August 18, 2018

The virome of California mosquitoes, effects of climate warming on grassland microbial communities, and a few “bacteria and art” entries including a 92-foot inflatable E. coli sculpture.

General microbiome

Communities of Niche-Optimized Strains: Small-Genome Organism Consortia in Bioproduction – Stephan Noack – Trends in Biotechnology

Growth tradeoffs produce complex microbial communities on a single limiting resource – Michael Manhart – Nature Communications

Human oral microbiome

Oral microbiome development during childhood: an ecological succession influenced by postnatal factors and associated with tooth decay – Majda Dzidic – The ISME Journal

Animal experiments

Loss of HDAC6 alters gut microbiota and worsens obesity – Arnon D Lieber – The FASEB Journal

Animal microbiome

Pre-print: CRISPR/Cas9-mediated gene deletion of the ompA gene in an Enterobacter gut symbiont impairs biofilm formation and reduces gut colonization of Aedes aegypti mosquitoes – Shivanand Hegde – bioRxiv

Plant, root, and soil microbiome

Climate warming leads to divergent succession of grassland microbial communities – Xue Guo – Nature Climate Change

Water and extremophile microbiome

Bacterial Diversity in Replicated Hydrogen Sulfide-Rich Streams – Scott Hotaling – Microbial Ecology

Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration – Sylvain Monteux – The ISME Journal

Phages and viruses

Virome of > 12 thousand Culex mosquitoes from throughout California – Mohammadreza Sadeghi – Virology

Comprehensive comparative analysis of methods and software for identifying viral integrations – Xun Chen – Briefings in Bioinformatics

Phage-inducible chromosomal islands are ubiquitous within the bacterial universe – Alfred Fillol-Salom – The ISME Journal

Metabolomics

Metabotypes Related to Meat and Vegetable Intake Reflect Microbial, Lipid and Amino Acid Metabolism in Healthy People – Runmin Wei – Molecular Nutrition & Food Research

More microbes

Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea – Michaeline B N Albright – Microbial Ecology

Bacteria art

Linen and Bacteria: The Hidden History of Microbiology – Clara Rodríguez Fernández – Labiotech.eu

Pomona Arts: Sara Parent Ramos: Jumble, Bunch, Grow – Inland Empire

Oxford Natural History exhibition explores benefits of bacteria – BBC News

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August 9, 2018

Horizontal gene transfer in microbiomes, metabolic study of the microbiota isolated from the camel rumen, a review on the bacteriophage virome in IBD.

General microbiome

Review: Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives – Rafael Pinilla-Redondo – Plasmid

Review: Learning from bacterial competition in the host to develop antimicrobials – Manuela Raffatellu – Nature Medicine

Pregnancy and early life

Early life colonization of the human gut: microbes matter everywhere – Katri Korpela – Current Opinion in Microbiology

Human respiratory microbiome

Determinants of the Nasal Microbiome: Pilot Study of Effects of Intranasal Medication Use – Vijay R Ramakrishnan – Allergy & Rhinology

Human skin microbiome

Sensitive scalp is associated with excessive sebum and perturbed microbiome – Li Ma – Journal of Cosmetic Dermatology

Animal experiments

Effects of host genetics and environmental conditions on fecal microbiota composition of pigs – Tereza Kubasova – PLOS ONE

Animal microbiome

A metagenomic analysis of the camel rumen’s microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation – Javad Gharechahi – Biotechnology for Biofuels

Plant, root, and soil microbiome

Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota – Allen Van Deynze – PLOS Biology

Brazilian Ironstone Plant Communities as Reservoirs of Culturable Bacteria With Diverse Biotechnological Potential – Washington L Caneschi – Frontiers in Microbiology

Water and extremophile microbiome

Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change – Trine Markussen – Environmental Microbiology

Pre-print: Resource diversity structures aquatic bacterial communities – Mario E Muscarella – bioRxiv

Pre-print: Modular assembly of polysaccharide-degrading microbial communities in the ocean – Tim N Enke – bioRxiv

Food microbiology

Review: Bakery yeasts, a new model for studies in ecology and evolution – Belen Carbonetto – Yeast

Inferences from inventories of microbes in ecological vineyard settings – Hans-Josef Schroers – International Journal of Environmental Quality

Phages and viruses

Review: Bacteriophage virome in IBD – Clemens Thoma – Nature Reviews Gastroenterology and Hepatology

Bioinformatics

Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis – Simon A Hardwick – Nature Communications

July 27, 2018

Diversity and stability of the oyster microbiota, earthworm gut bacteria contribute to silicon acquisition by maize, metabolic function and composition of the gut microbiota regulated by IgA, a review on engineering live biotherapeutics.

General microbiome

Review: Synthetic Biology and Engineered Live Biotherapeutics: Toward Increasing System Complexity – Tanel Ozdemir – Cell Systems

Pre-print: Fungal chromatin mapping identifies BasR, as the regulatory node of bacteria-induced fungal secondary metabolism – Juliane Fischer – bioRxiv

Multi-site human microbiome

Review: The Gut Microbiome as a Major Regulator of the Gut-Skin Axis – Iman Salem – Frontiers in Microbiology

Human respiratory microbiome

Identifying aerosolized cyanobacteria in the human respiratory tract: A proposed mechanism for cyanotoxin-associated diseases – Dominic N Facciponte – Science of the Total Environment

Human skin microbiome

Minor taxa in human skin microbiome contribute to the personal identification – Hikaru Watanabe – PLOS ONE

Animal experiments

Intestinal Microbiota Disruption Reduces Regulatory T Cells and Increases Respiratory Viral Infection Mortality Through Increased IFNγ Production – Mitchell H Grayson – Frontiers in Immunology

IgA regulates the composition and metabolic function of gut microbiota by promoting symbiosis between bacteria – Akira Nakajima – Journal of Experimental Medicine

Animal microbiome

Fecal bacterial communities from Mediterranean loggerhead sea turtles (Caretta caretta) – Elena Biagi – Environmental Microbiology Reports

Pre-print: Diversity and stability of microbiota are key factors associated to healthy and diseased Crassostrea gigas oysters – Camille Clerissi – bioRxiv

Plant, root, and soil microbiome

Earthworm gut bacteria increase silicon bioavailability and acquisition by maize – Lin Hu – Soil Biology and Biochemistry

Digging mammals contribute to rhizosphere fungal community composition and seedling growth – Shannon J Dundas – Biodiversity and Conservation

Soil amendment alters soil physicochemical properties and bacterial community structure of a replanted apple orchard – Bowen Liang – Microbiological Research

Water and extremophile microbiome

Microbiome functioning depends on individual and interactive effects of the environment and community structure – Chloé Orland – The ISME Journal

Microbes in space

Pre-print: Water quality and microbial load: a double-threshold identification procedure intended for space applications – Stefano Amalfitano – bioRxiv

Food microbiology

A low FODMAP diet is associated with changes in the microbiota and reduction in breath hydrogen but not colonic volume in healthy subjects – Tim J Sloan – PLOS ONE

Profiling white wine seed vinegar bacterial diversity through viable counting, metagenomic sequencing and PCR-DGGE – Vesna Milanović – International Journal of Food Microbiology

Probiotics/prebiotics

Review: Adipose tissue inflammation and metabolic syndrome. The proactive role of probiotics – Sebastian Torres – European Journal of Nutrition

Techniques

Recognizing the reagent microbiome – Marcus C de Goffau – Nature Microbiology

More microbes

Metabolically engineered Corynebacterium glutamicum for bio-based production of chemicals, fuels, materials, and healthcare products – Judith Becker – Metabolic Engineering

Pre-print: A dual motif mediates outer-membrane translocation and packing of glycosidases into Bacteroides Outer Membrane Vesicles – Ezequiel Valguarnera – bioRxiv

The outer membrane is an essential load-bearing element in Gram-negative bacteria – Enrique R Rojas – Nature

Microbes in the news

Viruses cooperate to defeat bacteria – Aude Bernheim – Nature

July 26, 2018

Altered intestinal phage populations in murine colitis, degradation of aromatic compounds by the wheat rhizosphere, barley products change the gut microbiota composition of rats.

General microbiome

Defining microbiome function – Jonathan L Klassen – Nature Microbiology

Electroactive microorganisms and microbial consortia – Enrico Marsili – Bioelectrochemistry

Humanome Versus Microbiome: Games of Dominance and Pan-Biosurveillance in the Omics Universe – Manousos E Kambouris – OMICS: A Journal of Integrative Biology

Human respiratory microbiome

The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens – Sophie Edouard – European Journal of Clinical Microbiology & Infectious Diseases

Human oral microbiome

Paired analysis of the microbiota between surface tissue swabs and biopsies from pediatric patients undergoing adenotonsillectomy – James Johnston – International Journal of Pediatric Otorhinolaryngology

Bacterial endotoxins and microorganisms in the oral cavities of patients on cancer therapy – J Mathews – Microbial Pathogenesis

Human gut microbiome

Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface – Marta Calatayud Arroyo – Journal of Visualized Experiments

Altered gut microbiota profile in patients with generalized anxiety disorder – Hai-yin Jiang – Journal of Psychiatric Research

Animal experiments

Beneficial changes of gut microbiota and metabolism in weaned rats with Lactobacillus acidophilus NCFM and Bifidobacterium lactis Bi-07 supplementation – Mengxia Wang – Journal of Functional Foods

Diammonium Glycyrrhizinate Protects against Non-Alcoholic Fatty Liver Disease in mice through modulation of gut microbiota and restoring intestinal barrier – Yun Li – Molecular Pharmaceuticals

Animal microbiome

Altering the Gut Microbiome of Cattle: Considerations of Host-Microbiome Interactions for Persistent Microbiome Manipulation – Brooke A Clemmons – Microbial Ecology

Plant, root, and soil microbiome

Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest – Julia C Haas – Soil Biology and Biochemistry

Diversity and Co-occurrence Patterns of Soil Bacterial and Fungal Communities in Seven Intercropping Systems – Sen Li – Frontiers in Microbiology

Metatranscriptome Analysis Deciphers Multifunctional Genes and Enzymes Linked With the Degradation of Aromatic Compounds and Pesticides in the Wheat Rhizosphere – Dhananjaya P Singh – Frontiers in Microbiology

Genome variations between rhizosphere and bulk soil ecotypes of a Pseudomonas koreensis population – Lucas Dantas Lopes – Environmental Microbiology

Water and extremophile microbiome

Comparative microbial communities in tidal flats sediment on Incheon, South Korea – Hye Jin Choi – The Journal of General and Applied Microbiology

Food microbiology

Fucoidan alleviates dyslipidemia and modulates gut microbiota in high-fat diet-induced mice – Min Liu – Journal of Functional Foods

Polyphenolic derivatives from mango (Mangifera Indica L.) modulate fecal microbiome, short-chain fatty acids production and the HDAC1/AMPK/LC3 axis in rats with DSS-induced colitis – Hyemee Kim – Journal of Functional Foods

Jaboticaba berry peel intake increases short chain fatty acids production and prevent hepatic steatosis in mice fed high-fat diet – Ângela Giovana Batista – Journal of Functional Foods

Bioavailability of Isoflavone Metabolites After Korean Fermented Soybean Paste (Doenjang) Ingestion in Estrogen‐Deficient Rats – Da-Hye Lee – Journal of Food Science

Barley Products of Different Fibre Composition Selectively Change Microbiota Composition in Rats – Cristina Teixeira – Molecular Nutrition & Food Research

Probiotics/prebiotics

A soy-based probiotic drink modulates the microbiota and reduces body weight gain in diet-induced obese mice – Juliana de Carvalho Marchesin – Journal of Functional Foods

Probiotics in cystic fibrosis patients: A double blind crossover placebo controlled study: Pilot study from the ESPGHAN Working Group on Pancreas/CF – Stephanie Van Biervliet – Clinical Nutrition ESPEN

Probiotics in Pediatric Gastroenterology: Emerging Indications – Elena Scarpato – Journal of Clinical Gastroenterology

Phages and viruses

Murine colitis reveals a disease-associated bacteriophage community – Breck A Duerkop – Nature Microbiology

Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins – Alexander P Hynes – Nature Communications

Bioinformatics

A marginalized two-part Beta regression model for microbiome compositional data – Haitao Chai – PLOS Computational Biology

Metabolomics

Simultaneous HS-SPME GC-MS determination of short chain fatty acids, trimethylamine and trimethylamine N-oxide for gut microbiota metabolic profile – Jessica Fiori – Talanta

Techniques

Balances: a New Perspective for Microbiome Analysis – J Rivera-Pinto – mSystems

Coupling magnetic-nanoparticle mediated isolation (MMI) and stable isotope probing (SIP) for identifying and isolating the active microbes involved in phenanthrene degradation in wastewater with higher resolution and accuracy – Jibing Li – Water Research

July 13, 2018

Comparing affects of host physiology and diet on primate gut microbiomes, oral bacterial and fungal dysbiosis in people with HIV, contribution of non-fermentable dietary fiber to prevention of autoimmune neurological disease via the gut microbiota.

General microbiome

Tools for engineering coordinated system behaviour in synthetic microbial consortia – Nicolas Kylilis – Nature Communications

Human oral microbiome

Dysbiosis in the oral bacterial and fungal microbiome of HIV-infected subjects is associated with clinical and immunologic variables of HIV infection – Pranab K Mukherjee – PLOS ONE

Human gut microbiome

Dietary non-fermentable fiber prevents autoimmune neurological disease by changing gut metabolic and immune status – Kerstin Berer – Scientific Reports

Physiology and central carbon metabolism of the gut bacterium Prevotella copri – Thomas Franke – Molecular Microbiology

Chemotaxis of Escherichia coli to major hormones and polyamines present in human gut – Joana G Lopes – The ISME Journal

Stool Microbiota Composition Differs in Patients with Stomach, Colon, and Rectal Neoplasms – Omar Youssef – Digestive Diseases and Sciences

Animal experiments

Of Mice and Men . . . and Microbes: Conclusions and Cautions from a Murine Study of the Lung Microbiome and Microbiome-Immune Interactions – John E McGinniss – American Journal of Respiratory and Critical Care Medicine

Modulation of gut microbiota by mulberry fruit polysaccharide treatment of obese diabetic db/db mice – Chun Chen – Food & Function

Evidence for the Role of the Cecal Microbiome in Maintenance of Immune Regulation and Homeostasis – Preeti Chhabra – Annals of Surgery

Human Milk Fortification with Bovine Colostrum Is Superior to Formula‐Based Fortifiers to Prevent Gut Dysfunction, Necrotizing Enterocolitis, and Systemic Infection in Preterm Pigs – Jing Sun – Journal of Parenteral & Enteral Nutrition

Fecal Microbiota Transplantation Is Effective in Relieving Visceral Hypersensitivity in a Postinfectious Model – Tao Bai – BioMed Research International

Animal microbiome

First report of foregut microbial community in proboscis monkeys: Are diverse forests a reservoir for diverse microbiomes? – Takashi Hayakawa – Environmental Microbiology Reports

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes – Katherine R Amato – The ISME Journal

The composition of the perinatal intestinal microbiota in cattle – Mohammad Jaber Alipour – Scientific Reports

Metagenomic evaluation of the effects of storage conditions on the bacterial microbiota of oysters Crassostrea gasar (Adanson, 1757) – Antonio Ostrensky – Journal of Applied Microbiology

16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus – Inga Reich – Scientific Reports

A Robust Noninvasive Approach to Study Gut Microbiota Structure of Amphibian Tadpoles by Feces – Xiaowei Song – Herpetology Research

Plant, root, and soil microbiome

Isolation and characterization of two phosphate-solubilizing fungi from rhizosphere soil of moso bamboo and their functional capacities when exposed to different phosphorus sources and pH environments – Yang Zhang – PLOS ONE

Water and extremophile microbiome

Hydrothermal chimneys host habitat-specific microbial communities: analogues for studying the possible impact of mining seafloor massive sulfide deposits – Yuchen Han – Scientific Reports

Food microbiology

Changes in Quality and Microbial Succession of Lightly Salted and Sugar-Salted Blunt Snout Bream (Megalobrama amblycephala) Fillets Stored at 4°C – Yan Li – Journal of Food Protection

Review: Novel approaches for Chemical and Microbiological shelf life extension of cereal crops – Marcus Schmidt – Critical Reviews in Food Science and Nutrition

Probiotics/prebiotics

The short-term impact of probiotic consumption on the oral cavity microbiome – Erik Dassi – Scientific Reports

Bioinformatics

The evolutionary signal in metagenome phyletic profiles predicts many gene functions – Vedrana Vidulin – Microbiome

More microbes

Pre-print: Listeria monocytogenes cell-to-cell spread in epithelia is heterogeneous and dominated by rare pioneer bacteria – Fabian E Ortega – bioRxiv

Microbes in the news

Gut microbiota: a new way to take your vitamins – João Carlos Gomes-Neto – Nature Reviews Gastroenterology & Hepatology

July 12, 2018

Bacteria in desert soils, mycobacteria in showerhead biofilms, metabolic diversity of microbes from commercial probiotics.

Human gut microbiome

Pre-print: Evaluating bacterial and functional diversity of human gut microbiota by complementary metagenomics and metatranscriptomics – Ravi Ranjan – bioRxiv

Animal microbiome

Pre-print: Olive fruit fly rearing procedures affect the vertical transmission of the bacterial symbiont Candidatus Erwinia dacicola – Patrizia Sacchetti – bioRxiv

Pre-print: Survey of bacteria associated with western corn rootworm life stages reveals no difference between insects reared in different soils – Dalton C Ludwick – bioRxiv

Plant, root, and soil microbiome

Influences of fertilization on soil environment and microorganism in continuous cropping based on high-throughput sequencing – Zhang YiJie – Journal of Agricultural Science and Technology

Review: Consortia of cyanobacteria/microalgae and bacteria in desert soils: an underexplored microbiota – Isiri Perera – Applied Microbiology and Biotechnology

Effects of cover crop in an apple orchard on microbial community composition, networks, and potential genes involved with degradation of crop residues in soil – Wei Zheng – Biology and Fertility of Soils

Microbial Community Level Physiological Profiles of Active Mud Volcano Soils in Andaman and Nicobar Islands – N Amaresan – National Academy Science Letters

Water and extremophile microbiome

Pre-print: Interspecies interactions mediated by conductive minerals in the sediments of the ferruginous Lake La Cruz, Spain – Amelia-Elena Rotaru – bioRxiv

Pre-print: Microbial community structure and microbial networks correspond to nutrient gradients within coastal wetlands of the Laurentian Great Lakes – Dean J Horton – bioRxiv

Pre-print: Hidden in plain sight – highly abundant and diverse planktonic freshwater Chloroflexi – Maliheh Mehrshad – bioRxiv

Built environment

Pre-print: Ecological analyses of mycobacteria in showerhead biofilms and their relevance to human health – Matthew Gebert – bioRxiv

Probiotics/prebiotics

Pre-print: Metabolic diversity of bacteria and yeast from commercial probiotic products illustrated by phenotypic profiling – Juliana Mastronunzio Ansari – bioRxiv

Phages and viruses

Pre-print: Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow – Antonin Bal – bioRxiv

More microbes

Species-specific activity of antibacterial drug combinations – Ana Rita Brochado – Nature

Science, career, and publishing

Hot streaks in artistic, cultural, and scientific careers – Lu Liu – Nature

Amy’s non-microbiology picks

Reprogramming human T cell function and specificity with non-viral genome targeting – Theodore L Roth – Nature

June 29, 2018

A variety of reviews on the human skin and gut microbiota, effects of probiotics on depressive behaviors, microbiota changes in deer populations in China.

Human skin microbiome

Review: Microbiome in the Gut-Skin Axis in Atopic Dermatitis – So-Yeon Lee – Allergy and Asthma Immunology Research

Human gut microbiome

Pre-print: The Genetic Basis for the Cooperative Bioactivation of Plant Lignans by a Human Gut Bacterial Consortium – Elizabeth N Bess – bioRxiv

Review: Mechanistic Insights in the Success of Fecal Microbiota Transplants for the Treatment of Clostridium difficile Infections – Amoe Baktash – Frontiers in Microbiology

Review: Reciprocal Interactions Between Gut Microbiota and Host Social Behavior – Emmanuelle Münger – Frontiers in Integrative Neuroscience

Review: Gut microbiota bile acid metabolism controls cancer immunosurveillance – Anna Dart – Nature Reviews Microbiology

Animal experiments

Pulmonary Arterial Hypertension Affects the Rat Gut Microbiome – María Callejo – Scientific Reports

Animal microbiome

Comparative Analysis of Gut Microbiota Changes in Père David’s Deer Populations in Beijing Milu Park and Shishou, Hubei Province in China – Meishan Zhang – Frontiers in Microbiology

Ixodes scapularis does not harbor a stable midgut microbiome – Benjamin D Ross – The ISME Journal

Plant, root, and soil microbiome

Different Height Forms of Spartina alterniflora Might Select Their Own Rhizospheric Bacterial Communities in Southern Coast of China – Li’an Lin – Microbial Ecology

Survey of sediment oxygenation in rhizospheres of the saltmarsh grass – Spartina anglica – Ketil Koop-Jakobsen – Science of the Total Environment

Probiotics/prebiotics

Probiotics decrease depressive behaviors induced by constipation via activating the AKT signaling pathway – Nana Xu – Metabolic Brain Disease

Phages and viruses

Pre-print: Seroprevalence of fourteen human polyomaviruses determined in blood donors – Sergio S Kamminga – bioRxiv

Bioinformatics

A distinct abundant group of microbial rhodopsins discovered using functional metagenomics – Alina Pushkarev – Nature

Techniques

Selection of validated hypervariable regions is crucial in 16S-based microbiota studies of the female genital tract – Simon Graspeuntner – Scientific Reports

More microbes

Cryo-EM structure of an essential Plasmodium vivax invasion complex – Jakub Gruszczyk – Nature

Microbes in the news

Genetically modified bacteria enlisted in fight against disease – Sara Reardon – Nature

A short course of laxatives has long-lasting effects on microbiome – Nature