Category Archives: Built Environment Microbiology

April 18, 2017

Posted on by

Today’s digest hosts a number of rhizosphere-related publications as well as a good amount of interesting microbiome-host-health science.  Coming up next week is BioData World West 2017, a conference focused on Genomics/Precision Medicine/AI that I will be attending – I’ll keep an eye out for anything microbiome-related!

Events and jobs

2017 Metagenomics Workshop – Edwards Lab Event (Bioinformatics)

BioData World West 2017 – Precision Medicine, AI, Genomics Conference

General microbiome

Biological Determinants of Health: Genes, Microbes, and Metabolism Exemplars of Nursing Science – Erin P. Ferranti – Nursing Outlook

* Microbiotal-Host Interactions and Hypertension – Sarah Galla – Physiology

Multi-site human microbiome

* The Landscape Ecology and Microbiota of the Human Nose, Mouth, and Throat – Diana M. Proctor – Cell Host & Microbe

Human respiratory microbiome

* The microbiome in respiratory medicine: current challenges and future perspectives – Rosa Faner – European Respiratory Journal

Human skin microbiome

Living in Peace: Host-Microbiota Mutualism in the Skin – Daniel J. Campbell – Cell Host & Microbe

Human gut microbiome

The Gut Microbiome: Connecting Spatial Organization to Function – Carolina Tropini – Cell Host & Microbe

Lactobacillus casei DG and its postbiotic reduce the inflammatory mucosal response: an ex-vivo organ culture model of post-infectious irritable bowel syndrome – Compare D – BMC Gastroenterology

Animal experiments

Age-Associated Microbial Dysbiosis Promotes Intestinal Permeability, Systemic Inflammation, and Macrophage Dysfunction – Netusha Thevaranjan – Cell Host & Microbe

Animal microbiome

PrePrint – Succession of embryonic and intestinal bacterial communities of Atlantic salmon – Jep Lokesh – bioRxiv

The Role of Rumen Microbiome on Feed Efficiency of Grazing Cattle [page 138] – Leluo Guan – 28th Annual Florida Ruminant Nutrition Symposium

Structure and dynamics of the gut bacterial microbiota of the bark beetle, Dendroctonus rhizophagus (Curculionidae: Scolytinae) across their life stages – Carlos Iván Briones-Roblero – PLOS One

Plant, root, and soil microbiome

The role of soil chemistry and plant neighbourhoods in structuring fungal communities in three Panamanian rainforests – Tyler Schappe – Journal of Ecology

Host plant compatibility shapes the proteogenome of Frankia coriariae – Amir Ktari – Frontiers in Microbiology

Managing and manipulating the rhizosphere microbiome for plant health: A systems approach – Matthew D. Wallenstein – Rhizosphere

In vitro and In vivo biofilm formation by Azotobacter isolates and its relevance to rhizosphere colonization – Mohd. Musheer Altaf – Rhizosphere

Metabolism of pyrene through phthalic acid pathway by enriched bacterial consortium composed of Pseudomonas, Burkholderia, and Rhodococcus (PBR) – Sagar Vaidya – 3 Biotech

Effects of titanium dioxide nanoparticles on soil microbial communities and wheat biomass – Janine Moll – Soil Biology and Biochemistry

The effect of simulated warming on root dynamics and soil microbial community in an alpine meadow of the Qinghai-Tibet Plateau – Changting Wang – Applied Soil Ecology

Water and extremophile microbiome

Impacts of sea-level rise on sediment microbial community structure and function in two New England salt marshes, USA – Matt R. Simon – Journals of Soils and Sediments

A critical assessment of the microorganisms proposed to be important to enhanced biological phosphorus removal in full-scale wastewater treatment systems – Mikkel Stokholm-Bjerregaard – Frontiers in Microbiology

Applicability of cryoconite consortia of microorganisms and glacier-dwelling animals in astrobiological studies – Krzysztof Zawierucha – Contemporary Trends in Geoscience

Built environment

Review – Microbiological diagnosis of device-related biofilm infections – Yijuan Xu – APMIS

Patent Application – MONITORING AND MANAGING A FACILITY MICROBIOME – Dillon, Harrison – Free Patents Online

Microbes in space

Origins of Life on Mars: NASA’s Rovers Were Never Sterilized – Rhawn Gabriel Joseph – Cosmology.com

Phages and viruses

Mini Review Article – Phages in the Human Body – Ferran Navarro – Frontiers in Microbiology

Bioinformatics

* A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes – Wontack Han – Research in Computational Molecular Biology. RECOMB 2017.

Techniques

Effect of environmental variation on estimating the bacterial species richness – Jongjian Chen – Frontiers in Microbiology

Thesis – USE OF MOLECULAR METHODS IN BIOTHREAT PREPAREDNESS – Katja Koskela – National Defense University: Research Publications No. 13

Microbes in the news

Pets During Pregnancy Trigger Gut Bacteria Changes for Infants That May Cut Obesity Risk, Study Finds

Gut microbiome dysregulation implicated in OCD

Microbes on the market

Innovative Microbiome-based IBD Therapeutics to Be Developed Under New Partnership

Microbiome drug candidate prevents recurrence of C. difficile infection

Ed’s non-microbiology picks

Climate change causes glacial river in Yukon to change direction

Self-taught artificial intelligence beats doctors at predicting heart attacks

Stroke rates appear to be rising steadily in young adults

Costs of Selective Attention: When Children Notice What Adults Miss – Daniel J. Plebanek – APS

California Dryness and Recovery Challenge Multi-Century Odds

April 15, 2017

Posted on by

Few interesting articles for your Saturday morning digest:   Urbanization alters the physicochemical environment: A new study suggests that urban soil archaeal and bacterial communities are not vulnerable to biodiversity loss, whereas global diversity loss of ectomycorrhizal fungi was observed.  Researchers believe they have found a method of hunting for buried landmines and explosive devices using a combination of engineered bacteria and lasers.    And another reason to be engaged in sports activities: a study highlights differences of microbiota and secondary metabolites in elite athletes.

General microbiome

Remote detection of buried landmines using a bacterial sensor – Shimshon Belkin – Nature Biotech

Next-generation approaches to understand and combat the antibiotic resistome – Terence S. Crofts – Nature Reviews

Human Oral Microbiome

Microbiomes of the normal middle ear and ears with chronic otitis media – Shujiro B. Minami – Laryngoscope

Human gut microbiome

The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level– Wiley Barton – Gut

The MS-Associated Gut Microbiome – Sergio E Baranzini – Multiple Sclerosis Journal

Mental Health

Oral treatment with Lactobacillus rhamnosus attenuates behavioral deficits and immune changes in chronic social stress – Aadil Bharwani – BMC Medicine

Animal microbiome

Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut – Janneke P. Ouwerkerk – Genome Announcements

Water and extremophile microbiome

Spatial variation in bacterial community in natural wetland-river-sea ecosystems –
Hongxia Zhang – J. of Basic Microbiology

Built environment

Urbanization erodes ectomycorrhizal fungal diversity and may cause microbial communities to converge – Dietrich JE Schmidt -Nature Ecology & Evolution

Prebiotics

Prebiotic evaluation of red seaweed (Kappaphycus alvarezii) using in vitro colon model – DM Bajury – International Journal of Food Sciences and Nutrition

April 13, 2017

Posted on by

Profiles of ulcerative colitis patients’ microbiota after fecal microbiota transplantation, a bioinformatics software package for rarefaction analysis, an artist who uses sweat and bacteria to create scents and sculptures.

General microbiome

Review: Microbial metabolites in nutrition, healthcare and agriculture – Rajendra Singh – 3 Biotech

Review: Modified Mediterranean Diet for Enrichment of Short Chain Fatty Acids: Potential Adjunctive Therapeutic to Target Immune and Metabolic Dysfunction in Schizophrenia? – Jamie Joseph – Frontiers in Neuroscience

Human respiratory microbiome

The Nasopharyngeal Microbiota of Children with Respiratory Infections in Botswana – Matthew S Kelly – Pediatric Infectious Disease Journal

Human gut microbiome

* Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation – Susana Fuentes – ISME Journal

Intestinal microbiome in children with severe and complicated acute viral gastroenteritis – Shih-Yen Chen – Scientific Reports

Unusual active site location and catalytic apparatus in a glycoside hydrolase family – Jose Munoz-Munoz – PNAS

Animal experiments

Enterococcus faecalis bacteriocin EntV inhibits hyphal morphogenesis, biofilm formation, and virulence of Candida albicans – Carrie E Graham – PNAS

The therapeutic protection of a living and dead Lactobacillus strain against aluminum-induced brain and liver injuries in C57BL/6 mice – Fengwei Tian & Leilei Yu – PLOS One

Microscale spatial analysis provides evidence for adhesive monopolization of dietary nutrients by specific intestinal bacteria – Yusuke Nagara – PLOS One

Review: Caspase recruitment domain 9, microbiota, and tryptophan metabolism: dangerous liaisons in inflammatory bowel diseases – Bruno Lamas – Current Opinion in Clinical Nutrition and Metabolic Care

Individual variation of natural D. melanogaster associated bacterial communities – Yun Wang – bioRxiv

Plant, root, and soil microbiome

A new polyketide glycoside from the rhizospheric Clonostachys rogersoniana associated with Panax notoginseng – Tian-Peng Yin – Journal of Asian Natural Products Research

Bacterial carbon use plasticity, phylogenetic diversity and the priming of soil organic matter – Ember M Morrissey – ISME Journal

Population and function analysis of cultivable bacteria associated with spores of arbuscular mycorrhizal fungus Gigaspora margarita – Liangkun Long – 3 Biotech

Water and extremophile microbiome

Exploring the ecological coherence between the spatial and temporal patterns of bacterioplankton in boreal lakes – Juan P. Niño García – Frontiers in Microbiology

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems – Sean P Jungbluth – PeerJ

Bacterial community composition and dynamics spanning five years in freshwater bog lakes – Alexandra M Linz – bioRxiv

Occurrence of high-diversity metazoan- to microbial-dominated bioconstructions in a shallow Kimmeridgian carbonate ramp (Jabaloyas, Spain) – G San Miguel – Facies

Expression patterns of elemental cycling genes in the Amazon River Plume – Brandon M Satinsky – ISME Journal

Built environment

Comparison of microbial community shifts in two parallel multi-step drinking water treatment processes – Jiajiong Xu – Applied Microbiology and Biotechnology

Probiotics/prebiotics

Engineered probiotic Escherichia coli can eliminate and prevent Pseudomonas aeruginosa gut infection in animal models – In Young Hwang – Nature Communications

Review: Unraveling the Differences between Gram-Positive and Gram-Negative Probiotics in Modulating Protective Immunity to Enteric Infections – Sukumar Kandasamy – Frontiers in Immunology

Bioinformatics

* RTK: efficient rarefaction analysis of large datasets – Paul Saary – Bioinformatics

A geographically-diverse collection of 418 human gut microbiome pathway genome databases – Aria S Hahn – Scientific Data

Metabolomics

Indolepropionic acid and novel lipid metabolites are associated with a lower risk of type 2 diabetes in the Finnish Diabetes Prevention Study – Vanessa D de Mello – Scientific Reports

More microbes

Influences of dissolved oxygen concentration on biocathodic microbial communities in microbial fuel cells – Laura Rago – Bioelectrochemistry

Microbes in the news

Waste-munching bacteria could make nuclear stores safer – Sam Wong – New Scientist

‘Young poo’ makes aged fish live longer – Ewen Callaway – Nature

Microbiology: Gut microbes augment neurodegeneration – Daniel Erny – Nature

* This Artist Turns Sweat and Bacteria Into Art – Annie Tittiger – Wired

Science, publishing, and career

* Why do scientists fabricate and falsify data? A matched-control analysis of papers containing problematic image duplications – Daniele Fanelli – bioRxiv

Amy’s non-microbiology picks

Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity – Danish Saleheen – Nature

April 8, 2017

Posted on by
General microbiome

Modeling The Consequences Of Heterogeneity In Microbial Population Dynamics – Helena Herrmann – BioRxiv

Human respiratory microbiome

16S rRNA Gene Sequencing Reveals Site-Specific Signatures Of The Upper And Lower Airways Of Cystic Fibrosis Patients – Sarah K. Lucas – BioRxiv

Review: Airway microbial dysbiosis in asthmatic patients: A target for prevention and treatment? – Kian Fan Chung – The Journal of Allergy and Clinical Immunology

Human skin microbiome

Toxification of polycyclic aromatic hydrocarbons by commensal bacteria from human skin – Juliane Sowada – Archives of Toxicology

Human gut microbiome

Long-term use of antibiotics and risk of colorectal adenoma – Yin Cao – Gut

Changes in Composition of the Gut Bacterial Microbiome after Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in a Pediatric Heart Transplant Patient – Kyle L. Flannigan – Frontiers in Cardiovascular Medicine

Animal experiments

Iron Supplements Modulate Colon Microbiota Composition and Potentiate the Protective Effects of Probiotics in Dextran Sodium Sulfate-induced Colitis – Marco Constante – Inflammatory Bowel Diseases

Animal microbiome

Intestinal microbiota of healthy and unhealthy Atlantic salmon Salmo salar L. in a recirculating aquaculture system – Chun Wang – Chinese Journal of Oceanology and Limnology

Identification and modes of action of endogenous bacteria in taphonomy of embryos and larvae – Justin L. Eagan – Palaios

Microbial community compositions in the gastrointestinal tract of Chinese Mongolian sheep using Illumina MiSeq sequencing revealed high microbial diversity – Yan Zeng – AMB Express

Skin microbiota differs drastically between co-occurring frogs and newts – Molly C. Bletz – The Royal Society Open Science

Amphibian skin microbiota exhibits temporal variation in community structure but stability of predicted Bd-inhibitory function – Molly C Bletz – ISME

Plant, root, and soil microbiome

Characterization of a metagenome-derived protease from contaminated agricultural soil microorganisms and its random mutagenesis – Chengjian Jiang – Folia Microbiologica

Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests – Luis E Castañeda – PeerJ

Initial nitrogen enrichment conditions determines variations in nitrogen substrate utilization by heterotrophic bacterial isolates – Suchismita Ghosh – BMC Microbiology

Sequential bioavailability of sedimentary organic matter to heterotrophic bacteria – Nagissa Mahmoudi – Environmental Microbiology

Seasonal and interannual dynamics of soil microbial biomass and available nitrogen in an alpine meadow in the eastern part of Qinghai-Tibet Plateau, China – Bo Xu – Biogeosciences

Microbial Functional Capacity Is Preserved Within Engineered Soil Formulations Used In Mine Site Restoration – Deepak Kumaresan – Scientific Reports

Keystone microbial taxa regulate the invasion of a fungal pathogen in agro-ecosystems – P. Trivedi – Soil Biology and Biochemistry

Water and extremophile microbiome

Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater – William B. Ludington – PLOS ONE

Hidden diversity revealed by genome-resolved metagenomics of iron-oxidizing microbial mats from Lō’ihi Seamount, Hawai’i – Heather Fullerton – ISME

Performance and microbial community analysis in a modified anaerobic inclining-baffled reactor treating recycled paper mill effluent – Haider M. Zwain – Environmental Science and Pollution Research

Microbial formation of labile organic carbon in Antarctic glacial environments – H. J. Smith – Nature Geoscience

Review: Cryospheric science: The power of glacial microbes – Elizabeth B. Kujawinski – Nature Geoscience

Taxonomic composition of Lake Baikal bacterioneuston communities – A. D. Galach’yants – Microbiology

Performance and microbial population dynamics during stable operation and reactivation after extended idle conditions in an aerobic granular sequencing batch reactor – Qiulai He – Bioresource Technology

Comparative metagenomics reveals insights into the deep-sea adaptation mechanism of the microorganisms in Iheya hydrothermal fields – Hai-liang Wang – Journal of Marine Systems

Built environment

Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City – Julia M. Maritz – PLOS ONE

Food microbiology

The Dynamic Microbiota Profile During Pepper (Piper nigrum L.) Peeling by Solid-State Fermentation – Qisong Hu – Current Microbiology

Molecular investigation of bacterial communities during the manufacturing and ripening of semi-hard Iranian Liqvan cheese – M. Ramezani – Food Microbiology

Identification of microbial communities, with a focus on foodborne pathogens, during kimchi manufacturing process using culture-independent and -dependent analyses – Hae-Won Lee – LWT – Food Science and Technology

Probiotics / prebiotics

Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial – Judit Villar-García – PLOS ONE

Phages and viruses

Taxonomic variability and functional stability in microbial communities infected by phages – Stilianos Louca – Environmental Microbiology

Bioinformatics

EzMap: A Simple Pipeline for Reproducible Analysis of the Human Virome – Patrick Czeczko – Bioinformatics

Microbes in the news

You Should Appreciate Germs – Bill Gates

Microbes on the market

The expanding ecosystem of microbiome startups – Juliet Preston – MedCity News

April 4, 2017

Posted on by

General microbiome

Diversity of fungus-growing termites (Macrotermes) and their fungal symbionts (Termitomyces) in the semiarid Tsavo Ecosystem, Kenya – R Vesala – Biotropica

Indole signalling and (micro)algal auxins decrease the virulence of Vibrio campbellii, a major pathogen of aquatic organisms – Q Yang – Environmental Microbiology

Large population study shows that adolescents with celiac disease have an increased risk of multiple autoimmune and nonautoimmune comorbidities –  A Assa – Acta Paediatrica

In vitro fermentation of oat β-glucan and hydrolysates by fecal microbiota and selected probiotic strains – JL Dong – Journal of the Science of Food and Agriculture

 

Human gut microbiome

Gastric microbiota features associated with cancer risk factors and clinical outcomes: A pilot study in gastric cardia cancer patients from Shanxi, China – G Yu – International Journal of Cancer

 

Animal microbiome

Host species shapes the co-occurrence patterns rather than diversity of stomach bacterial communities in pikas – H Li – Applied Microbiology and Biotechnology

 

Plant, root and soil microbiome

Phylloplane bacteria increase the negative impact of food limitation on insect fitness – GL Olson – Ecological Entomology

Bodyguards: Pathogen-Derived Decoys That Protect Virulence Factors – JK Paulus – Trends in Plant Science

Response of the rhizosphere prokaryotic community of barley (Hordeum vulgare L.) to elevated atmospheric CO2 concentration in open-top chambers – M Szoboszlay – Microbiology Open

Draft Genome Sequence of Pseudomonas putida Strain GM4FR, an Endophytic Bacterium Isolated from Festuca rubra L. – F Wemheuer – Genome Announcements

Phytoremediation of Petroleum-Contaminated Soil in Association with Soil Bacteria – P Pokethitiyook – Phytoremediation

Phytoremediation of Salt-Impacted Soils and Use of Plant Growth-Promoting Rhizobacteria (PGPR) to Enhance Phytoremediation – KE Gerhardt – Phytoremediation

Genomic identification and characterization of the elite strains Bradyrhizobium yuanmingense BR 3267 and Bradyrhizobium pachyrhizi BR 3262 recommended for cowpea inoculation in Brazil – J Leite – Brazilian Journal of Microbiology

Effect of elevated nitrate on biodegradation of pentabromodiphenyl ether (BDE-99) and change in microbial communities during groundwater recharge with tertiary-treated municipal wastewater – Y Yan – International Biodeterioration & Biodegradation

The tale of a neglected energy source: Elevated hydrogen exposure affects both microbial diversity and function in soil – M Khdhiri – Applied and Environmental Microbiology

 

Water and extremophile microbiome

Production and persistence of bacterial and labile organic matter at the hypoxic water–sediment interface of the St. Lawrence Estuary – M Hébert – Limnology and Oceanography

Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria – S Muthusamy – Environmental Microbiology

Spatiotemporal dynamics of bacterial community composition in large shallow eutrophic Lake Taihu: High overlap between free-living and particle-attached assemblages – X Tang – Limnology and Oceanography

 

Built environment

Coarse-graining bacteria colonies for modelling critical solute distributions in picolitre bioreactors for bacterial studies on single-cell level – C Westerwalbesloh – Microbial Biotechnology

 

Phages and Virus

Short-Sighted Virus Evolution and a Germline Hypothesis for Chronic Viral Infections – KA Lythgoe – Trends in Microbiology

Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria–plasmid–phage interaction – E Harrison – Molecular Ecology

 

Techniques

*Review: Bioelectrochemical Systems for Measuring Microbial Cellular Functions – HMM Selim – Electroanalysis

Engineering bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation – KNM Daeffler – Molecular Systems Biology

Impact of Contaminating DNA in Whole Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis – M Thoendel – Journal of Clinical Microbiology

Genomics and Metagenomics in Microbial Ecology: Recent Advances and Challenges  – T Narihiro – Microbes and Environments

A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam –  S Das – Genomics Data

Optimization of a bioassay to evaluate Escherichia coli stress responses – B Cunha – IEEE

 

More microbes

*Review: Shapeshifting to Survive: Shape Determination and Regulation in Caulobacter crescentus – SA Woldemeskel – Trends in Microbiology

 

Microbes in news

Antibiotic Resistant Bacteria Common in Diabetic Foot Ulcers – S Gupta – Endocrinology Advisor

Fighting Antibiotic-Resistant Bacteria in Food Animals – J Bartel – Veterinary Medicine News

Vets warn dog owners about potentially deadly bacteria lurking in water – A Lasker – Lifestyle

Magnetic brain stimulation causes weight loss by making gut bacteria healthier – The Endocrine Society – Science Daily

Vapour droplets from threatened orcas show pneumonia bacteria – Waterloo Region Record – TheRecord.com

Hitchhiking Earth bacteria could evolve to live on Mars – M Irving – New Atlas

Bionic leaf turns air, water, sunlight and bacteria into fertilizer – B Hays – UPI

Nicholls sophomore researches antibiotic-resistant bacteria – G Ohlmeyer – Houmatoday.com

What the Bacteria in Your Mouth May Reveal About Your Cancer Risk – SG Miller – Live Science

March 23, 2017

Posted on by

Today’s digest has quite a few papers in the human oral and gut microbiome with many interesting papers as the one from M. Lepczyńska addressing positive aspects of various diets on gut microbiota and its fight with parasites. In ‘Water microbiome’ you can take a look at Raquel S. Peixoto’s paper and beneficial microbes maintaining coral health, while in ‘Microbes in News’ you can read how team from Korea is tackling one of medicine’s most pressing problems – antibiotic resistance by using bacteria to fight bacteria.

General microbiome

Reduced microbial diversity in adult survivors of childhood acute lymphoblastic leukemia and microbial associations with increased immune activation – Ling Ling Chua -Microbiome

Pregnancy and early life

Manipulating the baby biome: What are the issues? – Lai-yang Lee – Australian and New Zealand Journal of Obstetrics and Gynaecology (ANZJOG)

Ex vivo infection of human placental chorionic villi explants with Trypanosoma cruzi and Toxoplasma gondii induces different Toll-like receptor expression and cytokine/chemokine profiles – Christian Castillo – American Journal of Reproductive Immunology (AJRI)

First foods and gut microbes – Martin F. Laursen – Frontiers in Microbiology

Reproductive microbiomes a new thread in the microbial network – Michael L. Power – Reproductive Sciences

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates – Matthew R Olm – Genome Research

 
Human Oral

 
Differential responses of human dendritic cells to metabolites from the oral/airway microbiome – K. Whiteson – Clinical & Experimental Immunology

Candida albicans alters the bacterial microbiome of early in vitro oral biofilms – M. M. Janus – Journal of Oral Microbiology

Probiotic Lactobacillus reuteri has antifungal effects on oral Candida species in vitro – Mette Rose Jørgensen – Journal of Oral Microbiology

Porphyromonas gingivalis is the most abundant species detected in coronary and femoral arteries – J-L. C. Mougeot – Journal of Oral Microbiology

Oral microbiome in HIV-associated periodontitis – Noguera-Julian – Medicine

Quorum sensing of Streptococcus mutans is activated by Aggregatibacter actinomycetemcomitans and by the periodontal microbiome – Szymon P. Szafrański – BMC Genomics

Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status – Jôice Dias Corrêa – Microbiome
Human nearly-sterile sites 

Alterations in gastric microbiota after H. Pylori eradication and in different histological stages of gastric carcinogenesis – Tung Hiu Li – Scientific Reports

Human gut microbiome

Oral iron supplementation: Potential implications for the gut microbiome and metabolome in patients with CKD – Guus A. M. Kortman – Hemodialysis International

Hugonella massiliensis gen. nov., sp. nov., genome sequence, and description of a new strictly anaerobic bacterium isolated from the human gut – Ziena Elsawi – Microbiology Open

Gut microbiota: Neonatal gut microbiota induces lung immunity against pneumonia – Sabrina Tamburini – Nature Reviews Gastroenterology & Hepatology

*Review: Blastocystis: how do specific diets and human gut microbiota affect its development and pathogenicity? – M. Lepczyńska – European Journal of Clinical Microbiology & Infectious Diseases

Dysbiosis and compositional alterations with aging in the gut microbiota of patients with heart failure – Takehiro Kamo – PLOS One

Complex pectin metabolism by gut bacteria reveals novel catalytic functions – Didier Ndeh – Nature

Proteobacteria explain significant functional variability in the human gut microbiome – Patrick H. Bradley  – Microbiome

Animal experiments

Rice- or pork-based diets with similar calorie and content result in different rat gut microbiota – Xiaozhe Qi – International Journal of Food Sciences and Nutrition

Perturbation of microbiota in one-day old broiler chickens with antibiotic for 24 hours negatively affects intestinal immune development – Dirkjan Schokker – BMC Genomics

Effects of dietary administration of Shewanella xiamenensis A-1, Aeromonas veronii A-7, and Bacillus subtilis, single or combined, on the Grass Carp (Ctenopharyngodon idella) intestinal microbiota – Kai Hao – Probiotics and Antimicrobial Proteins

Plant, root, and soil microbiome

Pseudomonas sesami sp. nov., a plant growth-promoting Gammaproteobacteria isolated from the rhizosphere of Sesamum indicum L. – Munusamy Madhaiyan – Antonie van Leeuwenhoek

The influence of environmental factors on communities of arbuscular mycorrhizal fungi associated with Chenopodium ambrosioides revealed by MiSeq sequencing investigation – Xihui Xu -Sceintific Reports

Compositional stability of the bacterial community in a climate-sensitive sub-Arctic peatland – James T. Weedon – Frontiers in Microbiology

Antibiotic and heavy metal tolerance of some indigenous bacteria isolated from petroleum contaminated soil sediments with a study – Jai Godheja – International Journal of Current Microbiology and Applied Science (IJCMAS)

Water and extremophile microbiome 

Genome reduction and microbe-host interactions drive adaptation of a sulfur-oxidizing bacterium associated with a cold seep sponge – Ren-Mao Tian – mSystems

Impact of hypoxia on gene expression patterns by the human pathogen, Vibrio vulnificus, and bacterial community composition in a North Carolina estuary – Britney L. Phippen – Geohealth

Distribution of anaerobic carbon monoxide dehydrogenase genes in deep subseafloor sediments – T. Hoshino – Letters in Applied Microbiology

Phytoplankton species richness, evenness, and production in relation to nutrient availability and imbalance – Sirpa Lehtinen – Limnology and Oceanography

Metagenomic and culture-dependent analysis of the bacterial diversity of a hot spring reservoir as a function of the seasonal variation – B. A. Kikani – International Journal of Environmental Research

Beneficial microorganisms for corals (BMC): Proposed mechanisms for coral health and resilience – Raquel S. Peixoto – Frontiers in Microbiology

High-throughput amplicon sequencing and stream benthic bacteria: identifying the best taxonomic level for multiple-stressor research – R. K. Salis – Scientific Reports

Highlighting of quorum sensing lux genes and their expression in the hydrothermal vent shrimp Rimicaris exoculata ectosymbiontic community. Possible use as biogeographic markers – Simon Le Bloa – PLOS One

Molecular insights on dissolved organic matter transformation by supraglacial microbial communities – Runa Antony – Environmental Science & Technology

An alternative polysaccharide uptake mechanism of marine bacteria – Greta Reintjes – ISME Journal

Viable cold-tolerant iron-reducing microorganisms in geographically diverse subglacial environments – Sophie L. Nixon – Biogeosciences

Different bacterial communities involved in peptide decomposition between normoxic and hypoxic coastal waters – Shuting Liu – Frontiers in Microbiology

Temperature- and size-scaling of phytoplankton population growth rates: Reconciling the Eppley curve and the metabolic theory of ecology – Colin T. Kremer – Limnology and Oceanography

Contrasting patterns of diversity of abundant and rare bacterioplankton in freshwater lakes along an elevation gradient – Huabing Li – Limnology and Oceanography

 Built environment 

Short-term effects of great cormorant droppings on water quality and microbial community of an artificial agricultural reservoir – Il Han – Journal of Environmental Quality

Probiotics / prebiotics

Review: Gut microbiota and bacterial translocation in digestive surgery: the impact of probiotics – Shunichiro Komatsu – Langenbeck’s Archives of Surgery

Techniques

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach – Bonnie L. Brown – Gigascience

Microbes in the news 

Diabetes patients can lower blood sugar through gut bacteria; fecal microbes found to have curative properties – The Science Times

Predatory bacteria as a new ‘living’ antibiotic -Phys Org

Achievements of the human microbiome project – News Medical Life Sciences

Warning: current ecological microbiome may be on the verge of disaster due to antibiotics – Nature World News

 

March 18, 2017

Posted on by
Events and jobs

Research Fellow in Omics analysis – King’s College London – Apply by April 12, 2017

Postdoctoral Research Position in Marine Microbial Ecology – University of Southern Mississippi

General microbiome

Microbial Influences in Cardio–Metabolic Diseases – Rachel Petersen – New York Academy of Sciences

*Review: Microbiota: a key orchestrator of cancer therapy – Soumen Roy – Nature Reviews Cancer

*Review: Caenorhabditis elegans as a model for microbiome research – Fan Zhang – Frontiers in Microbiology

Human respiratory microbiome

The relationship between nasopharyngeal CCL5 and microbiota on disease severity among infants with bronchiolitis – Kohei Hasegawa – Allergy

Human gut microbiome

The Food Contaminant Deoxynivalenol Exacerbates the Genotoxicity of Gut Microbiota – Delphine Payros – mBio

Delayed utilization of some fast-fermenting soluble dietary fibers by human gut microbiota when presented in a mixture – Yunus E. Tuncil – Journal of Functional Foods

Animal experiments

Deciphering the combinatorial influence of diet and the microbiota on experimental colitis – Sean R. Llewellyn – bioRxiv

The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish – Keaton Stagaman – ISME J

Animal microbiome

Comparison of bacterial populations in bedding material, on teat ends, and in milk of cows housed in compost bedded pack barns – R. L. Albino – Animal Production Science

Community analysis of microbial sharing and specialization in a Costa Rican ant–plant–hemipteran symbiosis – Elizabeth G. Pringle – Proceedings of the Royal Society Biological Sciences

Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment – Till Röthig – Scientific Reports

Plant, root, and soil microbiome

Root microbiota drive direct integration of phosphate stress and immunity – Gabriel Castrillo – Nature

Striking alterations in the soil bacterial community structure and functioning of the biological N cycle induced by Pennisetum setaceum invasion in a semiarid environment – G. Rodríguez-Caballero – Soil Biology and Biochemistry

Plant growth promoting rhizobacteria are more effective under drought: a meta-analysis – Rachel L. Rubin – Plant and Soil

Effect of biodynamic soil amendments on microbial communities in comparison with inorganic fertilization – Sibylle Faust – Applied Soil Ecology

Water and extremophile microbiome

Bacterial diversity in fumarole environments of the Paricutín volcano, Michoacán (Mexico) – Miguel Medrano-Santillana – Extremophiles

Prokaryotic Abundance and Activity in Permafrost of the Northern Victoria Land and Upper Victoria Valley (Antarctica) – Rosabruna La Ferla – Microbial Ecology

Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data – Michelle A. Allen – Scientific Reports

A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater – Flavia Flaviani – Viruses

Built environment

Microbial dynamics in anaerobic digestion reactors for treating organic urban residues during the start-up process – Rocio J. Alcántara-Hernández – Letters in Applied Microbiology

Variability of airborne bacteria in an urban Mediterranean area (Thessaloniki, Greece) – Savvas Genitsaris – Atmospheric Environment

*Review: A review of microscopy and comparative molecular-based methods to characterize “Plastisphere” communities – Caroline De Tender – Analytical Methods

Techniques

*Review: Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data – Jian Xu – Engineering

*Review: Metaproteomic strategies and applications for gut microbial research – Mingming Xiao – Applied Microbiology and Biotechnology

Microbes in the news

Bacteria-Enriched Lotion Battles Skin Infections – Jenna Flannigan – Live Science

Frozen, Freeze-dried Products for Fecal Microbiota Transplantation as Effective as Fresh? – Pharmacy Times

Study by Irish scientists finds porridge to be good for the heart and gut – RTE

Certain Bacteria Within Gut Microbiome May Halt Inflammation Naturally, Study Says – Patricia Inacio – IBD News Today

Antibiotic overuse might be bad for bees – Mary Beth Griggs – Popular Science

Microbiome research Studies aim to help health, environment – David Wahlberg – The Times Record

My cats poop for science – Jonathan M. Giltin – ars Technica

Microbes on the market

Seres doubles down on a microbiome do-over as the FDA clears a make-or-break study – John Carroll – Endpoint News

Bacteria Hysteria

Revealed: Which supermarket’s chicken is most likely to contain food poisoning bacteria? – Tom Belger – Liverpool Echo

March 17, 2017

Posted on by

Circadian clocks are ubiquitous timing systems that induce rhythms of biological activities in synchrony with night and day.In the first highlighted paper the authors present the structural basis of the day-night transition in a cyanobacterial circadian clock. The second highlighted paper evaluated the effects of antibiotic treatment on the honeybee gut microbiome. The authors found that exposure to antibiotics significantly alters the honeybee gut microbial community structure and leads to decreased survival.

General microbiome

Biohybrid Microtube Swimmers Driven by Single Captured Bacteria – Morgan M. Stanton – Small

Structural basis of the day-night transition in a bacterial circadian clock – Roger Tseng – Science

Pregnancy and early life

Breast Milk Polyamines and Microbiota Interactions: Impact of Mode of Delivery and Geographical Location – C Gómez-Gallego  – Annals of Nutrition and Metabolism

 
Human respiratory microbiome

Modulation of behaviour and virulence of a high alginate expressing Pseudomonas aeruginosa strain from cystic fibrosis by oral commensal bacterium Streptococcus anginosus – RD Waite  – PLOS One

Human gut microbiome

Transfer of dysbiotic gut microbiota has beneficial effects on host liver metabolism – Simon Nicolas – Molecular Systems Biology

Fecal microbiota transplantation induces hepatitis B virus e-antigen (HBeAg) clearance in patients with positive HBeAg after long-term antiviral therapy – Yan-Dan Ren – Hepatology

The Microbiome and Host Behavior – Vuong HE – Annual Review of Neuroscience

Nonalcoholic Fatty Liver Disease, the Gut Microbiome, and Diet – Zeinab Mokhtari – Advances in Nutrition

Animal experiments

Intestinal transcriptome modulation by functional diets in rainbow trout: A high-throughput sequencing appraisal to highlight GALT immunomodulation – Ana Teresa Gonçalves – Fish & Shellfish Immunology

Effects of Gliadin consumption on the Intestinal Microbiota and Metabolic Homeostasis in Mice Fed a High-fat Diet – Li Zhang – Scientific Reports

Oral administration of synthetic porcine beta-defensin-2 improves growth performance and cecal microbial flora and down-regulates the expression of intestinal toll-like receptor-4 and inflammatory cytokines in weaned piglets challenged with enterotoxigenic Escherichia coli – Zhiru Tang – Animal Science Journal

RNA-Based Stable Isotope Probing Suggests Allobaculum spp. as Particularly Active Glucose Assimilators in a Complex Murine Microbiota Cultured In Vitro – Elena Herrmann – BioMed Research International

Animal microbiome

Antibiotic exposure perturbs the gut microbiota and elevates mortality in honeybees – Kasie Raymann – PLOS Biology

Plant, root, and soil microbiome

Accessing the Carbofuran Degradation Ability of Cultures From Natural River Biofilms in Different Environments – Chien-Jung Tien – CLEAN – Soil, Air, Water

Impact of Agri-Usable Nanocompounds on Soil Microbial Activity: An Indicator of Soil Health – Priyanka Khati – CLEAN – Soil, Air, Water

Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites – Mitja N.P. Remus-Emsermann – SIGS Standards in Genomic Sciences

Is the methanogenic community reflecting the methane emissions of river sediments?—comparison of two study sites – Prem Prashant Chaudhary – Microbiology Open

Water and extremophile microbiome

Characterizing and predicting cyanobacterial blooms in an 8-year amplicon sequencing time-course – Nicolas Tromas – bioRxiv

Effect of pesticides on microbial communities in container aquatic habitats – Ephantus J. Muturi – Scientific Reports

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH – KI Twing – Frontiers in Microbiology

Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer – Ping Zhang – Environmental Science & Technology

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment – Pauliina Rajala – Frontiers in Microbiology

Built environment

Nanoscale zero-valent iron/persulfate enhanced upflow anaerobic sludge blanket reactor for dye removal: Insight into microbial metabolism and microbial community – Fei Pan – Scientific reports

Probiotics / prebiotics

Achieving High Yield of Lactic Acid for Antimicrobial Characterization in Cephalosporin-Resistant Lactobacillus by the Co-Expression of the Phosphofructokinase and Glucokinase – Gong Y – Journal of Microbiology and Biotechnology

Phages and viruses

Inflammation boosts bacteriophage transfer between Salmonella spp.– Médéric Diard – Science

Bioinformatics

microclass: an R-package for 16S taxonomy classification – Kristian Hovde Liland – BMC Bioinformatics

Microbes in the news

Team finds new way that bacteria lay siege to neighboring cells by hijacking two factors involved in protein synthesis – Phys.Org

 

March 4th, 2017

Posted on by
Events and jobs

Head, Microbiome Discovery Research – Johnson & Johnson

Multi-site human microbiome

Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients – Jessica R. Galloway-Peña – Genome Medicine

Human gut microbiome

Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use – K. Korpela – Microbiome

Animal experiments

Metaproteogenomics reveals taxonomic and functional changes between cecal and fecal microbiota in mouse – Alessandro Tanca – Frontiers in Microbiology

Animal microbiome

Cultivable gut bacteria provide a pathway for adaptation of Chrysolina herbacea to Mentha aquatica volatiles – Graziano Pizzolante – BMC Plant Biology

Gut bacteria oversee the special relationship between the green mint leaf beetle and watermint – BMC Series Blog

Effects of tussah immunoreactive substances on growth, immunity, disease resistance against Vibrio splendidus and gut microbiota profile of Apostichopus japonicus – Shuhui Ma – Fish & Shellfish Immunology

Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses – Holly H. Ganz – mSystems

The microbiome of the ant-built home: the microbial communities of a tropical arboreal ant and its nest – Jane Lucas – Ecosphere

*Perspective: Gut microbiome transmission in lizards – Timothy J. Colston – Molecular Ecology

Plant, root, and soil microbiome

Microbial communities in soil chronosequences with distinct parent material: the effect of soil pH and litter quality – Fernando D. Alfaro – Journal of Ecology

Water and extremophile microbiome

Volcanic ash supports a diverse bacterial community in a marine mesocosm – V. Witt – Geobiology

Methylamine as a Nitrogen Source for Microorganisms from a Coastal Marine Environment – Martin Taubert – Environmental Microbiology

Built environment

Response of microbial community structure to pre-acclimation strategies in microbial fuel cells for domestic wastewater treatment – Younghyun Park – Bioresource Technology

Food microbiology

Viable microbial loads on citrus carpoplane during packhouse processing and survival of foodborne pathogens in reconstituted postharvest fungicides – A. Gomba – Journal of Food Safety

Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage – Lysiane Duniere – BMC Microbiology

Probiotics / prebiotics

Microbiome dynamic modulation through functional diets based on pre- and probiotics (mannan-oligosaccharides and Saccharomyces cerevisiae) in juvenile rainbow trout (Oncorhynchus mykiss) – Ana Teresa Gonçalves – Journal of Applied Microbiology

Exploration of the effect of probiotics supplementation on intestinal microbiota of food allergic mice – Bo Yang – American Journal of Translational Research

Phages and viruses

Human norovirus binding to select bacteria representative of the human gut microbiota – Erin A. Almand – PLoS ONE

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean – Yosuke Nishimura – mSphere

Bioinformatics

REPARATION: Ribosome Profiling Assisted (Re-)Annotation of Bacterial
genomes – Elvis Ndah – BioRxiv

Normalization and microbial differential abundance strategies depend upon data characteristics – Sophie Weiss – Microbiome

How conserved are the conserved 16S-rRNA regions? – Marcel Martinez-Porchas – PeerJ

Microbes in the news

Gut bacteria affect intestines and brain in IBS patients – Medical News Today

Intestinal Bacteria Alter Gut and Brain Function – Neuroscience News

Why Are People Sending Poop Through the Mail? For Their Health – GQ Magazine

Microbes on the market

Next-gen microbiome drugs are now on sale, should you buy them? – New Scientist

 

February 24, 2017

Posted on by

Bioassay-guided metabolomics reveal new polyketide macrolactams from termite-associated actinomycete, the microbiota affects host antibody repertoire, artist makes agar molds of her face and grows bacteria on them, the fecal microbiota of Old World vultures.

Events and jobs

“Research Instructor – Microbiology & Immunology” at the Medical University of South Carolina

General microbiome

Review: Carcinogenesis and therapeutics: the microbiota perspective – Matthew C. B. Tsilimigras – Nature Microbiology

Pregnancy and early life

Review: Microbiome, autoimmunity, allergy, and helminth infection: The importance of the pregnancy period – Xian Chen – American Journal of Reproductive Immunology

Impact of microbial invasion of amniotic cavity and the type of microorganisms on short-term neonatal outcome in women with preterm labor and intact membranes – Teresa Cobo – Acta Obstetricia et Gynecologica Scandinavica

Human oral microbiome

Betel nut chewing, oral premalignant lesions, and the oral microbiome – Brenda Y. Hernandez – PLOS One

Human gut microbiome

Review: Gut Microbiota: A Potential Regulator of Neurodevelopment – Paola Tognini – Frontiers in Cellular Neuroscience

New evidences on the altered gut microbiota in autism spectrum disorders – Francesco Strati – Microbiome

Massilioclostridium coli gen. nov., sp. nov., a new member of the Clostridiaceae family isolated from the left colon of a 27-year-old woman – C. I. Lo – New Microbes and New Infections

Impact of humic acids on the colonic microbiome in healthy volunteers – Alexander Swidsinski – World Journal of Gastroenterology

Animal experiments

* IgD class switching is initiated by microbiota and limited to mucosa-associated lymphoid tissue in mice – Jin Huk Choi – PNAS

An Intestinal Farnesoid X Receptor-Ceramide Signaling Axis Modulates Hepatic Gluconeogenesis in Mice – Cen Xie – Diabetes

Effects of xylanase supplementation on growth performance, nutrient digestibility, blood parameters, fecal microbiota, fecal score and fecal noxious gas emission of weaning pigs fed corn-soybean meal-based diet – Ruixia Lan – Animal Science Journal

Animal microbiome

Assessment of Ruminal Bacterial and Archaeal Community Structure in Yak (Bos grunniens) – Zhenming Zhou – Frontiers in Microbiology

Changes in Metabolically Active Bacterial Community during Rumen Development, and Their Alteration by Rhubarb Root Powder Revealed by 16S rRNA Amplicon Sequencing – Zuo Wang – Frontiers in Microbiology

Metataxonomics reveal vultures as a reservoir for Clostridium perfringens – Xiangli Meng – Emerging Microbes and Infections

The fecal microbiome of dogs with exocrine pancreatic insufficiency – Anitha Isaiah – Anaerobe

Plant, root, and soil microbiome

Host-parasite-bacteria triangle: the microbiome of the parasitic weed Phelipanche aegyptiaca and tomato-Solanum lycopersicum (Mill.) as a host – Lilach Iasur Kruh – Frontiers in Plant Science

Diversity of root-associated fungi of Vaccinium mandarinorum along a human disturbance gradient in subtropical forests, China – Yanhua Zhang – Journal of Plant Ecology

Effects of long-term heavy metals contamination on soil microbial characteristics in calcareous agricultural lands (Saiss plain, North Morocco) – A. Kouchou – Journal of Materials and Environmental Sciences

Global transcriptional response to salt shock of the plant microsymbiont Mesorhizobium loti MAFF303099 – Marta Laranjo – Research in Microbiology

Novosphingobium pokkalii sp nov, a novel rhizosphere-associated bacterium with plant beneficial properties isolated from saline-tolerant pokkali rice – Ramya Krishnan – Research in Microbiology

Assembly patterns of soil-dwelling lichens after glacier retreat in the European Alps – Juri Nascimbene – Journal of Biogeography

Soil classification predicts differences in prokaryotic communities across a range of geographically distant soils once pH is accounted for – Rachel Kaminsky – bioRxiv

Water and extremophile microbiome

Different types of diatom-derived extracellular polymeric substances drive changes in heterotrophic bacterial communities from intertidal sediments – Julio Bohorquez – Frontiers in Microbiology

Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core – Deborah C. A. Leite – Frontiers in Microbiology

Built environment

Microbial diversity of a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment: integration of 16S rRNA gene amplicon and shotgun metagenomic sequencing – Tiago Palladino Delforno – MicrobiologyOpen

Metabolomics

* Macrotermycins A−D, Glycosylated Macrolactams from a Termite- Associated Amycolatopsis sp. M39 – Christine Beemelmanns – Organic Letters

compMS2Miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets – William Matthew Bell Edmands – Analytical Chemistry

More microbes

Indole production provides limited benefit to Escherichia coli during co-culture with Enterococcus faecalis – Shelly L. Pringle – Archives of Microbiology

Microbes in the news

* Art Grows on You – Lara Medlam – Nouse

Beware! Are bacteria raising your oxidative stress? – Purna Kashyap – Science Translational Medicine

Microbes on the market

Finch Therapeutics Announces Strategic Collaboration with OpenBiome to Develop Microbiome Therapies for FDA Approval – Business Wire