Category Archives: Pregnancy and birth

December 21, 2015

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Vacuum cleaning, anorexia, chronic fatigue syndrome, celiac disease, and social preferences in mice.

Pregnancy and birth

Potential association of vacuum cleaning frequency with an altered gut microbiota in pregnant women and their 2-year-old children – Ekaterina Avershina – Microbiome

Placental infection with Ureaplasma species is associated with histologic chorioamnionitis and adverse outcomes in moderate and late preterm infants – Emma L. Sweeney – The Journal of Infectious Diseases

Polymicrobial Amniotic Fluid Infection with Mycoplasma/Ureaplasma and Other Bacteria Induces Severe Intra-Amniotic Inflammation Associated with Poor Perinatal Prognosis in Preterm Labor – Noriko Yoneda – American Journal of Reproductive Immunology

The Development of Extremely Preterm Infants Born to Women Who Had Genitourinary Infections During Pregnancy – Alan Leviton – American Journal of Epidemiology

Human skin microbiome

Skin microbiome in melanomas and melanocytic nevi – Alexander Salava- European Journal of Dermatology

Human oral microbiome

Commentary: A New Association for the Oral Metagenome – Nicholas S. Jakubovics – Oral Diseases

Human respiratory microbiome

No evidence for viral sequences in five lepidic adenocarcinomas (former “BAC”) by a high-throughput sequencing approach – Nicolas Berthet – BMC Research Notes

Human gastric and gut microbiome

Gut Dysbiosis in Patients with Anorexia Nervosa – Chihiro Morita – PLOS ONE

Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) – Sanjay K. Shukla – PLOS ONE

From an imbalance to a new imbalance: Italian-style gluten-free diet alters the salivary microbiota and metabolome of African celiac children – Danilo Ercolini – Scientific Reports

Bacterial overgrowth and diversification of microbiota in gastric cancer – Wang, Lili – European Journal of Gastroenterology & Hepatology

Review: Endocannabinoids — at the crossroads between the gut microbiota and host metabolism – Patrice D. Cani – Nature Reviews Endocrinology

Review: Disruption of the Gut Microbiome: Clostridium difficile Infection and the Threat of Antibiotic Resistance – Priscilla A. Johanesen – MDPI Genes

Review: Obesity: An overview of possible role(s) of gut hormones, lipid sensing and gut microbiota – Alok Kumar Mishra – Metabolism

Review: Microbiome and Beyond: Non-Viable Food Microbes and Human Health – James W. Daily III – Journal of Medicinal Food

Review: Microbial translocation and microbiome dysbiosis in HIV-associated immune activation – Zevin, Alexander S – Current Opinion in HIV and AIDS

Animal and other models

Calcium supplementation modulates gut microbiota in a prebiotic manner in dietary obese mice – Alice Chaplin – Molecular Nutrition & Food Research

Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries – Joel D. Rudney – Microbiome

Innate immune responses to gut microbiota differ between threespine stickleback populations – Kathryn Milligan-Myhre – Disease Models & Mechanisms

Host microbiota modulates development of social preference in mice – Tim Arentsen – Microbial Ecology in Health and Disease

Gut barrier impairment by high-fat diet in mice depends on housing conditions –
Veronika Maria Müller – Molecular Nutrition & Food Research

A Strategy for the Targeted Metabolomics Analysis of 11 Gut Microbiota-host Co-metabolites in Rat Serum, Urine and Feces by Ultra Performance Liquid Chromatography—Tandem Mass Spectrometry – Waner Hou – Journal of Chromatography A

Editorial: Small but Mighty: Selected Commensal Bacterial Species Determine the Effectiveness of Anti-cancer Immunotherapies – Jose R. Conejo-Garcia – Immunity

Fecal Microbiota Transplant Restores Mucosal Integrity in a Murine Model of Burn Injury – Kuethe, Joshua W – Shock

Animal microbiome

Isolation, identification and fibrolytic characteristics of rumen fungi grown with indigenous methanogen from yaks (Bos grunniens) grazing on the Qinghai-Tibetan Plateau – Ya-Qin Wei – Journal of Applied Microbiology

Molecular characterization of midgut microbiota of Aedes albopictus and Aedes aegypti from Arunachal Pradesh, India – Kamlesh K. Yadav – Parasites & Vectors

Plant, root, and soil microbiome

Soil microbial community structure explains the resistance of respiration to a dry–rewet cycle, but not soil functioning under static conditions – Kate H. Orwin – Functional Ecology

Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems – Elizaveta Pershina – PLOS ONE

Succession of bacterial communities, coxL genotypes and carbon monoxide oxidation activity in soil microcosms to identify unknown carboxydovore bacteria dominating deciduous forest soil – Isabelle Lalonde – Applied and Environmental Microbiology

Commentary: Disentangling the factors shaping microbiota composition across the plant holobiont – Stéphane Hacquard – New Phytologist

Significant alteration of soil bacterial communities and organic carbon decomposition by different long-term fertilization management conditions of extremely low-productivity arable soil in South China – Weibing Xun – Environmental Microbiology

Water and extremophile microbiome

Physical and chemical controls on habitats for life in the deep subsurface beneath continents and ice – John Parnell – Philosophical Transactions A

Temporal succession in carbon incorporation from macromolecules by particle-attached bacteria in marine microcosms – Xavier Mayali – Environmental Microbiology Reports

Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic alaska – J. Kao-Kniffin – Scientific Reports

Built environment microbiome

Assessment of indoor environmental quality in existing multi-family buildings in North–East Europe – Liuliu Du – Environment International

Alas, no access for me, but sounds cool: Analysis of the incidence fungi in a crypt cemetery – Cecylia Łukaszuk – Journal of the Air & Waste Management Association

Monitoring sulfide-oxidizing biofilm activity on cement surfaces using non-invasive self-referencing microsensors – Liqiu Cheng – Water Research

Metagenomics and bioinformatics

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED – James Kaminski – PLOS Computational Biology

Techniques

Meta3C analysis of a mouse gut microbiome – Martial Marbouty, Lyam Baudry, Axel Cournac, Romain Koszul – BioRxiv

 

Microbes in the news

Podcast: Drugged Gut Microbiome Cuts Heart Risk in Mice – Christopher Intagliata – Scientific American

Are Antibiotics Making People Larger? Overuse of the drugs seems to make us gain weight—even when we don’t take them – James Hamblin – The Atlantic

Petri-Dishing the Dirt for Science and Education at Worcester Polytechnic Institute – PR Web

Men and women deposit different types of bacteria – Tim Sandle – Digital Journal

Mediterranean Diet Impacts Microbiome’s Influence on Heart Disease – Genengnews

Science, publishing, and career

Rejection of rejection: a novel approach to overcoming barriers to publication: Tired of rejections? Cath Chapman and Tim Slade offer a simple way to fight back – The BMJ

365 days: Nature’s 10 – Ten people who mattered this year – Nature

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December 16, 2015 #2

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Role of Lactobacillus in early pregnancy, skin microbiome of psoriasis patients before and after a spa treatment, retroviruses in coprolites, colonization of germ-free cockroach guts, more decomposing pigs, kitty poop, and de novo clustering methods are just better. So many papers, I had to do a second installment today.

General human microbiome

Review: Human Microbiome and Its Association With Health and Diseases – Asmaa Althani – Journal of Cellular Physiology

Review: Microbiota, Parasites and Immunity – Judith Allen – Parasite Immunology

Pregnancy and birth (and vaginal microbiome)

Role of Lactobacillus Species in the Intermediate Vaginal Flora in Early Pregnancy: A Retrospective Cohort Study – Alex Farr – PLOS ONE

Human Breast Milk miRNA, Maternal Probiotic Supplementation and Atopic Dermatitis in Offspring – Melanie Rae Simpson – PLOS ONE

Review: The Infant Microbiome: Implications for Infant Health and Neurocognitive Development – Yang, Irene – Nursing Research

Human oral microbiome

Association between Herpesviruses and Chronic Periodontitis: A Meta-Analysis Based on Case-Control Studies – Ce Zhu – PLOS ONE

Short-term Effects of Povidone Iodine and Sodium Fluoride Therapy on Plaque Levels and Microbiome Diversity – Cavan Reilly – Oral Diseases

Review: Saliva and viral infections – Paul L. A. M. Corstjens – Periodontology 2000

Review: The physiology of salivary secretion – Gordon B. Proctor – Periodontology 2000

Human skin microbiome

Skin Microbiome in Patients With Psoriasis Before and After Balneotherapy at the Thermal Care Center of La Roche-Posay – Richard Martin – Journal of Drugs in Dermatology

Importance of Lid Hygiene Before Ocular Surgery: Qualitative and Quantitative Analysis of Eyelid and Conjunctiva Microbiota – Peral, Assumpta – Eye & Contact Lens

Human gut microbiome

Coprolites: Retroviral DNA Sequences as a Means for Determining Ancient Diets – Jessica I. Rivera-Perez – PLOS ONE

Model microbiome

The deterministic assembly of complex bacterial communities in germ-free cockroach guts – Aram Mikaelyan – Applied and Environmental Microbiology

The piglet as a model for studying dietary components in infant diets: effects of galacto-oligosaccharides on intestinal functions – A. Alizadeh – British Journal of Nutrition

Lactobacillus crispatus inhibits growth of Gardnerella vaginalis and Neisseria gonorrhoeae on a porcine vaginal mucosa model – Laura M. Breshears – BMC Microbiology

Vancomycin treatment and butyrate supplementation modulate gut microbe composition and severity of neointimal hyperplasia after arterial injury – Karen J. Ho – Physiological Reports

Necrobiome: the microbiome of death

Shifts in soil biodiversity—A forensic comparison between Sus scrofa domesticus and vegetation decomposition – Ayodeji O. Olakanye – Science & Justice

Animal microbiome

A Longitudinal Study of the Feline Faecal Microbiome Identifies Changes into Early Adulthood Irrespective of Sexual Development – Oliver Deusch – PLOS ONE

Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata – Dustin W. Kemp – PLOS ONE

Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks – Khin K. Z. Mon – Frontiers in Veterinary Science

Niche Limits of Symbiotic Gut Microbiota Constrain the Salinity Tolerance of Brine Shrimp – Odrade Nougué – The American Naturalist

Opinion: Blurred lines: pathogens, commensals, and the healthy gut – Paul Wigley – Frontiers in Veterinary Science

Review: The gut microbiome and its potential role in the development and function of newborn calf gastrointestinal tract – Nilusha Malmuthuge – Frontiers in Veterinary Science

Review: An introduction to the avian gut microbiota and the effects of yeast-based prebiotic-type compounds as potential feed additives – Stephanie M. Roto – Frontiers in Veterinary Science

Plant, root, and soil microbiome

Biological attributes of rehabilitated soils contaminated with heavy metals – Jessé Valentim dos Santos – Environmental Science and Pollution Research

Comparison between cultivated and total bacterial communities associated with Cucurbita pepo using cultivation-dependent techniques and 454 pyrosequencing – N. Eevers – Systematic and Applied Microbiology

Euphorbia plant latex is inhabited by diverse microbial communities – Manjula Gunawardana – American Journal of Botany

Bioreactor and waste microbiology

Systematic investigation and microbial community profile of indole degradation processes in two aerobic activated sludge systems – Qiao Ma – Scientific Reports

Pretreatment of piggery wastewater by a stable constructed microbial consortium for improving the methane production – Jian Cai – Water Science & Technology

Bioinformatics and metagenomics

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units – Sarah L. Westcott – PeerJ

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database – Jarmo Ritari – BMC Genomics

RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis – Elisabeth Navarro – BioTechniques

Review: Metagenomics: Retrospect and Prospects in High Throughput Age – Satish Kumar – Biotechnology Research International

Microbes in the news

Human-gut-on-a-chip model offers hope for IBD sufferers – Kat J McAlpine – Harvard

Metagenomics Explainer, with Emory geneticist Tim Read – Lab Land, Emory Health Sciences Research blog

Your Face Is Covered in Mites, and It’s Your Parents’ Fault – Matt Simon – Wired

Science, publishing, and career

Plenty of moustaches but not enough women: cross sectional study of medical leaders – Mackenzie R Wehner – BMJ
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December 15, 2015

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Self-tracking the microbiome (quantified self), a human gut-on-a-chip model, indoor air bacteria in residences in the San Francisco Bay Area, and using probiotics on corals during oil spills.

General microbiome

Biometrics’ new identity—measuring more physical and biological traits: Research into the characteristics that are unique to an individual is addressing the need to correctly identify people in a variety of medical, social and security contexts – Andrea Rinaldi – EMBO Reports

Commentary: Self-tracking the microbiome: where do we go from here? – Carine Gimbert – Microbiome

Conference abstracts: 3th ISM World Congress on Targeting Microbiota – Journal of International Society of Microbiota Volume 1 No. 1

Pregnancy and birth

Buccal administration of human colostrum: impact on the oral microbiota of premature infants – K Sohn – Journal of Perinatology

Human mouth/ear microbiome

Pathophysiology of sinusitis of odontogenic origin – Silvio Taschieri – Journal of Investigative and Clinical Dentistry

Human gut microbiome

Different sub-type strains of Akkermansia muciniphila abundantly colonize in southern China – Xianfeng Guo – Journal of Applied Microbiology

Simultaneous fecal microbial and metabolite profiling enables accurate classification of pediatric irritable bowel syndrome – Vijay Shankar – Microbiome

Mucosal Barrier Depletion And Loss Of Bacterial Diversity Are Primary Abnormalities In Paediatric Ulcerative Colitis – Misagh Alipour – Journal of Crohn’s and Colitis

Systematic review with meta-analysis: long-term outcomes of faecal microbiota transplantation for Clostridium difficile infection – Y.-T. Li – Alimentary Pharmacology & Therapeutics

Microbiome models

Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip – Hyun Jung Kim – PNAS

Effects of antibiotics (oxytetracycline, florfenicol or tulathromycin) on neonatal calves’ faecal microbial diversity – J. Oultram – Veterinary Record

Animal microbiome

Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken and Human Feces – Liping Ma – Environmental Science & Technology

The impact of rearing environment on the development of gut microbiota in tilapia larvae – Christos Giatsis – Scientific Reports

The characterization and manipulation of the bacterial microbiome of the Rocky Mountain wood tick, Dermacentor andersoni – Katie A. Clayton – Parasites & Vectors

Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota – Henrique Fragoso ados Santos – Scientific Reports

Plant, root, and soil microbiome

Stronger warming effects on microbial abundances in colder regions – Ji Chen – Scientific Reports

Seasonal dynamics of the microbiome of chernozems of the long-term agrochemical experiment in Kamennaya Steppe – T. I. Chernov – Eurasian Soil Science

Water and extremophile microbiome

Metagenome-assembled genomes uncover a global brackish microbiome – Luisa W. Hugerth – Genome Biology

Similar microbial communities found on two distant seafloor basalts – Esther Singer – Frontiers in Microbiology

Microbial communities on seafloor basalts at Dorado Outcrop reflect level of alteration and highlight global lithic clades – Michael D. Lee – Frontiers in Microbiology

Bacterioplankton dynamics within a large anthropogenically impacted urban estuary – Thomas C. Jeffries – Frontiers in Microbiology

Marine microbial community structure assessed from combined metagenomic analysis and ribosomal amplicon deep-sequencing – Savvas Genitsaris – Marine Biology Research

Groundwater isolation governs chemistry and microbial community structure along hydrologic flowpaths – Sarah Ben Maamar – Frontiers in Microbiology

Review: Forged Under the Sun: Life and Art of Extremophiles from Andean Lakes – Virginia Helena Albarracín – Photochemistry and Photobiology

Food microbiology

Comparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations – Jinshui Zheng – Scientific Reports

Built environment microbiology

Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences – Marzia Miletto – Microbiome

Review: Antibiotic resistance in urban aquatic environments: can it be controlled? – Célia M. Manaia – Applied Microbiology and Biotechnology

Metagenomics, phages, and bioinformatics

Computational approaches to predict bacteriophage–host relationships – Robert A. Edwards – FEMS Microbiology Reviews

Partial least squares regression can aid in detecting differential abundance of multiple features in sets of metagenomic samples – Ondrej Libiger – Frontiers in Genetics

Techniques

A new fungal large subunit ribosomal RNA primer for high throughput sequencing surveys – Rebecca C Mueller – FEMS Microbiology Ecology

Biofilms

Classic Spotlight: Before They Were Biofilms – George A. O’Toole – Journal of Bacteriology

Microbes in the news

How Bacteria and Brown Fat Can Spur Weight Loss – Mandy Oaklander – Time

A cultural revolution in the study of the gut microbiome – Medical Xpress

Why Your Body Is Like A Rainforest… Micro-Macro Exhibition at Eden features artwork from students at local secondary schools – PirateFM

Italian olive trees are withering from this deadly bacteria – PBS Newshour

Behind the scenes: Microbial biogeography of a university campus – Ashley Ross – MicroBEnet

Irish company makes biggest breakthrough for microbiology testing in dairy industry in 100 years – Independent Ireland

Bacteria, Archaea – Some Methane In Hydraulic Fracturing Is Even More Natural Than Assumed – Science 2.0

Sweet and sticky: Bacteria use sugars to bind to human cells – Phys.org

Science, publishing, and career

The Unwritten Code of Conduct: Each day this week, my supervisor has walked into my office and made verbal demands that I remove content from my beloved blog – The Research Whisperer

A lesson on misleading graphs from the National Review – Lenny Teytelman – The Spectroscope

Women in STEM research: Better Data and Information Sharing Could Improve Oversight of Federal Grant-making and Title IX Compliance – US Government Accountability Office

Why do scientists like anonymity? Lenny Teytelman – Protocols

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December 9, 2015

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Student activity about the microbiome that uses pasta, nutritional supplementation in Malawian infants, fungi and drywall, and microbial aerosols from soiled hospital linens.

General microbiome

Cool student activity: Modeling the Dynamic Digestive System Microbiome – Anne M. Estes – Journal of Microbiology & Biology Education

Pregnancy and birth

Persistent microbial dysbiosis in preterm premature rupture of membranes from onset until delivery – Elizabeth A. Baldwin – PeerJ

No effect of supplementation: Gut microbiota in Malawian infants in a nutritional supplementation trial – Yin Bun Cheung – Tropical Medicine & International Health

Human vaginal microbiome

Bacterial vaginosis and inflammatory response showed association with severity of cervical neoplasia in HPV-positive women – Juçara Maria de Castro-Sobrinho – Diagnostic Cytopathology

Human gut microbiome

Review: Gut Microbiota Modulation and Mucosal Immunity: Focus on Rifaximin – Loris R. Lopetuso – Mini-Reviews in Medicinal Chemistry

Animal microbiome

The effects of omeprazole therapy on bacterial colonization of the pharynx in healthy dogs – Lauren A. Sullivan – Journal of Veterinary Emergency and Critical Care

Water microbiome

Spatial Patterns in Biofilm Diversity across Hierarchical Levels of River-Floodplain Landscapes – Marc Peipoch – PLOS ONE

 

Built environment microbiome

Moisture parameters and fungal communities associated with gypsum drywall in buildings – Sandra Dedesko – Microbiome

A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses – Thomas Weinmaier – Microbiome

Microbial aerosol liberation from soiled textiles isolated during routine residuals handling in a modern health care setting – Alina Handorean – Microbiome

Phages and viruses

Better together: bacteriophage combinations significantly reduce Clostridium difficile growth in vitro and proliferation in vivo – Janet Y. Nale – Antimicrobial Agents and Chemotherapy

Infection and transplantation

A genetic modifier of the gut microbiome influences the risk of GVHD and bacteremia following HSCT – Ahmad Rayes – Biology of Blood and Marrow Transplantation

World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis – Martyn D. Kirk – PLOS Medicine

Functional foods

A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods – Remco Kort – Microbial Cell Factories

Changes in the Milk Metabolome of the Giant Panda (Ailuropoda melanoleuca) with Time after Birth – Three Phases in Early Lactation and Progressive Individual Differences – Tong Zhang – PLOS ONE

Bioinformatics and metagenomics

Small Sample Kernel Association Tests for Human Genetic and Microbiome Association Studies – Jun Chen – Genetic Epidemiology

Microbes in the news

Questions About the Science Of Beer – Matt Shipman – NC State University News

Guest Post – Stadium Seat Bacteria – PeerJ – David Coil

How microbes in your gut today hold clues to tomorrow’s medicines: For the second episode of “Science Happens,” we hung out with Pamela Silver, a scientist who wants to hack the microbiome – Carl Zimmer – STAT news

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December 8, 2015

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The CF microbiome, microbes attaching to glycoproteins in sweat, gut bacteria make cockroach poop smell attractive for other cockroaches, mycobiome of South African Cabernet vines, and seasonality of Japanese cherry orchard soil fungi.

General microbiome

Perspective: Behavioral Microbiomics: A Multi-Dimensional Approach to Microbial Influence on Behavior – Adam C.-N. Wong – Frontiers in Microbiology

Research highlight: Microbiota-based nutrition plans – Cláudio Nunes-Alves – Nature Reviews Microbiology

Pregnancy and birth

Maternal risk factors for abnormal vaginal flora during pregnancy – Cecilia Tibaldi – International Journal of Gynecology & Obstetrics

Human respiratory microbiome

MiniReview: The cystic fibrosis microbiome in an ecological perspective and its impact in antibiotic therapy – Andreia P. Magalhães – Applied Microbiology and Biotechnology

Human oral microbiome

Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China – Xingdong Chen – PLOS ONE

Human skin microbiome

Sweating the small stuff: Glycoproteins in human sweat and their unexplored potential for microbial adhesion – Robyn A Peterson – Glycobiology

Human gut microbiome

Gut microbiota manipulation with prebiotics in patients with non-alcoholic fatty liver disease: a randomized controlled trial protocol – BMC Gastroenterology

Review: Current roles of specific bacteria in the pathogenesis of inflammatory
bowel disease – Lucy McMullen – Microbiology

Animal and bioreactor models

Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease – M Llopis – Gut

Development of a Laboratory Model of a Phototroph-Heterotroph Mixed-Species Biofilm at the Stone/Air Interface – Federica Villa – Frontiers in Microbiology

Animal microbiome

Gut bacteria mediate aggregation in the German cockroach – Ayako Wada-Katsumata – PNAS

The deep-sea glass sponge Lophophysema eversa harbors potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur – Ren-Mao Tian – Environmental Microbiology

Plant, root, and soil microbiome

The Anti-Phytophthora Effect of Selected Potato-Associated Pseudomonas Strains: From the Laboratory to the Field – Anouk Guyer – Frontiers in Microbiology

Defoliation reduces soil biota – and modifies stimulating effects of elevated CO2 – Marie Dam – Ecology and Evolution

Sequence-based Analysis of the Vitis vinifera L. cv Cabernet Sauvignon Grape Must Mycobiome in Three South African Vineyards Employing Distinct Agronomic Systems – Mathabatha E. Setati – Frontiers in Microbiology

Paradox of plant growth promotion potential of rhizobacteria and their actual promotion effect on growth of barley (Hordeum vulgare L.) under salt stress – Massimiliano Cardinale – Microbiological Research

Survey of Annual and Seasonal Fungal Communities in Japanese Prunus mume Orchard Soil by Next-Generation Sequencing – Yoshinao Aoki – Advances in Microbiology

Actinobacterial Diversity in the Sediments of Five Cold Springs on the Qinghai-Tibet Plateau – Jian Yang – Frontiers in Microbiology

Bacterial diversity assessment of pristine mangrove microbial community from dhulibhashani, sundarban using 16S rRNA gene tag sequencing – Pijush Basak – Genomics Data

Microbialites in the shallow-water marine environments of the Holy Cross Mountains (Poland) in the aftermath of the Frasnian–Famennian biotic crisis – Michał Rakociński – Global and Planetary Change

No tillage combined with crop rotation improves soil microbial community composition and metabolic activity – Bingjie Sun – Environmental Science and Pollution Research

Assessing the contribution of fallen autumn leaves to airborne fungi in an urban environment – Peter J. Irga – Urban Ecosystems

Water and extremophile microbiome

Weak Coherence in Abundance Patterns Between Bacterial Classes and Their Constituent OTUs Along a Regulated River – Clara Ruiz-González – Frontiers in Microbiology

Combined Culture-Based and Culture-Independent Approaches Provide Insights into Diversity of Jakobids, an Extremely Plesiomorphic Eukaryotic Lineage – Tomáš Pánek – Frontiers in Microbiology

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics – Kuei-Han Lin – BMC Genomics

Waste treatment

Microbial community structure associated with the high loading anaerobic codigestion of olive mill and abattoir wastewaters – Hana Gannoun – Bioresource Technology

Microbial analysis of in situ biofilm formation in drinking water distribution systems: implications for monitoring and control of drinking water quality – Isabel Douterelo – Environmental Biotechnology

Food microbiology

Pyrosequencing reveals bacterial diversity in Korean traditional wheat-based nuruk – Jyotiranjan Bal – Journal of Microbiology

Metagenomics and bioinformatics

Hunting Down Frame Shifts: Ecological Analysis of Diverse Functional Gene Sequences – Michal Strejcek – Frontiers in Microbiology

GenomeTester4: a toolkit for performing basic set operations – union, intersection and complement on k-mer lists – Lauris Kaplinski – GigaScience

Microbes in the news

Cockroaches communicate via bacteria in their feces – Elizabeth Pennisi – Science Magzine

MSU professor trekking to the Amazon to study bacteria of insects that spread disease
– Anne Cantrell, MSU News Service – Bozeman Daily

Bacterial Biofilms: A Charged Environment – Kathryn Calkins – Biomedical Beat

Maintaining Wellness, Starting From Your Gut – Julie Chen – Huffington Post

Fall into Fungi – Alex Alexiev – MicroBEnet

Caps can play a part in cleaning water, not just bottling it – Jim Johnson – Plastic News

Dirty Yamuna water harbours drug-resistant bacteria – Neetu Chandra Sharma – Daily Mail India

Cooperating bacteria isolate cheaters – Phys.org

What you should know about this ‘new’ STD: interview with Raquel Dardik – Kristine Thomason – CNN

Bacteria Hysteria

Bacteria tests: What’s growing beneath your feet? – Alex Osiadacz – KLTV

Science, publication, and career

Five selfish reasons to work reproducibly – Florian Markowetz – Genome Biology

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December 3, 2015

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Microbiomes of gallstones, soil along a bike trip, nematodes in cattle, kiddie pools, and 100 years of phage research.

Pregnancy and birth

Prophages of the genus Bifidobacterium as modulating agents of the infant gut microbiota – Gabriele Andrea Lugli – Environmental Microbiology

Gut microbiota analysis reveals a marked shift to bifidobacteria by a starter infant formula containing a synbiotic of bovine milk-derived oligosaccharides and Bifidobacterium animalis subsp. lactis CNCM I-3446 – Umberto Simeoni – Environmental Microbiology

Human skin microbiome

Alas no pictures: Microbial colonization of normal skin: direct visualization of 194 skin biopsies – Anika C. Jahns – Anaerobe

Human gut microbiome

Structural robustness of the gut mucosal microbiota is associated with Crohn’s disease remission after surgery – S Mondot – Gut

Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria – Hongzhang Shen – Scientific Reports

Improvement in Human Immune Function with Changes in Intestinal Microbiota by Salacia reticulata Extract Ingestion: A Randomized Placebo-Controlled Trial – Yuriko Oda – PLOS ONE

Establishing a Fecal Microbiota Transplant Service for the treatment of Clostridium difficile Infection – Samuel P. Costello – Clinical Infectious Diseases

Review: From Hype to Hope: The Gut Microbiota in Enteric Infectious Disease –
Peter T. McKenney – Cell

Research Highlight: Can Your Microbiome Tell You What to Eat? – Jairam K.P. Vanamala – Cell Metabolism

Review: Nutrition in cancer patients with cachexia: a role for the gut microbiota? – Laure B. Bindels – Clinical Nutrition Experimental

Review: What’s bugging the gut in OCD? A review of the gut microbiome in obsessive-compulsive disorder – Jasmine Turna – Depression and Anxiety

Book Chapter: Bile Acids, the Microbiome and Metabolic Disease-Implications for Surgery – Cyrus Jahansouz – Metabolic Syndrome and Diabetes

Animal and bioreactor models

Gut Microbiota Orchestrates Energy Homeostasis during Cold – Claire Chevalier – Cell

Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling – Maayan Levy – Cell

Levan Enhances Associated Growth of Bacteroides, Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota – Kaarel Adamberg – PLOS ONE

Animal microbiome

Cattle: Exploring the Gastrointestinal “Nemabiome”: Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities – Russell W. Avramenko – PLOS ONE

Seals: Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event – Stephanie M. Rosales – PLOS ONE

Shrimp: Bacterial concentration and diversity in fresh tropical shrimps (Penaeus notialis) and the surrounding brackish waters and sediment – D. Sylvain Dabadé – International Journal of Food Microbiology

Plant, root, and soil microbiome

Science and art: Soil microbial communities along the route of a venturous cycling trip – Magdalena Nagler – Applied Soil Ecology

Disease suppression in winter wheat from novel symbiosis with forest fungi – Mary Ridout – Fungal Ecology

Multifunctionality and diversity of culturable bacterial communities strictly associated with spores of the plant beneficial symbiont Rhizophagus intraradices – Fabio Battini – Microbiological Research

Plant Host Species and Geographic Distance Affect the Structure of Aboveground Fungal Symbiont Communities, and Environmental Filtering Affects Belowground Communities in a Coastal Dune Ecosystem – Aaron S. David – Plant Microbe Interactions

The impact of charcoal and soil mixtures on decomposition and soil microbial communities in boreal forest – Nathalie Pluchon – Applied Soil Ecology

Endophytic Actinobacteria and the Interaction of Micromonospora and Nitrogen Fixing Plants – Martha E. Trujillo – Frontiers in Microbiology

The microbiome and functions of black soils are altered by dibutyl phthalate contamination – Zhigang Wang – Applied Soil Ecology

Microbiological and faunal soil attributes of coffee cultivation under different management systems in Brazil – D.R. Lammel – Brazilian Journal of Biology

Spatial Patterns in Biofilm Diversity across Hierarchical Levels of River-Floodplain Landscapes – Marc Peipoch – PLOS ONE

Extremophile microbiome

Bacterial biogeography influenced by shelf–basin exchange in the Arctic surface sediment at the Chukchi Borderland – Dukki Han – Environmental Microbiology

Built environment microbiology

First microbiota assessments of children’s paddling pool waters evaluated using 16S rRNA gene-based metagenome analysis – Toko Sawabe – Journal of Infection and Public Health

Summary of Sloan symposium: healthy buildings 2015-Europe – Hal Levin – Microbiome

Waste microbiology

Characterization of a microbial consortium that converts mariculture fish waste to biomethane – Brigit Quinn – Aquaculture

More microbiology

Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus – Carey Lambert – Nature Communications

Phages and viruses

In retrospect: A century of phage lessons – Forest Rohwer & Anca M. Segall – Nature

Science, publishing, and career

Scientific Misconduct: Red Flags: Warning signs that scandal might be brewing in your lab – John R. Thomas Jr – The Scientist

Explaining Retractions: Editors and publishers should use a standardized form to detail why they are pulling papers from the scientific literature – Hervé Maisonneuve and Evelyne Decullier – The Scientist

Self Correction: What to do when you realize your publication is fatally flawed – Kerry Grens – The Scientist

Microbes in the news

Why It’s Time to Map the Microbiome (Kavli Roundtable) – Alan Brown, The Kavli Foundation – LiveScience

Scientists Argue Appendix Might Not Be ‘Irrelevant’ to Our Health, Propose This as the Organ’s Current Function – Liz Klimas – The Blaze

Immune cells make appendix ‘silent hero’ of digestive health – Walter and Eliza Hall Institute – EurekAlert

Bugs Against Disease: Could bacteria help fight colorectal cancer? A collaborative group of Tufts researchers hope to find out – Jacqueline Mitchell – Tufts Now

New research: Intestinal bacteria are affected by antidiabetic drugs – EurekAlert
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December 1, 2015

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African gut microbiota and Entamoeba colonization, cuticular bacteria in social spiders, Arabidopsis leaf and root microbiota, the mineralosphere, bacteria in operating rooms and on a university campus.

Pregnancy and birth

The role of gut microbiota in fetal methylmercury exposure: insights from a pilot study – Sarah E. Rothenberg – Toxicology Letters

Human respiratory microbiome

Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways – Darcy R. Denner – The Journal of Allergy and Clinical Immunology

Human gut microbiome

Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence – Elise R. Morton – PLOS Genetics

Not yet on Nature website: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota – Forslund K – Nature

Gut microbiome in health and disease: Linking the microbiome-gut-brain axis and environmental factors in the pathogenesis of systemic and neurodegenerative diseases – Shivani Ghaisas – Pharmacology & Therapeutics

Book Chapter: Microbiome in the Critically Ill – Meredith Barrett – Nutrition Support for the Critically Ill

Review: The gut microbiome, diet, and links to cardiometabolic and chronic disorders – Judith Aron-Wisnewsky & Karine Clément – Nature Reviews Nephrology

Microbiome and bioreactor models

A distributed cell division counter reveals growth dynamics in the gut microbiota –
Cameron Myhrvold – Nature Communications

Polymicrobial Oral Infection with Four Periodontal Bacteria Orchestrates a Distinct Inflammatory Response and Atherosclerosis in ApoEnull Mice – Sasanka S. Chukkapalli – PLOS ONE

Aflatoxin B1 induced compositional changes in gut microbial communities of male F344 rats – Jincheng Wang – Toxicological Sciences

PhD thesis: Advanced Computational Tools for Analyzing Microbial Communities for Energy Production Environments – Adam Robbins-Pianka – University of Colorado at Boulder

Escherichia coli Nissle 1917 enhances bioavailability of serotonin in gut tissues through modulation of synthesis and clearance – Jonathan Nzakizwanayo – Scientific Reports

Animal microbiome

Cuticular bacteria appear lethal to social spiders in mixed but not monoculture inoculations – Carl N. Keiser – Current Zoology

Plant, root, and soil microbiome

Not yet on Nature website: Functional overlap of the Arabidopsis leaf and root microbiota – Bai Y – Nature

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities – Stephane Uroz – Trends in Microbiology

Impact of lowland rainforest transformation on diversity and composition of soil prokaryotic communities in Sumatra (Indonesia) – Dominik Schneider – Frontiers in Microbiology

The assessment of epiphytic yeast diversity in sugarcane phyllosphere in Thailand by culture-independent method – Rujikan Nasanit – Fungal Biology

Changes in soil physicochemical and microbial properties along elevation gradients in two forest soils – Lei Hu – Scandinavian Journal of Forest Research

Influence of Cadmium and Glucose on Soil Microbial Communities – Aliya Gilmullina – American Journal of Applied Sciences

Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems – Xiaofeng Xu – Scientific Reports

Water microbiome

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages – Magali Lescot – ISME Journal

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river – Siavash Atashgahi – Scientific Reports

Built environment microbiology

The first microbial environment of infants born by C-section: the operating room microbes – Hakdong Shin – Microbiome

Microbial biogeography of a university campus – Ashley A. Ross and Josh D. Neufeld – Microbiome

Only on Pubmed as of now: Biofilms in churches built in grottoes – Cennamo P – Science of the Total Environment

Molecular Analysis of Microbial Community Structures in Nigerian Oil Production and Processing Facilities in order to Access Souring Corrosion and Methanogenesis – Chuma Okoro – Corrosion Science

Water heater temperature set point and water use patterns influence Legionella pneumophila and associated microorganisms at the tap – William J. Rhoads – Microbiome

Food microbiology

Selection of aroma compounds for the differentiation of wines obtained by fermenting musts with starter cultures of commercial yeast strains – Florin Vararu – Food Chemistry

Metagenomics and bioinformatics

MetaQUAST: evaluation of metagenome assemblies – Alla Mikheenko – Bioinformatics

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires – Eugen Bauer – Microbiome

Book Chapter: Predicting the Metagenomics Content with Multiple CART Trees – Dante Travisany – Mathematical Models in Biology

Enhanced virome sequencing using targeted sequence capture – Todd N. Wylie – Genome Research

Biofilms and infection

Multi-species biofilms in ecology, medicine, and biotechnology – A. N. Nozhevnikova – Microbiology

Bacterial infection remodels the DNA methylation landscape of human dendritic cells –
Alain Pacis – Genome Research

Survival with a Helping Hand: Campylobacter and Microbiota – Ivana Indikova – Frontiers in Microbiology

Microbes in the news

Microbiome Startup uBiome Will Sequence Poop for the CDC – Sarah Zhang – Wired

Dr. Elizabeth Lindsey, gastroenterologist: FACES of Nashville – Liza Graves – Style

Microbiome Monday: The Bacteria and “The Guinea Pig Doctor” – American Museum of Natural History

The beloved pioneer bread that smells like feet and breaks food safety rules – Natalie Zarrelli – Atlas Obscura

Peer review

Want me to review your manuscript for free? Then be polite… – Ian M Mackay – Virology Down Under
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November 26, 2015

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Happy Thanksgiving, everyone! NCBI’s Pubmed nor Google Alerts did not take any holiday, so here is a post stuffed (pun intended) with new papers. For today, I got the microbiome of turkey, red wine, and coprolites. And strain-level variation in human-associated bacteria, cat periodontitis, and historical penguin activity too!

General microbiome

Nurturing the microbiome field: It is exciting to see the nucleus of a grand vision for the field, but we must make the fundamentals of the scientific method central to our mission – Pat Schloss – Science

Book: Microbial Endocrinology: Interkingdom Signaling in Infectious Disease and Health
Chapters include:

Pregnancy and birth

Preterm gut microbiota and metabolome following discharge from intensive care – Christopher J. Stewart – Scientific Reports

The role of gut microbiota in fetal methylmercury exposure: Insights from a pilot study – Toxicology Letters

Assessing the Intestinal Microbiota in the SHINE Trial – Ethan K. Gough – Clinical Infectious Diseases

Gravidas with Class III Obesity: Evaluating the Abdominal Skin Microbiota Above and Below the Panniculus – Rodney K Edwards – The Journal of Maternal-Fetal & Neonatal Medicine
Review: A Review of Antibiotic Use in Pregnancy – P. Brandon Bookstaver – Pharmacotherapy

Review: On the origin of species: Factors shaping the establishment of infant’s gut microbiota – Niels van Best – Birth Defects Research Part C: Embryo Today: Reviews

Review: Molecular characterization of the human microbiome from a reproductive perspective – Amir Mor – Fertility and Sterility

Review: Reproductive tract microbiome in assisted reproductive technologies – Jason M. Franasiak – Fertility and Sterility

Review: Gynecologic health and disease in relation to the microbiome of the female reproductive tract – Katherine A. Green – Fertility and Sterility

Human skin microbiome

Genetic associations and shared environmental effects on the skin microbiome of Korean twins – Jiyeon Si – BMC Genomics

Human respiratory microbiome

The Sputum Microbiome in Chronic Obstructive Pulmonary Disease Exacerbations
Yvonne J. Huang – Annals of the American Thoracic Society

Review: Clinical Insights into Pulmonary Exacerbations in Cystic Fibrosis from the Microbiome. What Are We Missing? – Fiona J. Whelan – Annals of the American Thoracic Society

Human oral microbiome

Microbiome of titanium and zirconia dental implants abutments – Cássio do Nascimento – Dental Materials

Human gut microbiome

Microbiota and food residues including possible evidence of pre-mammalian hair in Upper Permian coprolites from Russia – Piotr Bajdek – Lethaia

Red wine polyphenols modulate fecal microbiota and reduce markers of the metabolic syndrome in obese patients – Moreno-Indias Isabel – Food & Function

The human gut microbial ecology associated with overweight and obesity determines ellagic acid metabolism – María V. Selma – Food & Function

The severity of NAFLD is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota – Jérôme Boursier – Hepatology

Differences of microbiota in small bowel and faeces between irritable bowel syndrome patients and healthy subjects – Chen-Shuan Chung – Scandinavian Journal of Gastroenterology

Methodology, Not Concept of Fecal Microbiota Transplantation, Affects Clinical Findings – Bota Cui – Gastroenterology

The Gut-Liver Axis in Primary Sclerosing Cholangitis – Bertus Eksteen – Clinics in Liver Disease

Animal models

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota – Marie Vétizou – Science

Antepartum Antibiotic Treatment Increases Offspring Susceptibility to Experimental Colitis: A Role of the Gut Microbiota – Peris Mumbi Munyaka – PLOS ONE

Metabolomic study on the faecal extracts of atherosclerosis mice and its application in a Traditional Chinese Medicine – Feng Tian – Journal of Chromatography B

Animal microbiome

Temporal Relationships Exist Between Cecum, Ileum, and Litter Bacterial Microbiomes in a Commercial Turkey Flock, and Subtherapeutic Penicillin Treatment Impacts Ileum Bacterial Community Establishment – Jessica L. Danzeisen – Frontiers in Veterinary Science

A Pyrosequencing Investigation of Differences in the Feline Subgingival Microbiota in Health, Gingivitis and Mild Periodontitis – Stephen Harris – PLOS ONE

Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species – Katherine R. Amato – Oecologia

Plant, root, and soil microbiome

Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile – Renbin Zhu – Scientific Reports

Elk, sagebrush, and saprotrophs: indirect top-down control on microbial community composition and function – Anna R. Peschel – Ecology

Effect of soil salinity and nutrient levels on the community structure of the root-associated bacteria of the facultative halophyte, Tamarix ramosissima, in southwestern United States – Takeshi Taniguchi – Journal of General and Applied Microbiology

Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots – Bao-Yu Tia – Scientific Reports

Effect of rice straw application on microbial community and activity in paddy soil under different water status – Fuxia Pan – Environmental Science and Pollution Research

Mapping the Centimeter-Scale Spatial Variability of PAHs and Microbial Populations in the Rhizosphere of Two Plants – Amélia Bourceret – PLOS ONE

Diversity of bacterial endophytes in 3 and 15 year-old grapevines of Vitis vinifera cv. Corvina and their potential for plant growth promotion and phytopathogen control – Marco Andreolli – Microbiological Research

Review: Functions, mechanisms and regulation of endophytic and epiphytic microbial communities of plants – Charles W. Bacon – Symbiosis

Review: Culture-independent discovery of natural products from soil metagenomes – Micah Katz – Journal of Industrial Microbiology & Biotechnology

Built environment microbiology

ISS: Extracellular Lipase and Protease Production from a Model Drinking Water Bacterial Community Is Functionally Robust to Absence of Individual Members – Graham G. Willsey – PLOS ONE

Food microbiology

Bacterial Ecology of Fermented Cucumber Rising pH Spoilage as Determined by Nonculture-Based Methods – Eduardo Medina – Journal of Food Science

Microbial Ecology

Complete nitrification by Nitrospira bacteria – Holger Daims – Nature

Does Microbial Diversity Confound General Predictions? – Marie Duhamel – Trends in Plant Science

Metagenomics and bioinformatics

Population genetic analyses of metagenomes reveal extensive strain-level variation in prevalent human-associated bacteria – Stephen Nayfach – BioRxiv

Techniques

Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi – Kevin V. Solomon – Anaerobe

Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies – Rashmi Sinha – Cancer Epidemiology, Biomarkers & Prevention

Microbes in the news

Is Double-Dipping Okay? CFUs in 4 types of dips after double dipping – Digg

New Research Reveals Bacteria Associated With Feline Gum Disease for the First Time – PR Newswire

Mission space food: Sugar-growing bacteria go into orbit – Clare Wilson – New Scientist

Your Coffee Machine Is a Breeding Ground for Caffeine-Resistant Bacteria – Matthew Braga – Motherboard

Your Poop Knows Best–New Study Shows Microbiome Can Help Predict Health Responses to Certain Foods – Patrick Mustain – Scientific American

Science, publishing, and career

China pursues fraudsters in science publishing – Mara Hvistendahl – Science
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November 25, 2015

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My apologies for 2 missed posts (due to overseas family circumstances). Gut microbiota of infants with botulism, gut microbial diversity in US Midwest population, decomposing pig carcasses, oil-degrading microbes and sunlight.

Events

5th Annual Microbiology of the Built Environment Conference – June 1-3 2016, Boulder, CO

Jobs

Our lab at Stanford University is hiring a Clinical Study Coordinator to be based out of UCSF School of Dentistry. Great position for someone who eventually wants to go to medical or dental school.

Pregnancy and birth

The relationship between early-life environment, the epigenome and the microbiota – Amber V Majnik – Epigenomics

Human oral microbiome

The impact of different DNA extraction methods on the analysis of microbial diversity of oral saliva from healthy youths by polymerase chain reaction-denaturing gradient gel electrophoresis – Ming Chen – Journal of Dental Sciences

Human gut microbiome

Characterizing the fecal microbiota of infants with botulism – T. Brian Shirey – Microbiome

Early-Life Exposure to Antibiotics, Alterations in the Intestinal Microbiome, and Risk of Metabolic Disease in Children and Adults – Sushmita G. Yallapragada – Pediatric Annals

Impact of demographics on human gut microbial diversity in a US Midwest population – Jun Chen – PeerJ Preprint

Review: Feeding the brain and nurturing the mind: Linking nutrition and the gut microbiota to brain development – Manu S. Goyal – PNAS

Review: Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome – Maayan Levy – Genome Medicine

Review: The relationship between early-life environment, the epigenome and the microbiota – Amber V Majnik – Future Medicine

Microbiome models

Gut Commensal E. coli Proteins Activate Host Satiety Pathways following Nutrient-Induced Bacterial Growth – Jonathan Breton – Cell Metabolism

Plant, root, and soil microbiome

From Rare to Dominant: A Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation – Sebastián Fuentes – Applied and Environmental Microbiology

Metabarcoding analysis of Phytophthora diversity using genus specific primers and 454 pyrosequencing – Maria I Prigigallo – Phytopathology

Structures of microbial communities in alpine soils: seasonal and elevational effects – Anna Lazzaro – Frontiers in Microbiology

Effects of long-term radionuclide and heavy metal contamination on the activity of microbial communities, inhabiting uranium mining impacted soils – Silvena Boteva – Environmental Science and Pollution Research

The community structures of prokaryotes and fungi in mountain pasture soils are highly correlated and primarily influenced by pH – Anders Lanzen – Frontiers in Microbiology

Water microbiome

Application of Microfluidic QPCR (MFQPCR) Technique to Monitor Bacterial Pathogens in Beach Water and Complex Environmental Matrices – Muruleedhara Byappanahalli – Environmental Science & Technology Letters

Natural sunlight shapes crude oil-degrading bacterial communities in northern Gulf of Mexico surface waters – Hernando P. Bacosa – Frontiers in MIcrobiology

Bacterioplankton community resilience to ocean acidification: evidence from microbial network analysis – Yu Wang – ICES Journal of Marine Sciences

Microbial Diversity and Bioactive Substances in Disease Suppressive Composts from India – C. M. Mehta – Compost Science & Utilization

Extremophile microbiome

Microbial metagenomics of oil sands tailings ponds: small bugs, big data – Julia M. Foght – Genome

Built environment microbiome

Changes in Microbes of the Built Environment in Early Stages of Urbanization – Maria Gloria Dominguez-Bello

Microbiome of death

The impact of carrion decomposition on the fatty acid methyl ester (FAME) profiles of soil microbial communities in southern Canada – Heloise Breton – Canadian Society of Forensic Science Journal

Metagenomics and bioinformatics

Assembly: a resource for assembled genomes at NCBI – Nucleic Acid Research

Web Resources for Metagenomics Studies – Pravin Dudhagara – Genomics, Proteomics & Bioinformatics

Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data – Martial Marbouty – Trends in Genetics

EBI metagenomics in 2016 – an expanding and evolving resource for the analysis and archiving of metagenomic data – Alex Mitchell – Nucleic Acids Research

probeBase—an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016 – Daniel Greuter – Nucleic Acids Research

Microbial ecology / more microbiology

Review: Microbial Invasions: The Process, Patterns, and Mechanisms – Cyrus Alexander Mallon – Trends in Microbiology

Review: Microbial diversity — exploration of natural ecosystems and microbiomes –
Sean M Gibbons – Current Opinion in Genetics & Development

Microbes As Friends, Not Foes: Shifting the Focus from Pathogenesis to Symbiosis – Sheila A. Homburger – The American Biology Teacher

Microbes in the news

Leading Antibiotic Doomsayer Mellows on Infection Armageddon – Michael Byrne – Motherboard
and
I believed we would face an antibiotics apocalypse – until now – Richard James – The Guardian

Tardigrades: Inside the Bizarre Genome of the World’s Toughest Animal – Ed Yong – The Atlantic

C&EN Talks With Microbiome Surveyor Stefanie Kandels-Lewis: The laboratory technician turned fixer kept the Tara Oceans project, an expedition to map the oceans’ microbial populations, afloat for four years – Sarah Everts – C&EN

Kiwi scientists invent stomach ulcer cure – Olivia Wannan – Stuff NZ

A Doctor Wrestles With Whether To Keep Wearing His White Coat – John Henning Schumann – NPR

When will the world wake up to the potential of poo power? – John Vidal – The Guardian

At TEDMED 2015: How microbiome studies could improve the future of humanity – ScopeBlog

Two Types of Diet May Protect Against Type 2 Through Regulation of Gut Microbiota – Diabetes in Control

Symberix lands two SBIRs for GI drug that targets the microbiome – Meghana Keshavan – MedCity News

Diet study overturns all we know about healthy eating – Israel21c

Liberia monitors over 150 Ebola contacts as virus re-emerges – James Harding Giahyue – Reuters

Now We Can Use Microbes to Make Designer Chocolate Flavors – Esther Inglis-Arkell – Gizmodo

Fossils show sign of ancient vampire microbes – Punctures in fossils suggest predation drove the evolution of self-defense systems – Thomas Sumner – Student Science

Science, publishing and career

Stepping Away from the Lab:Emilie, Can I Ask You? Why I made the decision to leave academic research and become an editor.- Cell

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November 19, 2015

Posted on by

Fungal dysbiosis in Crohn’s disease, a vagina monologue, stool sample storage, giraffe poop, Yellowstone lake, and extraction of bacteriophages.

Pregnancy and birth

Helminth infection, fecundity, and age of first pregnancy in women – Aaron D. Blackwell – Science

A Vagina Monologue: Mom’s Stress, Bugs, and Baby’s Brain – William A. Banks – Endocrinology

Human respiratory microbiome

The sinonasal bacterial microbiome in health and disease – Vijay R. Ramakrishnan – Current Opinion in Otolaryngology & Head & Neck Surgery

Human vaginal microbiome

Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity – A. Mitra – Scientific Reports

Human urinary tract microbiome

Role of the Gut Microbiome in Uremia: A Potential Therapeutic Target – Ali Ramezani – American Journal of Kidney Diseases

Human gut microbiome

Fungal dysbiosis in mucosa-associated microbiota of Crohn’s disease patients –
Giuseppina Liguori – Journal of Crohn’s and Colitis

Celiac Disease Genomic, Environmental, Microbiome, and Metabolomic (CDGEMM) Study Design: Approach to the Future of Personalized Prevention of Celiac Disease – Maureen M. Leonard – Nutrients

Sample storage conditions significantly influence faecal microbiome profiles – Jocelyn M Choo – Scientific Reports

Analysis of the Bacterial Diversity in Liver Abscess: Differences between
Pyogenic and Amoebic Abscesses – Miriam E. Reyna-Fabian – Am J Trop Med Hyg

Review: Gut microbiota regulates key modulators of social behavior – Arun Parashar – European Neuropsychopharmacology

Review: Metabolomic insights into the intricate gut microbial–host interaction in the development of obesity and type 2 diabetes – Magali Palau-Rodriguez – Frontiers in Microbiology

Animal models

The effect of microbial colonization on the host proteome varies by gastrointestinal location – Joshua S Lichtman – The ISME Journal

Animal microbiome

Analysis of the distal gut bacterial community by 454-pyrosequencing in captive giraffes (Giraffa camelopardalis) – Ousama AlZahal – Zoo Biology

Panamanian frog species host unique skin bacterial communities – Lisa K. Belden – Frontiers in Microbiology

Climate change stressors destabilize the microbiome of the Caribbean barrel sponge, Xestospongia muta – Michael P. Lesser – Journal of Experimental Marine Biology and Ecology

Plant, root, and soil microbiome

Bacteria in a wood fungal disease: characterization of bacterial communities in wood tissues of esca-foliar symptomatic and asymptomatic grapevines – Emilie Bruez – Frontiers in Microbiology

Water and extremophile microbiome

Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China – Qiufang Zhang – Frontiers in Microbiology

Distribution of cold adaptation proteins in microbial mats in Lake Joyce, Antarctica: Analysis of metagenomic data by using two bioinformatics tools – Hyunmin Koo – Journal of Microbiological Methods

Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function – William P. Inskeep – Frontiers in Microbiology

Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica – Tom O. Delmont – Frontiers in Microbiology

Book Chapter: Microbiological Monitoring of Lake Baikal – Valentina V. Parfenova – Novel Methods for Monitoring and Managing Land and Water Resources in Siberia

Waste microbiology

Effects of long-term radionuclide and heavy metal contamination on the activity of microbial communities, inhabiting uranium mining impacted soils – Silvena Boteva – Environmental Science and Pollution Research

Seasonal Changes in Bacterial Communities Cause Foaming in a Wastewater Treatment Plant – Ping Wang – Microbial Ecology

Temporal–spatial variation of bacterial diversity in estuary sediments in the south of Zhejiang Province, China – Xiao-Ming Lu – Applied Microbiology and Biotechnology

Viruses, metagenomics and bioinformatics

Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut – Josué L. Castro-Mejía – Microbiome

Comparison of Illumina de novo assembled and Sanger sequenced viral genomes: A case study for RNA viruses recovered from the plant pathogenic fungus Sclerotinia sclerotiorum – Mahmoud E. Khalifa – Virus Research

ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens – David Bonsall – F1000 Research

More microbiology

Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study – Yi-Yun Liu – The Lancet Infectious Diseases

Microbes in the news

Seafloor communities create electricity. In the digital age, we’re all connected by electricity — and some microbes are too – Meghan Bartels – ScienceLine

Microbe cheerleader: interview with Richard Roberts – Gijsbert Werner – Nature
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