the immune system: Moms, microbes and (missed) opportunities. – Nitya, J. et al., Gut Microbes

Delayed Establishment of Gut Microbiota in Infants Delivered by Cesarean Section. – Kim, G. et al., Frontiers in Microbiology

Human Respiratory Microbiome
Proteins produced by Streptococcus species in the lower respiratory tract can modify antiviral responses against influenza virus in respiratory epithelial cells. – Nishioka, K. et al., Microbes and Infection

Human Vaginal Microbiome
Vaginal host immune-microbiome interactions in a cohort of primarily African-American women who ultimately underwent spontaneous preterm birth or delivered at term. – Florova, V. et al., Cytokine

Human Oral Microbiome
Isolation and Characterization of Nitrate-Reducing Bacteria as Potential Probiotics for Oral and Systemic Health. – Rosier, B.T. et al., Frontiers in Microbiology

Human Gut Microbiome
Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans. – Ha, C.W.Y. et al., Cell

Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity. – Fang, X. et al., Inflammatory Bowel Diseases

Animal Experiments
α-Defensins Promote Bacteroides Colonization on Mucosal Reservoir to Prevent Antibiotic-Induced Dysbiosis. – Ou, J. et al., Frontiers in Immunology

In situ reprogramming of gut bacteria by oral delivery. – Hsu, B.B. et al., Nature Communications

The intestinal microbial metabolite desaminotyrosine is an anti‐inflammatory molecule that modulates local and systemic immune homeostasis. – Wei, Y. et al., The FASEB Journal

Modulation of experimental autoimmune encephalomyelitis through colonisation of the gut with Escherichia coli. – Libbey, J.E. et al., Beneficial Microbes

Molecular patterns from a human gut-derived Lactobacillus strain suppress pathogenic infiltration of leukocytes into the central nervous system. -Sanchez, J.M.S. et al., Journal of Neuroinflammation

Plant, Root, and Soil Microbiome
Soil-microorganism-mediated invasional meltdown in plants. – Zhang, Z. et al., Nature Ecology and Evolution

Microbiome Management by Biological and Chemical Treatments in Maize Is Linked to Plant Health. – Kusstatscher, P. et al., Microorganisms

Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease. – Lee, S-M. et al., The ISME Journal

Keystone Microbiomes Revealed by 14 Years of Field Restoration of the Degraded Agricultural Soil Under Distinct Vegetation Scenarios. – Zhang, Z. et al., Frontiers in Microbiology

Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds. – Wang, M. et al., Frontiers in Microbiology

Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis. – Harbort, C.J. et al., Cell Host & Microbe

Review: Pinpointing secondary metabolites that shape the composition and function of the plant microbiome. – Jacoby, R.P. et al., Journal of Experimental Botany

Water and Extremophile Microbiome
Microbiomes of fish, sediment and seagrass suggest connectivity of coral reef microbial populations. – León-Zayas, R. et al., PeerJ

Size Shapes the Active Microbiome of Methanogenic Granules, Corroborating a Biofilm Life Cycle. – Trego, A.C. et al., mSystems

Self-regulating microbiome networks ensure functional resilience of biofilms in sand biofilters during manganese load fluctuations. – Zhao, X. et al., Water Research

Review: Groundwater Microbial Communities in Times of Climate Change. -Retter, A. et al., Current Issues in Molecular Biology

Probiotics/Prebiotics
Combining IL-2-based immunotherapy with commensal probiotics produces enhanced antitumor immune response and tumor clearance. – Shi, L. et al., Journal for the ImmunoTherapy of Cancer

Mom’s diet matters: Maternal prebiotic intake in mice reduces anxiety and alters brain gene expression and the fecal microbiome in offspring. – Hebert, J.C. et al., Brain, Behavior, and Immunity

Prophylactic effects of oral administration of Lactobacillus casei on house dust mite-induced asthma in mice. – Lingzhi, L. et al., Food & Function

Bioinformatics
INTEDE: interactome of drug-metabolizing enzymes. – Yin, J. et al., Nucleic Acid Research.

GIMICA: host genetic and immune factors shaping human microbiota. – Tang, J. et al., Nucleic Acid Research

metaFlye: scalable long-read metagenome assembly using repeat graphs. – Kolmogorov, M. et al., Nature Methods

Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models. – Scarborough, M.J. et al., mSystems

Education
The Bean Beetle Microbiome Project: A Course-Based Undergraduate Research Experience in Microbiology. – Zelaya, A.J. et al., Frontiers in Microbiology