Category Archives: Human gut

July 5, 2017

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General microbiome

Letter to the editor: Introducing the sporobiota and sporobiome – George Tetz – Gut Pathogens

Human oral microbiome

Oropharyngeal and Sputum Microbiomes Are Similar Following Exacerbation of Chronic Obstructive Pulmonary Disease – Hai-Yue Liu – Frontiers in Microbiology

Human respiratory microbiome

Review: Respiratory microbiota and lower respiratory tract disease – Miguel Lanaspa – Expert Review of Anti-infective Therapy

Human gut microbiome

Review: Feeding the microbiota: transducer of nutrient signals for the host – Fergus Shanahan – Gut

Animal microbiome

Early Postnatal Diets Affect the Bioregional Small Intestine Microbiome and Ileal Metabolome in Neonatal Pigs – Brian D Piccolo – The Journal of Nutrition

Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major) – Lucie Kropáčková – Plos One

Temperature variation, bacterial diversity, and fungal infection dynamics in the amphibian skin – Ana V. Longo – Molecular Ecology

Early-Life Diet Affects Host Microbiota and Later-Life Defenses Against Parasites in Frogs – Sarah A. Knutie – Integrative & Comparitive Biology

Animal experiments

Relative variations of gut microbiota in disordered cholesterol metabolism caused by high-cholesterol diet and host genetics – Tao Bo – Microbiology Open

Plant, root, and soil microbiome

Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities – Kelly Gravuer – Frontiers in Microbiology

Long-term rock phosphate fertilization impacts the microbial communities of maize rhizosphere – Ubiana C. Silva – Frontiers in Microbiology

Global change and the soil microbiome: A human-health perspective – Raúl Ochoa-Hueso – Frontiers in Ecology and Evolution

The Impact of Hydration and Temperature on Bacterial Diversity in Arid Soil Mesocosms – Adam Št’ovíček – Frontiers in Microbiology

Contrasting bacterial communities in two indigenous Chionochloa (Poaceae) grassland soils in New Zealand – Jocelyn C. Griffith – Plos One

Water and extremophile microbiome

Bacterial diversity and population shifts driven by spotlight wastewater micropollutants in low-temperature highly nitrifying activated sludge – Antonina Kruglova – JScience of The Total Environment

Probiotics / prebiotics

The potential synergistic behaviour of inter- and intra-genus probiotic combinations in the pattern and rate of short chain fatty acids formation during fibre fermentation – Warnakulasuriya M. A. D. B. Fernando – International Journal of Food Sciences and Nutrition

Review: Structural features underlying prebiotic activity of conventional and potential prebiotic oligosaccharides in food and health – Subin R. C. K. Rajendran – Journal of Food Biochemistry

Phages and viruses

Case control comparison of enteric viromes in captive rhesus macaques with acute or idiopathic chronic diarrhea – Beatrix Kapusinszky – Journal of Virology

A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections – Samuele Bovo – Plos One

Bioinformatics

Does colorectal cancer significantly influence the assembly of gut microbial communities? – Lin Dai – PeerJ

Review: Using metagenomics to investigate human and environmental resistomes – Johan Bengtsson-Palme – Journal of Antimicrobial Chemotherapy

RRmix: A method for simultaneous batch effect correction and analysis of metabolomics data in the absence of internal standards – Stephen Salerno Jr – Plos One

Predicting the ecological quality status of marine environments from eDNA metabarcoding data using supervised machine learning – Tristan Cordier – Environmental Science and Technology

Anitha’s non-microbiology picks

AI is changing how we do science. Get a glimpse

Scientists explain ancient Rome’s long-lasting concrete

July 3, 2017

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Pregnancy and early life
Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission – Sabrina Duranti –  Microbiome

 
Mini Review: The microbiome and disorders of the central nervous system – Valeria D. Felice – Pharmacology Biochemistry and Behavior

 
Human respiratory microbiome

 
Short Report: The metabolic footprint of the airway bacterial community in cystic fibrosis – Vaishnavi Narayanamurthy – Microbiome

 
Human gut microbiome

 
Gut microbial transformation of the dietary imidazoquinoxaline mutagen MeIQx reduces its cytotoxic and mutagenic potency – Jianbo Zhang –  Toxicological Science

 
Review: Practical considerations for large-scale gut microbiome studies – Doris Vandeputte – FEMS Microbiology Reviews

 
Association of altered gut microbiota composition with chronic urticaria – Edris Nabizadeh – Annals of Allergy, Asthma & Immunology

 
Animal microbiome 

 
A genomic investigation of ecological differentiation between free-living and Drosophila-associated bacteria – Nathan J. Winans –  Molecular Ecology

 
The Gut Bacterial Community Composition of Wild Cervus albirostris (White-Lipped Deer) Detected by the 16S Ribosomal RNA Gene Sequencing – Jun-gang Li –  Current Microbiology

 
Microbial influence on Drosophila biology – ME Martino – Current Opinion in Microbiology

 
Plant, root, and soil microbiome

 
Organic carbon and nitrogen availability determine bacterial community composition in paddy fields of the Indo-Gangetic plain – Arvind Kumar –  Biotech

 

Water and extremophile microbiome

 
Spatiotemporal Dynamics of the Bacterial Microbiota on Lacustrine Cladophora glomerata (Chlorophyta) – Michael J. Braus –  bioRxiv

 
Quantity and quality of particulate organic matter controls bacterial production in the Columbia River estuary – Byron C. Crump – Limnology and Oceanography

 
Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa – Marta Cobo-Simón –  BMC Genomics

 
Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing – Natàlia Corcoll – FEMS Microbiology Letters

 
Food microbiology

 

Cleaning and disinfection of biofilms composed of Listeria monocytogenes and background microbiota from meat processing surfaces – Annette Fagerlund – Applied and Environmental Microbiology

 

Probiotics / prebiotics

 
A human gut commensal ferments cranberry carbohydrates to produce formate – Ezgi Özcan – Applied and Environmental Microbiology

 
Review: Lifestyles in transition: evolution and natural history of the genus Lactobacillus – Rebbeca M. Duar – FEMS Microbiology Reviews

 
Phages and viruses

 
Synergistic elimination of bacteria by phage and the innate immune system – Chung Yin (Joey) Leung – Journal of Theoretical Biology

 
Biotechnology

 
Effect of zinc oxide nanoparticles on nitrogen removal, microbial activity and microbial community of CANON process in a membrane bioreactor – Xiaojing Zhang – Bioresource Technology

 
Microbes in the news

 
A new approach to tackling drug-resistant bacteria

New technology to cool the body: make the clothes made of microorganisms

 
Microbes on the market (news about biotech companies)

 
New Belgian Biotech will use Microorganisms to Replace Pesticides and Fertilizers

July 1, 2017

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General microbiome

The microbiome in hematopoietic stem cell transplant recipients and cancer patients: Opportunities for clinical advances that reduce infection – AY Koh – PLoS Pathogens

Research Highlight: New insights into the BAT–liver–gut axis – A Morris – Nature Reviews

Biodiversity and ecosystem function: making sense of numerous species interactions in multi-species communities – C Brophy – Ecology

Obstruction of pilus retraction stimulates bacterial surface sensing – CK Ellison – bioRxiv

 

Human gut microbiome

Hospital association of the gut microbiota mobilome in preterm infants – A Ravi – Pediatric Research

 

Human respiratory microbiome

Maturation of the Infant Respiratory Microbiota, Environmental Drivers and Health Consequences: A Prospective Cohort Study – AATM Bosch – Am J Respir Crit Care Med.

Review: Perna canaliculus and the Intestinal Microbiome – ET Saltzman – Marine Drugs

 

 

Animal microbiome

Host-specific associations affect the microbiome of Philornis downsi, an introduced parasite to the Galápagos Islands – MY Ben – Molecular Ecology

Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus – JA Yang – Journal of Microbiology

 

Plant, root and soil microbiome

Ammonia oxidizer populations vary with nitrogen cycling across a tropical montane mean annual temperature gradient – S Pierre – Ecology

Bacterial periphytic communities related to mercury methylation within aquatic plant roots from a temperate freshwater lake (South-Western France) – S Gentès – Environ Sci Pollut Res Int.

Consistently inconsistent drivers of microbial diversity and abundance at macroecological scales – JN Hendershot – Ecology

Living cover crops have immediate impacts on soil microbial community structure and function – DM Finney – Journal of Soil and Water Conservation

Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus “Hitchhiker” from the Soybean Rhizosphere – GL Lozano – Genome Announcements

Colonization and Maize Growth Promotion Induced by Phosphate Solubilizing Bacterial Isolates – Y Li – International Journal of Molecular Sciences

Biogeography and ecological diversity patterns of rare and abundant bacteria in oil-contaminated soils – S Jiao – Molecular Ecology

 

Water microbiome and extremophiles

Organohalide respiration with chlorinated ethenes under low pH conditions – Y Yang – Environmental Science & Technology

 

Microbes in news

These Cleaning Bots Can Zap Bacteria Out of Your Water Supply in Minutes – D Nield – Science Alert

Four strains of bacteria work together to produce pigment for food and cosmetics industry – ML Martialay – Phys.org

Texas: Fecal bacteria levels at Gulf beaches ahead of Fourth of July holiday weekend – K Bradshaw – mySA

Gut microbiome’s link to the brain – S Downing – Nine.com

Breast Milk Bacteria are Important for Establishing Infant Gut Microbiome – S Parmar – Medical News Bulletin

Fig Enzyme could Help to fight Infection and Heal Wounds – DN Gameiro – Labiotech.eu

Gut Health: The Next Mega-Trend in Health and Wellness – H Schieber – Researchci

I spent three days as a hunter-gatherer to see if it would improve my gut health – T Spector – Medical Xpress

Altering gut bacteria pathways may stimulate fat tissue to prevent obesity – Medical Xpress

The broiler chicken intestine – an apt target for proteomic studies – E O’Reilly – BMC Blog Network

June 30, 2017

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A few gut microbiome reviews, apparently a simple bacterial community in bullet ants, circadian rhythm of rhizosphere bacterial communities, and you might want to think twice before you step into the ocean for a swim this summer.

General microbiology

Mapping quorum sensing onto neural networks to understand collective decision making in heterogeneous microbial communities – Tahir Yusufaly & James Q. Boedicker – ePub in Physical Biology, first in arXiv

Cheating fosters species co-existence in well-mixed bacterial communities – Anne Leinweber, R Fredrik Inglis and Rolf Kümmerli – ISME Journal

One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas – Rosaria Campilongo et al. – PLoS Genetics

PrePrint: Statistics and simulation of growth of single bacterial cells: illustrations with B. subtilis and E. coli – Johan H. van Heerden et al. – bioRxiv

Performance of electro-spun carbon nanofiber electrodes with conductive poly(3,4-ethylenedioxythiophene) coatings in bioelectrochemical systems – Juan J.L. Guzmana & Meryem O. Pehlivaner Kara et al. – Journal of Power Sources

Press: Bacteria-coated nanofiber electrodes digest pollutants – Blaine Friedlander – Phys.org

Human skin microbiome

Review: Keratinocytes as sensors and central players in the immune defense against Staphylococcus aureus in the skin – Katharina Bitschar et al. – Journal of Dermatological Science

Human gut microbiome

Review: The nutrition-gut microbiome-physiology axis and allergic diseases – Craig McKenzie – Immunological Reviews

16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease – Ashton JJ et al. – Medicine (Baltimore)

Review: The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology – Nathan T. Porter and Eric C. Martens – Annual Reviews of Microbiology

Review: Gut Microbiota as a Target for Preventive and Therapeutic Intervention against Food Allergy – Rosita Aitoro et al. – Nutrients

Two distinct metacommunities characterize the gut microbiota in Crohn’s disease patients – Qing He & Yuan Gao et al. – GigaScience

Animal experiments

PrePrint: Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut microbiomes – Matthew L Jenior et al. – bioRxiv

Animal microbiome

PrePrint: Bacterial community profiles and Vibrio parahaemolyticus abundance in individual oysters and their association with estuarine ecology – Ashley L. Marcinkiewicz et al. – bioRxiv

Diversity and Persistence of the Gut Microbiome of the Giant Neotropical Bullet Ant – Corrie S. Moreau & Benjamin E. R. Rubin – Integrative and Comparative Biology

PrePrint: Gut microbiota in the burying beetle, Nicrophorus vespilloides, provide colonization resistance against larval bacterial pathogens – Yin Wang & Daniel Rozen – bioRxiv

Plant, root and soil microbiome

Effects of habitat constraints on soil microbial community function – Naoise Nunan et al. – Scientific Reports

Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism – Christopher Staley et al. – Microbiome

Biological control of Pythium, Rhizoctonia and Sclerotinia in lettuce: the plant protective activity of the bacterium Paenibacillus alvei K165 is associated with the induction of systemic resistance – G. Fatouros et al. – Plant Pathology

Water and extremophile microbiome

Membrane biofilm communities in full-scale membrane bioreactors are not randomly assembled and consist of a core microbiome – Gerald K. Matar & Samik Bagchi et al. – Water Research

Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica – Hyunmin Koo et al. – Journal of Microbiological Methods

Built environment

Hospital Building and Healthcare Associated Infections (HAIs) in terms of total contamination data and cases grouped by department/areas – Shadha M. Abbas Al Asadi – Scientific Journal of Medical Research

Microbes in the news

The Bugs That Keep Us Safe – Maria-Luisa Alegre – American Journal of Transplantation

Study on human skin microbiome finds archaea abundance associated with age – Phys.org

The Dust Storm Microbiome – Weismann Institute of Science – Laboratory Equipment

Starbucks’ iced coffee may have fecal bacteria in it — so do all these other things – Donovan Harrell – Miami Herald (BBC investigation)

Bacteria change a liquid’s properties and escape entrapment – Gail Mccormick – Phys.org

Only association: Gut feelings are real: Some people have stomach bacteria that makes them more anxious and stressed, study shows – DailyMail

Elevated bacteria counts found at 4 Island beaches – Rick Kelley – Valley Morning Star

Plasmids: traffickers of antibiotic resistance – Modernising Medical Microbiology – University of Oxford

Microbes on the market

Diabetes: J&J and Seventure Partners launch investment – tg – European Biotechnology

Global Microbiome Drugs Market 2017- Pfizer, Second Genome , Seres Therapeutics, MaaT Pharma, Enterome Bioscience – Nakul Shirke – Daily Hover

June 28, 2017

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Human vaginal microbiome

Vaginal seeding or vaginal microbial transfer from the mother to the cesarean born neonate: a commentary regarding clinical management – Thor Haahr – BJOG

Human gut microbiome

*Review: The resilience of the intestinal microbiota influences health and disease – Felix Sommer – Nature Reviews Microbiology

Other human microbiome

Urinary catheter-associated microbiota change in accordance with treatment and infection status – Laetitia Bossa – PLOS ONE

Dynamics of the Oral Microbiota as a Tool to Estimate Time Since Death – Joe Adserias Garriga – Molecular Oral Microbiology

Animal experiments

Tuftsin-Phosphorylcholine maintains normal gut microbiota in collagen induced arthritic mice – Hila Ben-Amram – Frontiers in Microbiology

Animal microbiome

The Diet and Gut Microbial Communities of Two Closely Related Combtooth Blennies, Chasmodes saburrae and Scartella cristata – Peter J. Hundt – Copeia

Variation in the microbiome of the urogenital tract of koalas (Phascolarctos cinereus) with and without “wet bottom” – Alistair R. Legione – bioRxiv

Plant, root, and soil microbiome

Dominant Groups of Potentially Active Bacteria Shared by Barley Seeds become Less Abundant in Root Associated Microbiome – Luhua Yang – Frontiers in Plant Science

Understanding the variation of microbial community in heavy metals contaminated soil using high throughput sequencing – Honghong Guo – Ecotoxicology and Environmental Safety

Root Hair Mutations Displace the Barley Rhizosphere Microbiota – Senga Robertson-Albertyn – Frontiers in Plant Science

*Review: Below-ground connections underlying above-ground food production: a framework for optimising ecological connections in the rhizosphere – Franciska T. de Vries – Journal of Ecology

Rhizosphere microorganisms affected by soil solarization and cover cropping in Capsicum annuum and Phaseolus lunatus agroecosystems – Nancy Kokalis-Burelle – Applied Soil Ecology

Bacterial community dynamics in the rhizosphere of a long-lived, leguminous shrub across a 40-year age sequence – Xiaofan Na – Journal of Soils and Sediments

Microbial populations of stony meteorites: Substrate controls on first colonisers – Alastair W. Tait – Frontiers in Microbiology

Water and extremophile microbiome

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage – Wenkai Teng – Minerals

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer – Donald Pan – Frontiers in Microbiology

Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat – Jackson Z Lee – bioRxiv

Bioinformatics

Mixed Effect Dirichlet-Tree Multinomial for Longitudinal Microbiome Data and Weight Prediction – Yunfan Tang – arXiv

Segal’s Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project – James B. Pettengill – PeerJ

Techniques

Assembly and Tracking of Microbial Community Development within a Microwell Array Platform – Andrea C. Timm – JOVE

June 27, 2017

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Water microbiome focus today: The effects of terrestrially derived dissolved organic matter on the arctic microbiome, a characterization of deep terrestrial biosphere biofilms, and the microbiome of glaciers and ice sheets.

  • General microbiome

Review: Perspectives and Challenges in Microbial Communities Metabolic Modeling – Emanuele Bosi – Frontiers in Genetics

  • Human respiratory microbiome

Ecological networking of cystic fibrosis lung infections – Robert A Quinn – NPJ Biofilms and Microbiomes

  • Human oral microbiome

Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment – Katy Califf – mSystems

Educational strategies and ART effect on salivary characteristics: a controlled clinical trial – Camila Nobre de Freitas – Oral Diseases

Linkages between oral commensal bacteria and atherosclerotic plaques in coronary artery disease patients – Jyoti Chhibber-Goel – NPJ Biofilms and Microbiomes

Next generation sequencing of oral microbiota in Type 2 diabetes mellitus prior to and after neem stick usage and correlation with serum monocyte chemoattractant-1 – Rubini Anbalagan – Diabetes Research and Clinical Practice

Pyrosequencing Analysis of Cryogenically Ground Samples from Primary and Secondary/Persistent Endodontic Infections – Cangül Keskin – Journal of Endodontics

  • Human gut microbiome

Heat-stabilised rice bran consumption by colorectal cancer survivors modulates stool metabolite profiles and metabolic networks: a randomised controlled trial – Dustin Brown – British Journal of Nutrition

Two rheumatoid arthritis-specific autoantigens correlate microbial immunity with autoimmune responses in joints – Annalisa Pianta – The Journal of Clinical Investigation

Distinct patterns in the gut microbiota after surgical or medical therapy in obese patients – Daniel Medina – PeerJ

Immune-modulating effects in mouse dendritic cells of lactobacilli and bifidobacteria isolated from individuals following omnivorous, vegetarian and vegan diets – Diomira Luongo – Cytokine

  • Animal microbiome

Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands – Ross Cunning – PeerJ

Microbial bioenergetics of coral-algal interactions – Ty Roach – Peer J

Gut symbiont enhances insecticide resistance in a significant pest, the oriental fruit fly Bactrocera dorsalis – Daifeng Cheng – Microbiome

  • Plant, root, and soil microbiome</b

Temporal dynamics of the compositions and activities of soil microbial communities post-application of the insecticide chlorantraniliprole in paddy soils – Meng Wu – Ecotoxicology and Environmental Safety

Disease Suppressive Soils: New Insights from the Soil Microbiome – Daniel Schlatter – Phytopathology

Bacillus subtilis biofilm development in the presence of soil clay minerals and iron oxides – Wenting Ma – NPJ Biofilms and Microbiomes

  • Water and extremophile microbiome

Review: Constraint-based metabolic modelling of marine microbes and communities – Marco Fondi – Marine Genomics

* Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters – Xiaofen Wu – Microbiome

* The microbiome of glaciers and ice sheets – Alexandre M. Anesio – NPJ Biofilms and Microbiomes

* Microbial Community Response to Terrestrially Derived Dissolved Organic Matter in the Coastal Arctic – Rachel Sipler – Frontiers in Microbiology

  • Built environment

New insights into the spatial variability of biofilm communities and potentially negative bacterial groups in hydraulic concrete structures – Wei Cai – Water Research

Architecture, component, and microbiome of biofilm involved in the fouling of membrane bioreactors – Tomohiro Inaba – NPJ Biofilms and Microbiome

  • Techniques

Orthogonal Comparison of GC-MS and 1H NMR Spectroscopy for Short Chain Fatty Acid Quantitation – Jingwei Cai – Anal Chem

June 25, 2017

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Lots of interesting pre-prints in this post that might be worth following! Also a blog post on some cool science art with kombucha, as well as a lot of articles on rhizosphere-microbe interactions.

Events and jobs

Research Opportunities in Molecular Microbiology – Washington University in St. Louis

PhD scholarship in Metagenomics analysis and systems biology – Danmarks Tekniske Universitet

General microbiome

Microbiome yarns: microbial forensics for auditing provenance in global food chains – Timmis et al. – Microbial Biotechnology

Adjuncts and alternatives in the time of antibiotic resistance and in-feed antibiotic bans – Brüssow – Microbial Biotechnology

Human gut microbiome

Bacteria facilitate viral co-infection of mammalian cells and promote genetic recombination – Erickson et al. – bioRXiv

Chemical transformation of xenobiotics by the human gut microbiota – Koppel et al. – Science

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer – Purcell et al. – bioRXiv

Animal microbiome

Whole genome sequencing-based detection of antimicrobial resistance and virulence in non-typhoidal Salmonella enterica isolated from wildlife – Thomas et al. – bioRXiv

 

Plant, root, and soil microbiome

Antagonism between two root-associated beneficial Pseudomonas strains does not affect plant growth promotion and induced resistance against a leaf-chewing herbivore – Pangesti et al. – FEMS Microbiology Ecology

Bioelectrochemical approach for control of methane emission from wetlands – Liu et al. – Bioresource Technology

The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks – Duke et al. – BMC Genomics

Delftia rhizosphaerae sp. nov. isolated from the rhizosphere of Cistus ladanifer – Carro et al. – International Journal of Systematic and Evolutionary Microbiology

Synthesis and Secretion of Isoflavones by Field-Grown Soybean – Sugiyama et al. – Plant Cell Physiology

The Variation in the Rhizosphere Microbiome of Cotton with Soil Type, Genotype and Developmental Stage – Qiao et al. – Scientific Reports

Complete Genome Sequence of Bacillus paralicheniformis MDJK30, a Plant Growth -Promoting Rhizobacterium with Antifungal Activity – Wang et al. – Genome Anouncements

Extensive Overlap of Tropical Rainforest Bacterial Endophytes between Soil, Plant Parts, and Plant Species – Haruna et al. – Microbial Ecology

Phytoavailability of Cr in Silene vulgaris: The role of soil, plant genotype and bacterial rhizobiome – García-Gonzalez et al. – Ecotoxicology and Environmental Safety

Water and extremophile microbiome

Sulfolobus islandicus meta-populations in Yellowstone National Park hot springs – Campbell et al. – Environmental Microbiology

Bottled aqua incognita: Microbiota assembly and dissolved organic matter diversity in natural mineral waters – Lesaulnier et al. – bioRXiv

Techniques

Rapid whole genome amplification and sequencing of low cell numbers in a bacteraemia model – Anscombe et al. – bioRXiv

Microbes in the news

Do Probiotics Really Work? – Ferris Jabr – Scientific American

Fungi and bacteria team up in dental plaque – Evans – LabRoots

Scientists spy on the secret inner life of bacteria – Saey – Science News

Biofilms: The eradication has begun – McGill University Health Centre – Science Daily

Bacteria and Mental Health: Gut Bacteria Linked to Bipolar Disorder – Villamil – Medical News Bulletin

The Kombucha Craze Steps into Art and the Science of the Microbiome – Fernández – Labiotech

Microbes on the market

Global Microbiome Drugs Industry Market Research Report 2017 – Medgadget

June 24, 2017

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An early life focus today: Interesting papers on the effects of a pre-term cesarian birth on the gut microbiome and the impact of the infant gut microbiome on food allergies. Also highlighted, the relationship between the gut microbiome and social stress vulnerability in mice, the role of the gut microbiome in mosquito development, and evidence of a permanent transfer of prokaryotic virus sequences to the mammalian brain.

  • Pregnancy and early life

Review: Perinatal Group B Streptococcal Infections: Virulence Factors, Immunity, and Prevention Strategies – Jay Vornhagen – Trends in Microbiology

* Cesarean or Vaginal Birth Does Not Impact the Longitudinal Development of the Gut Microbiome in a Cohort of Exclusively Preterm Infants – Christopher Stewart – Frontiers in Microbiology

* A prospective microbiome-wide association study of food sensitization and food allergy in early childhood – Jessica Savage – Allergy

  • Human respiratory microbiome

Psl Produced by Mucoid Pseudomonas aeruginosa Contributes to the Establishment of Biofilms and Immune Evasion – Christopher Jones – mBio

  • Human skin microbiome

Isotretinoin and lymecycline treatments modify the skin microbiota in acne – Hanna-Lenna Kelhala – Experimental Dermatology

  • Human oral microbiome

Potassium is a key signal in host-microbiome dysbiosis in periodontitis – Susan Yost – PLOS Pathogens

  • Human gut microbiome

The TMAO-Producing Enzyme Flavin-Containing Monooxygenase 3 Regulates Obesity and the Beiging of White Adipose Tissue – Rebecca Schugar – Cell Reports
In vitro modulation of gut microbiota by whey protein to preserve intestinal health – Sanchez-Moya – Food and Function

Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis – Gregory Young – Frontiers in Cellular and Infection Microbiology

NOD2 genetic variants predispose one of two familial adenomatous polyposis siblings to pouchitis through microbiome dysbiosis – Kathleen Schieffer – Journal of Crohn’s and Colitis

The Bacteroides fragilis pathogenicity island links virulence and strain competition – Benjamin Casterline – Gut Microbes

Diversity analysis of gut microbiota in osteoporosis and osteopenia patients – Jihan Wang – PeerJ

Gut microbiota of liver transplantation recipients – Li-Ying Sun – Scientific Reports

Review: Microbiome: A Potential Component in the Origin of Mental Disorders – George Stefano – Medical Science Monitor

Review: Impact of mycotoxins on the intestine: are mucus and microbiota new targets? – Herve Robert – Journal of Toxicology and Environmental Health

Review: Microbiota, Inflammation and Colorectal Cancer – Cecily Lucas – International Journal of Molecular Sciences

Review: The Enteric Network: Interactions between the Immune and Nervous Systems of the Gut – Bryan Yoo – Immunity

  • Cadaver microbiome

Function of bacterial community dynamics in the formation of cadaveric semiochemicals during in situ carcass decomposition – Javier Pascual – Environmental Microbiology

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  • Animal experiments

* Implications of the gut microbiota in vulnerability to the social avoidance effects of chronic social defeat in male mice – Joanna Kasia Szyszkowicz – Brain, Behavior, and Immunity

Intestinal microbial dysbiosis aggravates the progression of Alzheimer’s disease in Drosophila – Shih-Cheng Wu – Nature Communications

Fructo-oligosaccharides and intestinal barrier function in a methionine-choline-deficient mouse model of nonalcoholic steatohepatitis – Kotaro Matsumoto – PLOS One

Spirulina Protects against Hepatic Inflammation in Aging: An Effect Related to the Modulation of the Gut Microbiota? – Audrey Neyrinck – Nutrients

Antrodia cinnamomea reduces obesity and modulates the gut microbiota in high-fat diet-fed mice – C.J Chang – International Journal of Obesity

Topical antimicrobial treatments can elicit shifts to resident skin bacterial communities and reduce colonization by Staphylococcus aureus competitors – Adam SanMiguel – Antimicrobial Agents and Chemotherapy

Temporal microbiota changes of high-protein diet intake in a rat model – Chunlong Mu – Anaerobe

  • Animal microbiome

Microbiome dynamics in early life stages of the scleractinian coral Acropora gemmifera in response to elevated pCO2 – Guowei Zhou – Environmental Microbiology

Effects of dietary supplementation of red pepper (Schinus terebinthifolius Raddi) essential oil on performance, small intestinal morphology and microbial counts of weanling pigs – Pedro Leon Gomes Cairo – Science of Food and Agriculture

Identification of Bufadienolides from the Boreal Toad, Anaxyrus boreas, Active Against a Fungal Pathogen – Kelly Barnhart – Microbial Ecology

* Bacteria-mediated hypoxia functions as a signal for mosquito development – Kerri Coon – PNAS

  • Plant, root, and soil microbiome

The Microbiome of Eucalyptus Roots under Different Management Conditions and Its Potential for Biological Nitrogen Fixation – Eduardo de Siva Fonseca – Microbial Ecology

  • Water and extremophile microbiome

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses – Vera Thiel – Frontiers in Microbiology

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  • Phages and viruses

* A prokaryotic viral sequence is expressed and conserved in mammalian brain – Yang-Hui Yeh – PNAS

  • Techniques

Solid Sampling with a Diode Laser for Portable Ambient Mass Spectrometry – Yeni Yung – Analytical Chemistry

June 22, 2017

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Effects of weight loss treatment on gut microbiota and serum metabolites, mouse gut microbiota can alter visceral sensitivity, a review discussing the microbiota’s ability to shape the maternal immune system.

Pregnancy and early life

Review: The unique immunological and microbial aspects of pregnancy – Gil Mor – Nature Reviews Immunology

Human oral microbiome

Review: Microbiome and Microbial Biofilm Profiles of Peri-Implantitis: A Systematic Review – Gloria Inés Lafaurie – Journal of Periodontology

Human gut microbiome

Bifidobacterium-Rich Fecal Donor May Be a Positive Predictor for Successful Fecal Microbiota Transplantation in Patients with Irritable Bowel Syndrome – S Mizuno – Digestion

Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests – Francesca Borgo – PLOS ONE

Animal experiments

Fructo-oligosaccharides and intestinal barrier function in a methionine–choline-deficient mouse model of nonalcoholic steatohepatitis – Kotaro Matsumoto – PLOS ONE

Microbiota regulates visceral pain in the mouse – Pauline Luczynski – eLife

Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle – Milton Thomas – bioRxiv

Animal microbiome

Combining ‘omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut – Angela Kruse – PLOS ONE

Plant, root, and soil microbiome

Application of struvite alters the antibiotic resistome in soil, rhizosphere, and phyllosphere – Qing-Lin Chen – Environmental Science & Technology

Water and extremophile microbiome

Synergistic hydrolysis of xylan using novel xylanases, β-xylosidases, and an α-l-arabinofuranosidase from Geobacillus thermodenitrificans NG80-2 – Di Huang – Applied Microbiology and Biotechnology

Longitudinal variation of microbial communitiesin benthic biofilms and association with hydrological and physicochemical conditions in glacier-fed streams – Ze Ren – Freshwater Science

Control of Sulfide Production in High Salinity Bakken Shale Oil Reservoirs by Halophilic Bacteria Reducing Nitrate to Nitrite – Biwin A An – Frontiers in Microbiology

Phages and viruses

Viral and Bacterial Communities of Colorectal Cancer – Geoffrey D Hannigan – bioRxiv

Plasmids, Viruses, And Other Circular Elements In Rat Gut – Tue Sparholt Jørgensen – bioRxiv

Bioinformatics

The metagenomic data life-cycle: standards and best practices – Petra ten Hoopen – GigaScience

PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies – Ludovic Mallet – Bioinformatics

Metabolomics

Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention – Ruixin Liu – Nature Medicine

Integrating Microbiome and Metabolome Data to Understand Infectious Airway Disease – Robert A Quinn – American Journal of Respiratory and Critical Care Medicine

Coupling targeted and untargeted mass spectrometry for metabolome-microbiome-wide association studies of human fecal samples – Alexey V Melnik – Analytical Chemistry

Techniques

Incorporating comparative genomics into the Design-Test-Learn cycle of microbial strain engineering – Maria Sardi – FEMS Yeast Research

Different amplicon targets for sequencing-based studies of fungal diversity – Francesca De Filippis – Applied and Environmental Microbiology

Microbes in the news

Modified viruses deliver death to antibiotic-resistant bacteria – Sara Reardon – Nature

Microbes on the market

EnteroBiotix raises £500k in first round of equity funding – Philip Gates – Insider.co.uk

Microbiotica To Present At Microbiome Drug Development Summit – BioSpace

Bacteria art

MIT Researchers Use Light-Illuminated Bacteria to Make ‘Living’ Pictures – Kristin Fawcett – Mental Floss

The world’s art is under attack—by microbes – Kate Baggaley – Popular Science

Science, publishing, and career

Editorial: Don’t let Europe’s open-science dream drift – Nature

June 21, 201

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Today’s Microbiome Digest has quite a few articles from water environment. Both articles I would like to highlight are with cyanobacteria as stars. The first one from Anne D. Jungblut reports on Antarctic cynobacteria diversity, while the second one reveals the new freshwater cyanobacterial genome. One more thing to highlight come from news. Exxon Mobil Corps and Sintetic Genomics Inc have announced a new breakthrough with genetically modified algae which was able to convert 40% of CO2 to lipids, up from the previous 15%. Algae are still far away from being able to run the process at commercial scale and replace fossil fuels, but we love algae! Enjoy this summer reading.

Events and jobs

Microbiome Research Scientist (BS or MS or PhD) – St. John of God Foundation for Research and Teaching, Barcelona, Spain

Quality Associate Specialist – Merck, Durham, NC, US

Microbiology Manager OR Microbiology Laboratory Manager Opening, Madison, WI, US
General microbiome

A null model for microbial diversification – Timothy J. Straub – PNAS

Pregnancy and early life

Association between breast milk bacterial communities and establishment and development of the infant gut microbiome – JAMA Pediatrics
Human skin microbiome

Topical antimicrobial treatments can elicit shifts to resident skin bacterial communities and reduce colonization by competitors – Adam J. SanMiguel – Antimicrobial Agents and Chemotherapy
Human gut microbiome

Liver transplant modulates gut microbial dysbiosis and cognitive function in cirrhosis – Jasmohan S. Bajaj – Liver Transplatation

How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans – Alan Cartmell – PNAS

Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing – Kate Lawrence – PLOS
Animal microbiome 

The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish – Keaton Stagaman – The ISME Journal
Plant, root, and soil microbiome

Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions – Di Wang – The ISME Journal

Novel antibiotic resistance determinants from agricultural soil exposed to antibiotics widely used in human medicine and animal farming – Calvin Ho-Fung Lau – Applied and Environmental Microbiology
Water and extremophile microbiome 

Animal-like prostaglandins in marine microalgae – Valeria Di Dato – The ISME Journal

Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents – Dimitri V Meier – The ISME Journal

Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the methylated amine degradation pathway – Ian Lidbury – The ISME Journal

DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments – Anders Lanzén – PLOS

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters – David M Needham – The ISME Journal

Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics – Lucas Moitinho-Silva – The ISME Journal

Spontaneous mutations of a model heterotrophic marine bacterium – Ying Sun – The ISME Journal

Plastid thylakoid architecture optimizes photosynthesis in diatoms – Serena Flori –  Nature Communications

Evolutionary radiation of lanthipeptides in marine cyanobacteria – Andres Cubillos-Ruiz –  PNAS

Using Captain Scott’s Discovery specimens to unlock the past: has Antarctic cyanobacterial diversity changed over the last 100 years? – Anne D. Jungblut – Proceedings of the Royal Society B

Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs – Pedro J. Cabello-Yeves – Frontiers in Microbiology

Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment – Yu Wang – Frontiers in Microbiology

Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere through Submarine Mud Volcanoes – Tatsuhiko Hoshino – Frontiers in Microbiology
Phages and viruses

Effect of acute predation with bacteriophage on intermicrobial aggression by Pseudomonas aeruginosa – Patrick R. Secor
Bioinformatics

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data – Gerben Menschaert –

Microbes in the news 

Zombie bacteria and viruses in melting permafrost are waking up  

ExxonMobil and Synthetic Genomics Report Breakthrough in Algae Biofuel Research

Gut microbiome changes linked to numerous biomarkers of type 2 diabetes 

Funky tasting beer? Biofilms may be to blame, MSU researchers say

Bacteria in Your Coughs And Sneezes Can Stay Alive in The Air For Up to 45 Minutes

Microbes on the market

This Company Uses the Human Microbiome to Discover New Disease Mechanisms