Category Archives: Extremophiles

June 18, 2016

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Your Saturday Microbiome Digest: CSF metagenomics in multiple sclerosis, Caenorhabditis elegans responses to bacteria, and archaeal communities in permafrost.

Infection and microbes

Only microbial contamination found: Metagenomic Analysis of Cerebrospinal Fluid from Patients with Multiple Sclerosis – Karol Perlejewski – Advances in Experimental Medicine and Biology

Review: The regulation of host defences to infection by the microbiota – Rebecca L. Brown – Immunology

Animal and in vitro experiments

Microbial Community Transplant Results in Increased and Long-Term Oxalate Degradation – Aaron W. Miller – Microbial Ecology

Differential Utilization of Basic Proline-Rich Glycoproteins During Growth of Oral Bacteria in Saliva – Yuan Zhou – Applied and Environmental Microbiology

Caenorhabditis elegans responses to bacteria from its natural habitats – Buck S. Samuel – PNAS

Plant, root, and soil microbiome

Presence and persistence of viable, clinically relevant Legionella pneumophila bacteria in garden soil in the Netherlands – E. van Heijnsbergen – Applied and Environmental Microbiology

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons – C. Ryan Pento – Frontiers in Microbiology

Monitoring fungi in ecological restorations of coastal Indiana, U.S.A. – Peter G. Avis – Restoration Ecology

Review: Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing “Stress-on-Stress” Responses – Hamed Azarbad – MDPI International Journal of Molecular Sciences

Water and extremophile microbiome

Archaeal communities of Arctic methane-containing permafrost – Victoria Shcherbakova – FEMS Microbiology Ecology

Microbial community diversity, structure, and assembly across oxygen gradients in meromictic marine lakes, Palau – Matthew S. Meyerhof – Environmental Microbiology

Bioreactor microbiology

An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant – Vera Ortseifen – Journal of Biotechnology

Bioinformatics

Finds microbial interactions based on PubMed abstracts, so basically finding interactions that were already published (???): @MInter: Automated Text-mining of Microbial Interactions – Lim Kun Ming Kenneth – Bioinformatics

More microbiology

In situ replication rates for uncultivated bacteria in microbial communities – Christopher T Brown – bioRxiv

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities – Sebastian Germerodt – PLOS Computational Biology

Microbes in the news

UWM professor taking a deeper dive on beach pollution data – Milwaukee-Wisconsin Journal Sentinel

The medical revolution that delves into humans’ inner aliens – Robert Matthews – The National

Brewing on the wild side: IU’s Dr. Matthew L. Bochman – Rita Kohn – Nuvo.net

Fecal bacteria and antibiotic resistance genes found in water samples from fly-in Northern Manitoba – Ian Graham – Thompson Citizen

CosmosID, BioCollective Collaborate on Microbiome Analysis Kit – GenomeWeb

June 17, 2016

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Gastric bypass induces persistent gut microbiome changes, omnivorous lizards going vegetarian, new Borrelia species in Australian ticks, a free-living Bradyrhizobium, plant responses to phyllosphere commensals, and chemotrophic microbial populations in Yellowstone hot springs.

Events

HT: Jonathan Eisen: June 20-21 Meeting #2 for NAS Microbiomes of the Built Environment Study. Click here to register for the webcast (free!).

Human respiratory microbiome

Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children – Marcos Pérez-Losada – Microbiome

Human gut microbiome

Antibiotic-induced gut microbiota disruption during human endotoxemia: a randomised controlled study – Jacqueline M Lankelma – Gut
Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota – Albert Palleja – Genome Medicine

Review: Metabolomics of autism spectrum disorders: early insights regarding mammalian-microbial cometabolites – Michele Mussap – Expert Review of Molecular Diagnostics

Review: How the microbiota shapes rheumatic diseases – Tom Van de Wiele – Nature Reviews Rheumatology

Animal and other experiments

Physiological and microbial adjustments to diet quality permit facultative herbivory in an omnivorous lizard – Kevin D. Kohl – Journal of Experimental Biology

Press: How does a lizard go vegetarian? By growing its gut – Patrick Monahan – Science Magazine

Nasal commensal Staphylococcus epidermidis counteracts influenza virus – Hui-Wen Chen – Scientific Reports

Animal microbiome

Diversity, structure and convergent evolution of the global sponge microbiome – Torsten Thomas – Nature Communications

Does canine inflammatory bowel disease influence gut microbial profile and host metabolism? – Jia Xu – BMC Veterinary Research

Novel Borrelia species detected in echidna ticks, Bothriocroton concolor, in Australia – Siew-May Loh – Parasites & Vectors

Press: New bacteria discovered in Australian ticks – MedicalXpress

Plant, root, and soil microbiome

Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes – a genome comparison – Frances Patricia Jones – Scientific Reports

Press: Study unlocks surprising behaviour of soil bacteria – Mark Kinver – BBC

The Arabidopsis leaf transcriptome reveals distinct but also overlapping responses to colonization by phyllosphere commensals and pathogen infection with impact on plant health – Christine Vogel – New Phytologist

DNA from dust: comparative genomics of vaccine-break virus in the field – Utsav Pandey – bioRxiv

Water and extremophile microbiome

Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs – Daniel R. Colman – FEMS Microbiology Ecology

Large shifts among eukaryotes, bacteria, and archaea define the vertical organization of a lake sediment – Christian Wurzbacher – bioRxiv

Microbes in the news

Featuring an All Male Panel: That Gut Feeling: Part One. Dan Saladino discovers the world of the gut microbiota, the vast array of microbes within us all – BBC Radio

Bik’s Picks

Klinefelter’s syndrome (47,XXY) is in excess among men with Sjögren’s syndrome –
Valerie M. Harris – Clinical Immunology

Press: Does X mark the spot? A new clue why autoimmune diseases target women – Oklahoma Medical Research Foundation

June 15, 2016

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Microbiome evolution in vertebrates, post-antibiotic microbial competition for sugars, microbial networks in respiratory infections, bacteria in snow from Australian and Swiss Alps, Yucatan Black and Red soil microbes.

Human oral microbiome

Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-CF bronchiectasis patients – Michael J Cox – bioRxiv

Human skin microbiome

Comprehensive pyrosequencing analysis of the bacterial microbiota of the skin of patients with seborrheic dermatitis – Akiomi Tanaka – Microbiology and Immunology

Review: Can molecular DNA-based techniques unravel the truth about diabetic foot infections? – M. Malone – Diabetes/Metabolism Research and Reviews

Human respiratory microbiome

Mycoplasma pneumoniae and Streptococcus pneumoniae caused different microbial structure and correlation network in lung microbiota – Heping Wang – Journal of Thoracic Disease

Human gut microbiome

Ecophysiological consequences of alcoholism on human gut microbiota: implications for ethanol-related pathogenesis of colon cancer – Atsuki Tsuruya – Scientific Reports

Research highlight: Intimate gut interactions: helminths and the microbiota – Nicola L Harris – Cell Research

Review: Human Gut-on-a-Chip technology: Will this revolutionize our understanding of IBD and future treatments? – Jaewon Lee – Expert Review of Gastroenterology & Hepatology

Review: Dientamoeba fragilis, the Neglected Trichomonad of the Human Bowel – Damien Stark – Clinical Microbiology Reviews

Review: Akkermansia muciniphila: a novel functional microbe with probiotic properties – C. Gómez-Gallego – Beneficial Microbes

Review: Alterations of gut microbiota in patients with irritable bowel syndrome: A systematic review and meta-analysis – Xiaojun Zhuang – Journal of Gastroenterology and Hepatology

Animal and tissue culture experiments

Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion – Franziska Faber – Nature

News and Views: Microbiology: The dark side of antibiotics – Thibault G. Sana & Denise M. Monack – Nature

Genetic and transcriptional analysis of human host response to healthy gut microbiome – Allison L Richards – bioRxiv

The Microbiota Determines Susceptibility to Experimental Autoimmune Uveoretinitis – Jarmila Heissigerova – Journal of Immunology Research

Animal microbiome

Invited Review: Microbiome Evolution Along Divergent Branches of the Vertebrate Tree of Life: What’s Known and Unknown – Timothy J. Colston – Molecular Ecology

Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity – Swapnil Gaikwad – AMB Express

Plant, root, and soil microbiome

Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (Oryza sativa L.) – Wenfeng Wang – Microbiological Research

Yucatán in black and red: Linking edaphic analysis and pyrosequencing-based assessment of bacterial and fungal community structures in the two main kinds of soil of Yucatán State – Héctor Estrada-Medina – Microbiological Research

Water and extremophile microbiome

Global and local-scale variation in bacterial community structure of snow from the Swiss and Australian Alps – Tina Wunderlin – FEMS Microbiology Ecology

Waste, pollution, drinking water microbiology

Assessing the effects of heavy metals in ACC deaminase and IAA production on plant growth-promoting bacteria – Mendoza-Hernández José Carlos – Microbiological Research

Effect of Co-Composting Cattle Manure with Construction and Demolition Waste on the Archaeal, Bacterial, and Fungal Microbiota, and on Antimicrobial Resistance Determinants – Devin B. Holman – PLOS ONE

Anthropogenic impact on mangrove sediments triggers differential responses in the heavy metals and antibiotic resistomes of microbial communities – Lucélia Cabral – Environmental Pollution

Investigation of Archaeal and Bacterial community structure of five different small drinking water networks with special regard to the nitrifying microorganisms – Zsuzsanna Nagymáté – Microbiological Research

A survey of biofilms on wastewater aeration diffusers suggests bacterial community composition and function vary by substrate type and time – Peter A. Noble – Applied Microbiology and Biotechnology

DGGE: Synergistic effect of crude oil plus dispersant on bacterial community in a louisiana salt marsh sediment – Mohammed Al-Jawasim – FEMS Microbiology Letters

Food microbiology

Complexity and Dynamics of the Winemaking Bacterial Communities in Berries, Musts, and Wines from Apulian Grape Cultivars through Time and Space – Marinella Marzano – PLOS ONE

More microbiology

Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B – Caroline Chénard – mBio

Press: Virus Hacks Host Genome, Steals CRISPR to Protect Itself – GenEngNews
Virus uses ‘stolen’ CRISPR to hack its host’s immune system – Science Daily

Microbes in the news

Asgard archaea diversity in estuaries – Roy Rodriguez – REU in Subtropical Marine Ecosystems, University of Texas at Austin

Microbes in pressed grapes may predict flavor metabolites in the finished wine – American Society for Microbiology – EurekAlert

Nanoflowers can detect bacteria before they make you sick: The particles can spot even tiny amounts of E. coli – Mariella Moon – Engadget

BacteriaHysteria: Self-cleaning sheets do exist! Silvon launches bacteria-resistant bedding – Julie Pennell – Today

Science, publishing, and career

Predatory journals: Ban predators from the scientific record – Jeffrey Beall – Nature

Data sharing: A code of conduct for data on epidemics – Ilaria Capua – Nature

June 14, 2016

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Breastfeeding protects against antibiotics’ effect in infants, pediatric gut microbiome after surgery, microbial contribution to regional wine characteristics, microbial hotspots on glacial surfaces, foodwebs in your gut, and much more!

Pregnancy and birth

Association of Early-Life Antibiotic Use and Protective Effects of Breastfeeding – 
Role of the Intestinal Microbiota – Katri Korpela – JAMA Pediatrics

Press: Antibiotics May Blunt Breast-Feeding’s Benefits – Infants given the drugs were prone to infections and obesity in childhood, researchers say – WebMD

Human gut microbiome

The pediatric intestinal mucosal microbiome remains altered after clinical resolution of inflammatory and ischemic disease – Minna M. Wieck – Surgery

Press: Culture Crash: How Common Pediatric Diseases Affect the Healthy Intestinal Microbiome – Children’s Hospital Los Angeles

Systematic Review: Fecal Microbiota Transplantation for Ulcerative Colitis: A Systematic Review and Meta-Analysis – Yanqiang Shi – PLOS ONE

Animal and bioreactor experiments

Vancomycin Treatment Alters Humoral Immunity and Intestinal Microbiota in an Aged Mouse Model of Clostridium difficile Infection – Edward van Opstal – Journal of Infectious Diseases

The structural alteration of gut microbiota in low-birth-weight mice undergoing accelerated postnatal growth – Jingjing Wang – Scientific Reports

MALDI-TOF: Investigation of the interactions between Chrysanthemum morifolium flowers extract and intestinal bacteria from human and rat – Jin-hua Tao – Biomedical Chromatography

Substrate-driven convergence of the microbial community in lignocellulose-amended enrichments of gut microflora from the Canadian beaver (Castor canadensis) and North American moose (Alces americanus) – Mabel Ting Wong – Frontiers in Microbiology

Animal microbiome
Epimicrobiota Associated with the Decay and Recovery of Orbicella Corals Exhibiting Dark Spot Syndrome – Julie L. Meyer – Frontiers in Microbiology

Plant, root, and soil microbiome

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics – Nicholas A. Bokulich – mBio

Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm – Daiva Domenech Tupinambá – Archaea

Effects of Frangula alnus on soil microbial communities and biogeochemical processes in Wisconsin forests – Joel P. Stokdyk – Plant and Soil

Species-specific effects of plant invasions on activity, biomass, and composition of soil microbial communities – Anna M. Stefanowicz – Biology and Fertility of Soils

Water and extremophile microbiome

Review: Biofilms on glacial surfaces: hotspots for biological activity – Heidi J Smith – NPJ Biofilms and Microbiomes

Press: MSU doctoral student publishes research on microbial biofilms and carbon cycling on glacial surfaces – Montana State University

Diversity of culturable bacteria recovered from Pico Bolívar’s glacial and subglacial environments, at 4,950 m, in Venezuelan Tropical Andes – Johnma Rondón – Canadian Journal of Microbiology

Large differences in bacterial community composition among three nearby extreme waterbodies of the high Andean plateau – Pablo Aguilar – Frontiers in Microbiology

The Vertical Distribution of Sediment Archaeal Community in the “Black Bloom” Disturbing Zhushan Bay of Lake Taihu – Xianfang Fan – Archaea

Built environment microbiome / food microbiology

Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community – Stephan Thies – Scientific Reports

Characterization of specific spoilage organisms (SSOs) in vacuum-packed ham by culture-plating techniques and MiSeq next-generation sequencing technologies – Agnieszka Piotrowska-Cyplik – Journal of the Science of Food and Agriculture

Metagenomics and bioinformatics

Linking comparative genomics and environmental distribution patterns of microbial populations through metagenomics – Tom O Delmont – bioRxiv

Species–function relationships shape ecological properties of the human gut microbiome – Sara Vieira-Silva – Nature Microbiology

Press: Unraveling the food web in your gut – The Flanders Institute for Biotechnology – EurekAlert

Protocol: A Brief Review on the Ecological Network Analysis with Applications in the Emerging Medical Ecology – Zhanshan (Sam) Ma – Part of the series Springer Protocols Handbook

Review: The evolution of genome mining in microbes – a review – Nadine Ziemert – Natural Product Reports

Transcriptomics, metabolomics

Integrative analysis of transcriptomic and metabolomic data via sparse canonical correlation analysis with incorporation of biological information – Sandra E. Safo – arXiv

More microbiology

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity – Emanuele Bosi – PNAS

Microbes in the news

Bill Gates, Jennifer Doudna Will Take Podium at ASM Microbe – Ingrid Hein – Medscape

Insights into the ecology of the microbiome: dynamics of the gut, mouth and skin microbiomes of healthy subjects – Science Daily

Podcast: Profile Of A Scientist: Personalized Medicine, Gut Microbes And The Biology Of Space Travel, with Stanford biologist Mike Snyder – WBUR

WPI students may have discovered three new viruses in Worcester soil – Michael D. Kane – MassLive

Electronic sensor that tells dead bacteria from live by measuring ‘osmoregulation’ is potential future tool for medicine and food safety – Purdue University

Oral microbiome rich environment for study, product development, event attendees told – Hank Schultz – Nutraingredients

Take Care of Your Microbiome and Your Microbiome Will Take Care of You – Aaron M. Renn – Urbanophile

Science, publishing, and career

How to make your article easy to review – Part 4 – 25 tips from experienced reviewers on what to look out for before submitting your article – Elsevier

June 13, 2016

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Malassezia’s in horses’ ears, microbes in carnivorous plant pitchers, meta-analysis of arbuscular mycorrhizal fungi , and the metatranscriptome of an alkaline hot sulfur spring.

Pregnancy and birth

Early settlers – which E. coli strains do you not want at birth? – Thomas Secher – Am J Physiol Gastrointest Liver Physiol

Human gut microbiome

Intestinal Microbiota‐Generated Metabolite Trimethylamine‐N‐Oxide and 5‐Year Mortality Risk in Stable Coronary Artery Disease: The Contributory Role of Intestinal Microbiota in a COURAGE‐Like Patient Cohort – Vichai Senthong – Journal of the American Heart Association

Review: Gut microbiota, diet and obesity-related disorders – the good, the bad and the future challenges – Kevin J. Portune – Molecular Nutrition & Food Research

Animal experiments

Gut Microbiota are Linked to Increased Susceptibility to Hepatic Steatosis in Low Aerobic Capacity Rats Fed an Acute High Fat Diet – Matthew R Panasevich – Am J Physiol Gastrointest Liver Physiol

Animal microbiome

Don’t look a gift horse in the ear: Is Malassezia nana the main species in horses’ ear canal microbiome? – Ana Lúcia Aldrovandi – Brazilian Journal of Microbiology

Plant, root, and soil microbiome

Comparative Study of Bacterial Communities in Nepenthes Pitchers and Their Correlation to Species and Fluid Acidity – Pattanop Kanokratana – Microbial Ecology

Riparian reforestation: are there changes in soil carbon and soil microbial communities? – J.E. Mackay – Science of The Total Environment

Home-field advantage? evidence of local adaptation among plants, soil, and arbuscular mycorrhizal fungi through meta-analysis – Megan A. Rúa – BMC Evolutionary Biology

Associations between soil bacterial community structure and nutrient cycling functions in long-term organic farm soils following cover crop and organic fertilizer amendment – Adria L. Fernandez – Science of The Total Environment

Water and extremophile microbiome

Relationship of bacterial richness to organic degradation rate and sediment age in subseafloor sediment – Emily A. Walsh – Applied and Environmental Microbiology

Analysis of the metatranscriptome of microbial communities of an alkaline hot sulfur spring revealed different gene encoding pathway enzymes associated with energy metabolism – Swetaleena Tripathy – Extremophiles

Temperature effects on net greenhouse gas production and bacterial communities in arctic thaw ponds – Karita Negandhi – FEMS Microbiology Ecology

Differences in the sensitivity of fungi and bacteria to season and invertebrates affect leaf litter decomposition in a Mediterranean stream – Juanita Mora-Gómez – FEMS Microbiology Ecology

Microbes in the news

Living Bacteria Can Now Store Data – George Dvorsky – Gizmodo

Note that the images in this article have no sources, and that the second image is showing mice data instead of human: The Bacteria In Your Gut And Cancer – Jack Hidary – Huffington Post

The pioneering dental laser that blasts away bacteria – and could help millions of Brits eradicate chronic gum disease without the need for antibiotics – Hilary Freeman – Daily Mail

Science, publishing, and career

The Mistrust of Science – Commenceent Address at CalTech – Atul Gawande

June 11, 2016

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Microbiome and virome of FMT patient over time, how well do animal models predict natural microbial activities, goats!, Neolithic vs. modern soil, truffles, and a medieval church.

Human gut microbiome

Long-term microbiota and virome in a Zürich patient after fecal transplantation against Clostridium difficile infection – Felix Broecker – Annals of the New York Academy of Sciences

Perspective: Nutrition and the microbiome – Karin Moelling – Annals of the New York Academy of Sciences

Entitled denigrating view of African research, unclear background or IRB approval of volunteers from Africa: Significant pharmacokinetic differences of berberine are attributable to variations in gut microbiota between Africans and Chinese – Raphael N. Alolga – Scientific Reports

Conference report: A Summary of The First HIV Microbiome Workshop 2015 – Brett Williams – AIDS Research and Human Retroviruses

Infection and microbes

No mention of extraction or PCR controls, and most OTUs are shared between samples, so suspicious for contamination. Proceed with caution: High-throughput sequencing of microbial diversity in implant-associated infection – Xin Wang – Infection, Genetics and Evolution

Animal experiments

Metabolomics insights into the modulatory effects of long term low calorie intake in mice – Junfang Wu – Journal of Proteome Research

Perspective: A synthetic ecology perspective: how well does behavior of model organisms in the laboratory predict microbial activities in natural habitats? – Zheng Yu – Frontiers in Microbiology

Animal microbiome

Age and feeding system (supplemental feeding versus grazing) modulates colonic bacterial succession and host mucosal immune maturation in goats – J. Jiao – Journal of Animal Science

Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers – Phillip R. Myer – Journal of Microbiological Methods

Plant, root, and soil microbiome

A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation – Yong-Guan Zhu – Science Bulletin

Mycorrhizal detection of native and non-native truffles in a historic arboretum and the discovery of a new North American species, Tuber arnoldianum sp. nov. – Rosanne A. Healy – Mycorrhiza

Beneficial native bacteria improve survival and mycorrhization of desert truffle mycorrhizal plants in nursery conditions – Alfonso Navarro-Ródenas – Mycorrhiza

Nutrient limitation drives response of Calamagrostis epigejos to arbuscular mycorrhiza in primary succession – Jana Rydlová – Mycorrhiza
http://link.springer.com/article/10.1007/s00572-016-0712-5

Ectomycorrhizal and saprotrophic fungal diversity are linked to different tree community attributes in a field-based tree experiment – Nhu H. Nguyen – Molecular Ecology

Long-term effect of plastic film mulching and fertilization on bacterial communities in a brown soil revealed by high through-put sequencing – John Farmer – Archives of Agronomy and Soil Science

Resilience of Fungal Communities to Elevated CO2 – Stavros D. Veresoglou – Microbial Ecology

Review: Life in heaps: A review of microbial responses to variable acidity in sulfide mineral bioleaching heaps for metal extraction – D.W. Shiers – Research in Microbiology

Review: Giving back to the community: Microbial mechanisms of plant-soil interactions – Sur Herrera Paredes – Functional Ecology

Perspective: History Leaves Its Mark on Soil Bacterial Diversity – Jennifer B. H. Martiny – mBio

Water and extremophile microbiome

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

Response of a coastal tropical pelagic microbial community to changing salinity and temperature – Gurpreet Kaur-Kahlon – Inter-Research in Aquatic Microbial Ecology

Bacterial communities in Arctic first-year drift ice during the winter/spring transition – E. Eronen-Rasimus – Environmental Microbiology Reports

Diversity and distribution of prokaryotes within a shallow-water pockmark field – Donato Giovannelli – Frontiers in Microbiology

Mainly about animals: Life in a dark biosphere: a review of circadian physiology in “arrhythmic” environments – Andrew David Beale – Journal of Comparative Physiology B

Site-specific environmental factors control bacterial and viral diversity in stormwater retention ponds – Matthew A. Saxton – Inter-Research in Aquatic Microbial Ecology

Built environment microbiome

Profile of microbial communities on carbonate stones of the medieval church of San Leonardo di Siponto (Italy) by Illumina-based deep sequencing – Guglielmina Chimienti – Applied Microbiology and Biotechnology

Food microbiology

Cascade degradation of organic matters in brewery wastewater using a continuous stirred microbial electrochemical reactor and analysis of microbial communities – Haiman Wang – Scientific Reports

Bioinformatics and computational biology

Advancing microbial sciences by individual-based modelling – Ferdi L. Hellweger – Nature Reviews Microbiology

Microbes in the news

A Portrait of a Building and its External Inhabitants – Makayla Betts – MicroBEnet

Woman meets Winnipeg researchers whose Ebola treatment saved her life – Bill Redekop – Winnipeg Free Press

Tackling healthcare challenges in a changing world: an interview with Professor Jeremy Nicholson – News Medical

June 10, 2016

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Volunteers taking ETEC, 3 new E. coli phages, oral microbiomes of cats and dogs, skin microbes in Japanese amphibians, fungi and bacteria in floor dust.

Human oral microbiome

The oral microbiome of patients with axial spondyloarthritis compared to healthy individuals – Jordan E. Bisanz – PeerJ

Human vaginal microbiome

Association of Sexual Debut in Adolescents With Microbiota and Inflammatory Markers – Jespers, Vicky – Obstetrics & Gynecology

Human blood ‘microbiome’

Rapid identification of fungi in culture-negative clinical blood and respiratory samples by DNA sequence analyses – Farida Sidiq – BMC Research Notes

Human gut microbiome

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment – Mihai Pop – BMC Genomics

Mucosa-Associated Ileal Microbiota in New-Onset Pediatric Crohn’s Disease – Assa, Amit – Inflammatory Bowel Diseases

Three New Escherichia coli Phages from the Human Gut Show Promising Potential for Phage Therapy – Marion Dalmasso – PLOS ONE

“Free living females” sounded… weird. Soluble Corn Fiber Increases Calcium Absorption Associated with Shifts in the Gut Microbiome: A Randomized Dose-Response Trial in Free-Living Pubertal Females – Corrie M Whisner – Journal of Nutrition

Similar Fecal Microbiota Signatures in Patients With Diarrhea-predominant Irritable Bowel Syndrome and Patients With Depression – Yixuan Liu – Clinical Gastroenterology and Hepatology

DGGE: Differences in the Biodiversity of the Fecal Microbiota of Infants With Rotaviral Diarrhea and Healthy Infants – Peng Fei – Jundishapur Journal of Microbiology

Opinion: How Our Other Genome Controls Our Epi-Genome – Antonella Celluzzi – Trends in Microbiology

Review: The role of the gut microbiota in NAFLD – Christopher Leung – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Diet may influence the oral microbiome composition in cats – Christina J. Adler – Microbiome

Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules – James E. McDonald – PLOS ONE

Bacterial microbiomes from vertically-transmitted fungal inocula of the leaf-cutting ant Atta texana – Lucas A. Meirelles – Environmental Microbiology Reports

Defensive insect symbiont leads to cascading extinctions and community collapse – Dirk Sanders – Ecology Letters

Plant, root, and soil microbiome

Subalpine conifers in two different geographic locations host highly similar foliar bacterial endophyte communities – Alyssa A. Carrell – FEMS Microbiology Ecology

Effect of plant growth-promoting bacteria on the growth and fructan production of Agave americana L. – Neyser De La Torre-Ruiz – Brazilian Journal of Microbiology

Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region – Joana Sabino-Pinto – Microbial Ecology

Water and extremophile microbiome

Benthic protists: the under-charted majority – Dominik Forster – FEMS Microbiology Ecology

Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance – Maren Bornemann – FEMS Microbiology Ecology

Review: How mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes – Elena Kazamia – Ecology Letters

Review: All ecosystems potentially host electrogenic bacteria – Nicolas Chabert – Bioelectrochemistry

Pollution and waste and bioreactor microbiology

Arsenic metabolism and toxicity influenced by ferric iron in simulated gastrointestinal tract and the roles of gut microbiota – Haiyan Yu – Environmental Science & Technology

Pyrosequencing analysis of bacterial diversity in soils contaminated long-term with PAHs and heavy metals: Implications to bioremediation – Saranya Kuppusamy – Journal of Hazardous Materials

A strange combination of samples: Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies – Simon Güllert – Biotechnology for Biofuels

Monitoring the impact of bioaugmentation with a PAH-degrading strain on different soil microbiomes using pyrosequencing – S. Festa – FEMS Microbiology Ecology

Built environment microbiome

Fungal and bacterial growth in floor dust at elevated relative humidity levels – Karen C. Dannemiller – Indoor Air

Bioinformatics and statistics

An Introduction to Programming for Bioscientists: A Python-Based Primer – Berk Ekmekci – PLOS Computational Biology

Ten Simple Rules for Effective Statistical Practice – Robert E. Kass – PLOS Computational Biology

Bipartite Graphs for Visualization Analysis of Microbiome Data – Karel Sedlar – Evolutionary Bioinformatics

Techniques

The source of SYBR green master mix determines outcome of nucleic acid amplification reactions – Jianxin Yang – BMC Research Notes

More microbiology

Ancestral Tryptophan Synthase Reveals Functional Sophistication of Primordial Enzyme Complexes – Florian Busch – Cell Chemical Biology

Press: Ancient enzyme resurrected from the ancestor of all bacteria – Conor Gearin – New Scientist
Bacteria perfected protein complexes more than 3.5 billion years ago – Science Daily

Microbes in the news

Tufts microbiologist Cecilia A. Silva-Valenzuela, Ph.D., named Pew Latin American Fellow
Silva-Valenzuela, in Andrew Camilli’s lab, will investigate novel approaches to prevent cholera outbreaks – EurekAlert

Bio-statistician Albert Parker with MSU’s Center for Biofilm Engineering earns top EPA award – Amanda Eggert – Montana State University

Video series with James Hamblin – The Atlantic
Should You Map Your Microbiome? A visit to uBiome
Your Probiotics Aren’t Doing Anything (Yet)
You Probably Don’t Need to Shower – James Hamblin – The Atlantic

Banking on stool despite an uncertain future – Tina Amirtha – Science

Science, publishing, and career

In effort to understand continuing racial disparities, NIH to test for bias in study sections – Jeffrey Mervis – Science

Triplicated paper with multiplicated cells and images – Leonid Schneider – For Better Science
Author denies accusations of blatant duplication – Shannon Palus – Retraction Watch

Bik’s Picks (it’s not microbiology, but pretty cool)

RhizoTubes as a new tool for high throughput imaging of plant root development and architecture: test, comparison with pot grown plants and validation – Christian Jeudy – Plant Methods

June 9, 2016

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Salivary microbiome in Behcet’s disease, microbial RNA in human blood, acetate implied in metabolic syndrome, effects of fire retardant on plant–microbe interactions, and a book about the marine microbiome.

Events

ASM Microbe TweetUp: Friday June 17, 11.45-12:30, in the Peer-to-Peer Exchange Zone (in the Exhibition Hall)

Focused meeting: Molecular Biology of Archaea 5, London, UK, 1-3 August 2016

Pregnancy and birth

Infant Early Gut Colonization by Lachnospiraceae: High Frequency of Ruminococcus gnavus – Valeria Sagheddu – Frontiers in Pediatrics

Review: The microbiome during pregnancy and early postnatal life – Josef Neu – Seminars in Fetal and Neonatal Medicine

Review: The human milk microbiome and factors influencing its composition and activity – Carlos Gomez-Gallego – Seminars in Fetal and Neonatal Medicine

Human blood microbiome

Total RNA Sequencing reveals microbial communities in human blood and disease specific effects – Serghei Mangul – bioRxiv

Human mouth microbiome

A Study of the Variation in the Salivary Peptide Profiles of Young Healthy Adults Acquired Using MALDI-TOF MS – Andrei Prodan – PLOS ONE

Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet’s disease – Patrick Coit – Clinical Immunology

Human gut microbiome

Review: What’s bugging your teen? —The microbiota and adolescent mental health – Karen-Anne McVey Neufeld – Neuroscience & Biobehavioral Reviews

Bio-banking gut microbiome samples – Shankar Bolan – EMBO Reports

Animal experiments

Acetate mediates a microbiome–brain–β-cell axis to promote metabolic syndrome – Rachel J. Perry – Nature

Press: How altered gut microbes cause obesity – Science Daily
Fecal Transplant Shows Gut Microbes Cause Obesity – In Rats, Anyway – Science 2.0

Sex-specific Effects of Arsenic Exposure on the Trajectory and Function of the Gut Microbiome – Liang Chi – Chemical Research in Toxicology

Taxonomic assessment of rumen microbiota using total RNA and targeted amplicon sequencing approaches – Fuyong Li – Frontiers in Microbiology

Environmental filtering decreases with fish development for the assembly of gut microbiota – Qingyun Yan – Environmental Microbiology

Animal microbiome

Bacterial Community Diversity Harboured by Interacting Species – Mikaël Bili – PLOS ONE

Plant, root, and soil microbiome

Cascading effects of fire retardant on plant–microbe interactions, community composition, and invasion – Abigail Marshall – Ecological Applications

Temperature sensitivity of soil microbial communities: An application of macromolecular rate theory to microbial respiration – Charlotte J. Alster – Journal of Geophysical Research

Selection and evaluation of microorganisms for biocontrol of Verticillium dahliae in olive – A Varo – Journal of Applied Microbiology

Influence of plant genotype on the cultivable fungi associated to tomato rhizosphere and roots in different soils – Anna Poli – Fungal Biology

Arbuscular mycorrhizal fungal communities in buffelgrass pasture under intercropping and shading systems in Brazilian semiarid conditions – Karen M.S. Menezes – Agriculture, Ecosystems & Environment

Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression – Adam J. Book – PLOS Biology

Press: Chemistry lessons from bacteria may improve biofuel production – Science Daily

Review: Streptomyces as a plant’s best friend? – Tom Viaene – FEMS Microbiology Ecology

Water and extremophile microbiome

Light availability regulates the response of algae and heterotrophic bacteria to elevated nutrient levels and warming in a northern boreal peatland – Lily Y. Gu – Freshwater Biology

Metagenomic covariation along densely sampled environmental gradients in the Red Sea – Luke R Thompson – bioRxiv

Microbial community structure of Arctic seawater as revealed by pyrosequencing – Yang Li – Acta Oceanologica Sinica

A snapshot on spatial and vertical distribution of bacterial communities in the eastern Indian Ocean – Jing Wang – Acta Oceanologica Sinica

Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina – Laura T. Carney – Algal Research

Detection of antibiotic-resistant bacteria endowed with antimicrobial activity from a freshwater lake and their phylogenetic affiliation – Zothanpuia – PeerJ

Microbial diversity in lake–river ecotone of Poyang Lake, China – Xiaolan Huang – Environmental Earth Sciences

Book: The Marine Microbiome. An Untapped Source of Biodiversity and Biotechnological Potential – Lucal J. Stal, Mariana Silvia Cretoiu – Springer

Food microbiology

Bacterial dynamics and functional analysis of microbial metagenomes during ripening of Dutch-type cheese – Davide Porcellato – International Dairy Journal

Pollution and waste microbiology

Chronic exposure to triclosan sustains microbial community shifts and alters antibiotic resistance gene levels in anaerobic digesters – Daniel Carey – Environ Sci Processes Impacts

Computational models of microbiome research, bioinformatics

Synergistic elimination of bacteria by phage and the immune system – Chung Yin (Joey) Leung – bioRxiv

A new way to publish metagenomics studies – Folker Meyer – BioMed Central

Techniques

RNA-stable isotope probing: from carbon flow within key microbiota to targeted transcriptomes – Tillmann Lueders – Current Opinion in Biotechnology

More microbiology

Centenary of the death of Elie Metchnikoff: A visionary and an outstanding team leader –
Jean-Marc Cavaillon – Microbes and Infection

Microbes in the news

Worcester Polytechnic Institute Students Isolate Potentially Novel Soil-Dwelling Viruses – PR Web

Yuck factor may boost hand hygiene compliance: Interview with Ashley Gregory – EurekAlert

Europe orders Italians to cut down olive trees infected with bacteria – Nick Squires – The Telegraph

It’s Not Just Restaurants—Scientists Are Fascinated With Fermented Foods Too – Jane Lear – Take Part

Science, publishing, and career

Differences in incomes of physicians in the United States by race and sex: observational study – Dan P. Ly – British Medical Journal

Press: White male doctors earn 35 percent more than black male doctors – Jennifer Adaeze Okwerekwu – STAT News

June 6, 2016

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Human oral microbiome

Identification of oral bacteria on titanium implant surfaces by 16S rDNA sequencing – Fabiana de Melo – Clinical Oral Implants Research

Subgingival microbiota in individuals with severe chronic periodontitis – Chi-Ying Tsai – Journal of Microbiology, Immunology and Infection

Human gut microbiome

Gut to brain interaction in Autism Spectrum Disorders: a randomized controlled trial on the role of probiotics on clinical, biochemical and neurophysiological parameters – Elisa Santocchi – BMC Psychiatry

Review: Resource conflict and cooperation between human host and gut microbiota: implications for nutrition and health – Helen Wasielewski – Annals of the New York Academy of Sciences

Press: War and peace in the human gut: probing the microbiome -Biodesign

Animal and tissue culture experiments

Adult microbiota-deficient mice have distinct dendritic morphological changes: differential effects in the amygdala and hippocampus – Pauline Luczynski – European Journal of Neuroscience

Exposure to common respiratory bacteria alters the airway epithelial response to subsequent viral infection – Carla Bellinghausen – Respiratory Research

Animal microbiome

Gut microbiota of Busseola fusca (Lepidoptera: Noctuidae) – Maxi Snyman – World Journal of Microbiology and Biotechnology

Plant, root, and soil microbiome

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages – Shengjing Shi – Ecology Letters

Functional Role of Bacteria from Invasive Phragmites australis in Promotion of Host Growth – M. A. Soares – Microbial Ecology

Design defines the effects of nanoceria at a low dose on soil microbiota and the potentiation of impacts by canola plant – Mohamed Hamidat – Environmental Science & Technology

Water and extremophile microbiome

Taxon interactions control the distributions of cryoconite bacteria colonizing a High Arctic ice cap – Jarishma K. Gokul – Molecular Ecology

Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic – Sunil Mundra – MicrobiologyOpen

Microbial sedimentary imprint on the deep Dead Sea sediment – Camille Thomas – The Depositional Record

Characterization of the cyanobacteria and associated bacterial community from an ephemeral wetland in New Zealand – Nick H. Secker – Journal of Phycology

Abundance of sulfur-degrading bacteria in a benthic bacterial community of shallow sea sediment in the off-Terengganu coast of the South China Sea – Zahar Marziah – MicrobiologyOpen

Pollution and waste microbiology

Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing – Lei Wang – Marine Pollution Bulletin

Effects of erythromycin, trimethoprim and clindamycin on attached microbial communities from an effluent dominated prairie stream – M.J. Waiser – Ecotoxicology and Environmental Safety

Metagenomics and bioinformatics

MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data – Vladimir I. Ulyantsev – Bioinformatics

MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses – Vanni Bucci – Genome Biology

Microbes in the news

New Bacterial Research May Help Reduce Excessive Amounts Of Phosphorus In Lakes –
Catherine Cabral-Isabedra – Tech Times

About Nicholas Muzyczka, microbiology professor at the University of Florida: Inventor says fame is fine, but best reward is helping others – Anthony Clark – Gainesville.com

Bacteria has potential to clean up oil spills – Zia Lyle – Daily Texan Online

Clif Bars join list of products recalled over listeria concern – Debra Goldschmidt – CNN

Microbes in Space: JPL Researcher Explores Tiny Life – NASA

Jason Tetro aims to rehabilitate microbes’ bad reputation with The Germ Files – Rebecca Tucker – National Post

Science, publishing, and career

Publishing for academic refugees: Paul Ostwald: The Journal of Interrupted Studies – Emma Christie – Oxford Student

Postdoc mysteries: three recent developments raise puzzling uncertainties about postdocs’ present and future lives – Beryl Lieff Benderly – Science

June 4, 2016

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A very late Saturday digest, after a fun day at the pool and dinner with family. Germ-free jewel wasps, tooth extraction in horses, dormancy in lakes, subways and urban biomes.

Pregnancy and birth

Review: Fetal, neonatal, and infant microbiome: Perturbations and subsequent effects on brain development and behavior – Rochellys Diaz Heijtz – Seminars in Fetal and Neonatal Medicine

Determination of Bifidobacterium and Lactobacillus in breast milk of healthy women by digital PCR – L. Qian – Beneficial Microbes

Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants – Tali Raveh-Sadka – The ISME Journal

Human gut microbiome

Capturing One of the Human Gut Microbiome’s Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data – Patricio Jeraldo – Frontiers in Microbiology

Identification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract – Cedric C. Laczny – Frontiers in Microbiology

Cryptic functional variation in the human gut microbiome – Patrick H Bradley – bioRxiv Preprint

Review: The gut microbiome in human immunodeficiency virus infection – Gili Zilberman-Schapira – BMC Medicine

Review: The Gut Microbiome and Obesity – George Kunnackal John – Current Oncology Reports

Animal experiments

An optimized approach to germ-free rearing in the jewel wasp Nasonia – J. Dylan Shropshire – PeerJ Preprints

Bacteraemia before, during and after tooth extraction in horses in the absence of antimicrobial administration – I. Kern – Equine Veterinary Journal

Effects of Diets Supplemented with Ensiled Mulberry Leaves and Sun-Dried Mulberry Fruit Pomace on the Ruminal Bacterial and Archaeal Community Composition of Finishing Steers – Yuhong Niu – PLOS ONE

Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness – Hui Yang – Scientific Reports

Animal microbiome

Gut microbial communities associated with the molting stages of the giant freshwater prawn Macrobrachium rosenbergii – Eleni Mente

DGGE: A comparison of microbial profiles of different regions of the equine hindgut –
K. Fliegerova – Livestock Science

Diversity and composition of cultivable gut bacteria in an endemic island bird and its mainland sister species – Elisa Lobato – Symbiosis

Bacterial Community Diversity Harboured by Interacting Species – Mikaël Bili – PLOS ONE

Plant, root, and soil microbiome

Structure of Fungal Communities in Sub-Irrigated Agricultural Soil from Cerrado Floodplains – Elainy Cristina A. M. Oliveira – Diversity

Phylogenetic and multivariate analyses to determine the effect of agricultural land-use intensification and soil physico-chemical properties on N-cycling microbial communities in drained Mediterranean peaty soils – Valentina Ciccolini – Biology and Fertility of Soils

The impact of pasture systems on soil microbial biomass and community-level physiological profiles – Francisco Marques Cardozo Junior – Land Degradation & Development

Effect of Heavy Metals Pollution on Soil Microbial Diversity and Bermudagrass Genetic Variation – Yan Xie – Frontiers in Plant Science

Isolation, identification and oenological characterization of non-Saccharomyces yeasts in a Mediterranean island – G. Polizzotto – Letters in Applied Microbiology

Water and extremophile microbiome

Diversity and distribution of cultured endolichenic fungi in the Ny-Ålesund Region, Svalbard (High Arctic) – Tao Zhang – Extremophiles

Bacterial dormancy is more prevalent in freshwater than hypersaline lakes – Zachary T. Aanderud – Frontiers in Microbiology

Changes in the water quality and bacterial community composition of an alkaline and saline oxbow lake used for temporary reservoir of geothermal waters – Andrea K. Borsodi – Environmental Science and Pollution Research

Responses of aquatic bacteria to terrestrial runoff: effects on community structure and key taxonomic groups – Huong T. Le – Frontiers in Microbiology

Metagenomics accelerates species discovery and unravel great biodiversity of benthic invertebrates in marine sediments in Campos basin, Brazil – Milena Marcela D P Schettini – PeerJ Preprint

Built environment microbiome

Microbial communities in dairy processing environment floor-drains are dominated by product-associated bacteria and yeasts – Kerstin Schön – Food Control

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report – The MetaSUB International Consortium – Microbiome

Bioinformatics and metagenomics

The Pepsi Challenge, Metagenomics style? COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge – Yang Young Lu – Bioinformatics

Microbial Ecology

A stable genetic polymorphism underpinning microbial syntrophy – Tobias Großkopf – The ISME Journal

Microbes in the news

Two Stanford microbiology and immunology professors elected to National Academy of Sciences – Stanford Medicine

From the American Society of Clinical Oncology Annual Meeting in Chicago: Bacteria found in female upper reproductive tract, once thought sterile – Science Daily

Crowds of crows spread C. jejuni: Are humans vulnerable? – EurekAlert

Antimicrobial Kills E. Coli Within 30 Seconds – Greg Watry – RD Magazine