Author Archives: eliesbik

December 22, 2015

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Periodontal disease associated with increased chance for breast cancer, rifaximin treatment of IBS patients, bacteria on surface of 2 different grape varieties in Spain, and a reproducible research workflow in R.

Human oral microbiome

Periodontal Disease and Breast Cancer: Prospective Cohort Study of Postmenopausal Women – Jo L. Freudenheim – Cancer Epidemiology, Biomarkers & Prevention

Distributions of Synergistetes in clinically-healthy and diseased periodontal and peri-implant niches – Xiao-Lin Yu – Microbial Pathogenesis

Human gut microbiome

Modulation of the gut microbiota composition by rifaximin in non-constipated irritable bowel syndrome patients: a molecular approach – Sara Soldi – Clinical and Experimental Gastroenterology

Roles of Sphincter of Oddi Laxity in Bile Duct Microenvironment in Patients with Cholangiolithiasis: From the Perspective of the Microbiome and Metabolome –
Tingbo Liang – Journal of the American College of Surgeons

Book chapter: Influence of Gut Microbiota on Hepatic Lipogenesis and Disease Pathogenesis – Vishal Singh – Hepatic De Novo Lipogenesis and Regulation of Metabolism

Review: Metabolic Interactions in the Gastrointestinal Tract (GIT): Host, Commensal, Probiotics, and Bacteriophage Influences – Luis Vitetta – MDPI Microorganisms

Book chapter: Gut Microbiome and Stress – Winnie-Pui-Pui Liew – Beneficial Microorganisms in Medical and Health Applications

Review: Dietary and Lifestyle Factors Associated with Colorectal Cancer Risk and Interactions with Microbiota: Fiber, Red or Processed Meat and Alcoholic Drinks – Tuan J. – GastroIntestinal Tumors

Models of microbiomes

Effect of chito-oligosaccharides over human faecal microbiota during fermentation in batch cultures – Inmaculada Mateos-Aparicio – Carbohydrate Polymers

Changes in gastric microbiota induced by Helicobacter pylori infection and preventive effects of Lactobacillus plantarum ZDY 2013 against such infection – Mingfang Pan – Journal of Dairy Science

Glycan:glycan interactions: High affinity biomolecular interactions that can mediate binding of pathogenic bacteria to host cells – Christopher J. Day – PNAS

Research highlight: A ‘fit’ microbiota to potentiate cancer immunotherapy – Maria Rescigno – Genome Medicine

Animal microbiome

Ecological Succession in the Honey Bee Gut: Shift in Lactobacillus Strain Dominance During Early Adult Development – Kirk E. Anderson – Host Microbe Interactions

A diverse array of new viral sequences identified in worldwide populations of the Asian citrus psyllid (Diaphorina citri) using viral metagenomics – Shahideh Nouri – Journal of Virology

Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia – Jamal S. M. Sabir – Science

Comparison of Fecal Microbial Communities between White and Black Pigs – Robin B. Guevarra – Journal of Applied Biological Chemistry

Plant, root, and soil microbiome

Bacterial diversity of Grenache and Carignan grape surface from different vineyards at Priorat wine region (Catalonia, Spain) – Maria del Carmen Portillo – International Journal of Food Microbiology

Field Application of the Mycorrhizal Fungus Rhizophagus irregularis Increases the Yield of Wheat Crop and Affects Soil Microbial Functionalities – Sanâa Wahbi – American Journal of Plant Sciences

Arbuscular mycorrhizal fungi reduced the ratios of inorganic/organic arsenic in rice grains – H. Li – Chemosphere

Characteristics of rhizosphere and bulk soil microbial communities in rubber plantations in Hainan Island, China – Wang, W. B. – Journal of Tropical Forest Science

Microbial community structure and its temporal changes in Rehmannia glutinosa rhizospheric soils monocultured for different years – Linkun Wu – European Journal of Soil Biology

Exotic Plant Alnus trabeculosa Alters the Composition and Diversity of Native Rhizosphere Bacterial Communities of Phragmites australis – Xueping Chen – Pedosphere

Long-term chronological shifts in bacterial communities and hydrolytic extracellular enzyme activities in the forty years following a land-use change from upland fields to paddy fields – Nan Jiang – Pedobiologia

Water microbiome

Resilience of SAR11 bacteria to rapid acidification in the high latitude open ocean – Manuela Hartmann – FEMS Microbiology Ecology

Selective pressure of temperature on competition and cross-feeding within denitrifying and fermentative microbial communities – Anna Hanke – Frontiers in Microbiology

Bioinformatics

Reproducible Research Workflow in R for the Analysis of Personalized Human Microbiome Data – Benjamin Callahan – Pacific Symposium on Biocomputing

Techniques

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys – William Walters – mSystems

Protocol: Studying Protistan Communities in Hydrocarbon-Contaminated Environments – Julia Johnke – Springer Protocols Handbooks

Microbes in the news

Harmful bacteria can survive in sandwich crackers, cookies for months, UGA study finds – Online Athens

Tomorrow’s Heart Drugs Might Target Gut Microbes – Ed Yong – The Atlantic

Bik’s Picks

Pharmacy delivery vans targeted by thieves seeking painkillers – David Armstrong – STAT news

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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 18, 2015

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Influence of breast milk on infant gut microbiome, built environment microbiome and mental health, and a review on treatment strategies of bacterial vaginosis biofilms.

General microbiome

Review: The Microbiome and Musculoskeletal Conditions of Ageing: A Review of Evidence for Impact and Potential Therapeutics – Claire J Steves – Journal of Bone and Mineral Research

Pregnancy and birth

Human Breast Milk and Infant Formulas Differentially Modify the Intestinal Microbiota in Human Infants and Host Physiology in Rats – Zhenmin Liu – The Journal of Nutrition

Models for microbiome research

Effects and mode of action of chitosan and ivy fruit saponins on the microbiome, fermentation and methanogenesis in the rumen simulation technique – Alejandro Belanche – – FEMS Microbiology Ecology

The long-term effect of uranium and pH on the community composition of an artificial consortium – Ryann M. Brzoska – FEMS Microbiology Ecology

Human gut microbiome

Optimal screening and donor management in a public stool bank – Abbas Kazerouni – Microbiome

Human vaginal microbiome

Review: Bacterial vaginosis biofilms: challenges to current therapies and emerging solutions – Daniela Machado – Frontiers in Microbiology

Built environment microbiome

The microbiome of the built environment and mental health – Andrew J. Hoisington – Microbiome

Microbes in the news
Microorganisms Spreading Holiday Cheer – Laurie Kundrat – Microbiologics

Nanotech weapon against chronic bacterial infections in hospitals – EurekAlert

Bacteria battle: How one changes appearance, moves away to resist the other – EurekAlert

Science, publishing, and career

New approach needed for governance of risky research, scholars say – Steve Fyffe – MedicalXpress

Do drug firm ties affect researchers’ reporting of study results? – Charles Piller – STAT news

Kaiser Permanente’s Innovative Approach to Care Delivery Defines Its New National School of Medicine Opening in 2019 — Kaiser Permanente

365 days: The best science images of 2015 – From Pluto to viral structures, this year produced an array of dazzling pictures – Daniel Cressey – Nature
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December 17, 2015

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Effects of intranasal flu vaccine on nose microbiota, intestinal microbiota of Dutch children, fungi in dung, optical sensors, and diurnal time scales in drinking water.

General microbiome

Review: Intestinal Microbiota and Metabolic Diseases: Pharmacological Implications – Liang Shen – Trends in Pharmacological Sciences

Editorial: Immunotherapy Not Working? Check Your Microbiota – Nathan R. West – Cancer Cell

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

Infection and immunity

The microbiome of diabetic foot osteomyelitis – S. A. V. van Asten – European Journal of Clinical Microbiology & Infectious Diseases

A baleful weed and the king of fruits: tolerance, immunity, and the microbiome – Kairav Sinha – International Journal of Dermatology

Human oral microbiome

Salivary changes in oral mucosal diseases – Yazan Hassona – Periodontology 2000

Human respiratory microbiome

The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles – Y. Tarabichi – Microbiome

Editorial: Precision respiratory medicine and the microbiome – Geraint B Rogers – The Lancet Respiratory Medicine

Review: The microbiome and critical illness – Robert P Dickson – The Lancet Respiratory Medicine

Human urinary tract microbiome

Intracellular Bacterial Communities: A Potential Etiology for Chronic Lower Urinary Tract Symptoms – Victoria C.S. Scott – Urology

Review: The interplay of extracellular matrix and microbiome in urothelial bladder cancer – Massimo Alfano – Nature Reviews Urology

Human gut microbiome

Composition and stability of intestinal microbiota of healthy children within a Dutch population – Tim G. J. de Meij – The FASEB Journal

Long-term risk of cardiovascular and cerebrovascular disease after removal of the colonic microbiota by colectomy: a cohort study based on the Danish National Patient Register from 1996 to 2014 – Anders Boeck Jensen – BMJ Open

Adverse events in faecal microbiota transplant: a review of the literature –
M. Baxter – Journal of Hospital Infection

Editorial: Antidiabetic drug treatment confounds gut dysbiosis associated with type 2 diabetes mellitus – David Holmes – Nature Reviews Endocrinology

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

Microbiome models

Response of gut microbiota to salinity change in two euryhaline aquatic animals with reverse salinity preference – Meiling Zhang – Aquaculture

Destabilization of the gut microbiome marks the end-stage of simian immunodeficiency virus infection in wild chimpanzees – Hannah J. Barbian – American Journal of Primatology

Non-lethal Inhibition of Gut Microbial Trimethylamine Production for the Treatment of Atherosclerosis – Zeneng Wang – Cell

Editorial: Immunotherapy Meets Microbiota – Jiaying Tan – Cell

Editorial: Drug the Bug! – Annika Lindskog Jonsson – Cell

Functional anatomy of the colonic bioreactor: Impact of antibiotics and Saccharomyces boulardii on bacterial composition in human fecal cylinders – Alexander Swidsinski – Systematic and Applied Microbiology

The Murine Lung Microbiome Changes During Lung Inflammation and Intranasal Vancomycin Treatment – Kenneth Klingenberg Barfod – The Open Microbiology Journal

Animal microbiome

Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens – Heidi M. Luter – PeerJ

Review: Dung-inhabiting fungi: a potential reservoir of novel secondary metabolites for the control of plant pathogens – Sabrina Sarrocco – Pest Management Science

Book Chapter: Age-Related Variation in the Scent Pouch Bacterial Communities of Striped Hyenas (Hyaena hyaena) – Kevin R. Theis – Chemical Signals in Vertebrates 13

Plant, root, and soil microbiome

Effects of chemical and biological pesticides on plant growth parameters and rhizospheric bacterial community structure in Vigna radiata – Sunil Singh – Journal of Hazardous Materials

Experimental Evidence that Fungi are Dominant Microbes in Carbon Content and Growth Response to Added Soluble Organic Carbon in Moss-rich Tundra Soil – O. Roger Anderson

Fertilizing with Animal Manure Disseminates Antibiotic Resistance Genes to the Farm Environment – Matti Ruuskanen – Journal of Environmental Quality

Water microbiome

Microbiology: lessons from a first attempt at Lake Ellsworth – D. A. Pearce – Philosophical Transactions A

Comprehensive genomic analyses of the OM43 clade including a novel species from Red Sea indicate ecotype differentiation among marine methylotrophs – Francy Jimenez-Infante – Applied and Environmental Microbiology

Built environment microbiome

Exposure to culturable and total microbiota in cultural heritage conservation laboratories – Rafał L. Górny – Int J Occup Med Environ Health

The impact of sampling, PCR, and sequencing replication on discerning changes in drinking water bacterial community over diurnal time-scales – Quyen Melina Bautista-de los Santos – Water Research

Food microbiology

The impact of yeast starter cultures on the microbial communities and volatile compounds in cocoa fermentation and the resulting sensory attributes of chocolate – Nádia Nara Batista – Journal of Food Science and Technology

Techniques

Optical sensors for sensing microbial life on a surface – M. Fischer – Applied and Environmental Microbiology

Metagenomes, viruses, and bioinformatics

Rise of Microbial Culturomics: Noncontiguous Finished Genome Sequence and Description of Beduini massiliensis gen. nov., sp. nov. – Gaël Mourembou – OMICS: A Journal of Integrative Biology

A metagenomic approach from aphid’s hemolymph sheds light on the potential roles of co-existing endosymbionts – Caroline De Clerck – Microbiome

MeFiT: Merging and Filtering Tool for Illumina Paired-End Reads for 16S rRNA Amplicon Sequencing – Hardik I. Parikh – ArXiv

Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach – Philippe Bordron – MicrobiologyOpen

What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail?
Henrike Zschach – Viruses

MEEPTOOLS: A maximum expected error based FASTQ read filtering and trimming toolkit – Vishal N. Koparde – Arxiv

Microbes in the news

Book review: I, superorganism – learning to love your inner ecosystem – Jon Turney

Science, publishing, and career

South Korean professors charged over alleged plagiarism scheme: Prosecutors accuse academics of colluding with publishers to boost their standing and sell more books – David Matthews – Times Higher Education
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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 16, 2015

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Two papers showing no differences on soil/root microbiomes between transgenic and non-transgenic plants, a new technique to study bacterial interactions. Then, after a 5-day hiatus, I finally got a new NCBI’s Pubmed alert with 159 articles. Before I sort through all of these, here is what I have collected so far today. I might do another blog post later today or tonight to catch up.

Microbiome biotech company to watch: Osel Inc in Mountain View

Microbiome models

Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling – Pedro Dorado-Morales – Scientific Reports

Human respiratory microbiome

Review: The human microbiome, asthma, and allergy – Amund Riiser – Allergy, Asthma & Clinical Immunology

Human gut microbiome

Sequence-based methods for detecting and evaluating the human gut mycobiome – Mallory J. Suhr – Letters in Applied Microbiology

Alterations in the gut microbiotas of children with food sensitization in early life – Chien-Chang Chen – Pediatric Allergy and Immunology

Plants, roots, and soil microbiome

Community Structure of Arbuscular Mycorrhizal Fungi in Rhizospheric Soil of a Transgenic High-Methionine Soybean and a Near Isogenic Variety – Jingang Liang – PLOS ONE

Transgenic banana plants expressing Xanthomonas wilt resistance genes revealed a stable non-target bacterial colonization structure – Jean Nimusiima – Scientific Reports

Comparison of myxobacterial diversity and evaluation of isolation success in two niches: Kiritimati Island and German compost – Kathrin I. Mohr – MicrobiologyOpen

Community Analysis of Root- and Tuber-Associated Bacteria in Field-Grown Potato Plants Harboring Different Resistance Levels against Common Scab – Akira Kobayashi – Microbes and Environments

Water and extremophile microbiome

Microbial eukaryotic distributions and diversity patterns in a deep-sea methane seep ecosystem – Alexis L. Pasulka – Environmental Microbiology

Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise – Julie Reveillaud – Environmental Microbiology

Bacterial Community Analysis of Drinking Water Biofilms in Southern Sweden – Katharina Lührig – Microbes and Environments

Microbes in the news

Amy Apprill of the Woods Hole Oceanographic Institution studies the humpback microbiome – Science Magazine

Microbiology: Inflammatory evidence – Kirsten Weir – Nature Outlook

Microbiomes: Curating communities from plants – Gwyn A. Beattie – Nature News and Views

Everything you wanted to know about space poop – David Coil – MicroBEnet

U.S. Navy Recruits Gut Microbes to Fight Obesity and Disease:
The military is creating “smart” E. coli to combat a variety of disorders faced by warfighters – Jennifer Ackerman – Scientific American

Gut microbes: Burning calories while you sleep? Study links changes in gut bacteria to lower resting metabolic rate and weight gain in mice – Jennifer Brown – Iowa Now

Zinc deficiency alters gut bacteria makeup and function – Krishna Ramanujan – Cornell University

Our water pipes crawl with millions of bacteria – Lund University – EurekAlert

1 Percent Human, 99 Percent Bacteria – David Samadi – Huffington Post

Land use may weaken amphibian’s capacity to fight infection and disease – Case Western Reserve University – EurekAlert

Science, publishing, and career

Evelyn Witkin and the Road to DNA Enlightenment – Claudia Dreifus – NY Times

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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 14, 2015

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Not a lot of papers today; NCBI’s PubMed alerts has not come out for a couple of days (I will probably get an email tomorrow with 200 new papers…..). Today’s main paper is a not-very microbiological paper on the human gut metagenome.

Human gut microbiome

Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome – Volodymyr Kuleshov – Nature Biotechnology

Review: Microbiota–mitochondria inter-talk: consequence for microbiota–host interaction – Yann Saint-Georges-Chaumet – Pathogens and Disease

Animal microbiome

Toward a better understanding of mechanisms of probiotics and prebiotics action in poultry species – K. M. Ajuwon – Journal of Applied Poultry Research

Microbes in the news

Not sure what is stunning about the diversity they found but: Stunning diversity of gut bacteria uncovered by new approach to gene sequencing devised at Stanford – Jennie Dusheck – Stanford Medicine News Center

Bacteriophage: The Microscopic Black Market – Stefan Rollnick – Huffington Post

Intestinal bacteria are in command – Gemma K. Alderton – Nature Reviews Immunology

The bacteria among us – Jeffrey Perkel – Biotechniques

Antibiotic Use in Food Animals Continues to Rise: Soaring levels of drug use in livestock fuels concern about resistant bacteria, human health – Tom Polansek – Scientific American

Cambridge’s Seres targets ulcerative colitis with new drug based on gut bacteria – Don Seiffert – Boston Business Journal

Altered microbiome burns fewer calories – Study links changes in gut bacteria to lower resting metabolic rate and weight gain in mice – EurekAlert

“How microbial communities interact. It’s kind of like in economics”
Economies of Ail: How Bacteria Flourish – Jo Craven McGinty – Wall Street Journal (subscription required)
Shorter version here that does not require subscription:
Can economics explain our gut microbiome? – Genetic Literacy Project

World’s First Microbiome Fund Swells to €160M With Major Pharma Also Chipping In – LabioTech

Science, publishing, and career

Law ignored, patients at risk: failure to report results of human studies to ClinicalTrials.gov database – Charles Piller – STAT news
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December 13, 2015

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Apple juice or almond consumption, lessons from animal studies, distinguishing between live and dead methanogens.

Human gut microbiome

Comparative study of fecal microbiota in patients with type II diabetes after consumption of apple juice for 4 weeks – Gyu-Sung Cho – Food Science and Biotechnology

Diet quality improves for parents and children when almonds are incorporated into their daily diet: a randomized, crossover study – Alyssa M. Burns – Nutrition Research

Review: Diagnosis and treatment of small intestinal bacterial overgrowth – Francesca Romana Ponziania – Expert Review of Gastroenterology & Hepatology

Review: The enteric microbiome in hepatobiliary health and disease – James H. Tabibian – Liver International

Animal models

Review: The influence of the young microbiome on inflammatory diseases—Lessons from animal studies – Katja M. Bendtsen – Birth Defects Research Part C: Embryo Today: Reviews

Plant, root, and soil microbiome

Interaction between lithification and resource availability in the microbialites of Río Mesquites, Cuatro Ciénegas, México – J. R. Corman – Geobiology

The diversity and abundance of phytase genes (BPP) in bacterial communities of the maize rhizosphere – Simone Raposo Cotta – Letters in Applied Microbiology

Bring on the wheelbarrow: Transplanting soil microbiomes leads to lasting effects on willow growth, but not on the rhizosphere microbiome – Etienne Yergeau – Frontiers in Microbiology

Differential responses of soil bacterial taxa to long-term P, N, and organic manure application – Ying Wang – Journal of Soils and Sediments

Water and extremophile microbiome

Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin, Gulf of California – Luke McKay – Environmental Microbiology Reports

Oceanic fronts: transition zones for bacterioplankton community composition – Federico Baltar – Environmental Microbiology Reports

PhD thesis: Hydrothermal Habitats: Measurements of Bulk Microbial Elemental Composition, and Models of Hydrothermal Influences on the Evolution of Dwarf Planets – Marc Francois Luarent Neveu – Arizona State University

Metagenomics and bioinformatics

Network construction and structure detection with metagenomic count data – Zhenqiu Liu – BioData Mining

A simple algorithm for identifying integrons and gene cassettes in bacteria on next generation sequencing data – Guan-Jie Hua – International Journal of Data Mining and Bioinformatics (no access for me)

Techniques

Fluorescent in situ hybridization for the localization of viruses, bacteria and other microorganisms in insect and plant tissues – Adi Kliot – Methods

Propidium monoazide treatment to distinguish between live and dead methanogens in pure cultures and environmental samples – Janine Heise – Journal of Microbiological Methods

Microbes in the news

You’re Surrounded by Bacteria That Are Waiting for You to Die – Erika Engelhaupt – National Geographic

Does That Wine Smell Good? Bacteria in Your Saliva Deserve Some of the Credit
Study shows some wine aromatics aren’t released until they meet the bacteria in our mouths – Kasey Carpenter – Wine Spectator

San Jose: Hospital nurse had tuberculosis; hundreds of babies, moms need treatment or tests – Tracy Seipel – Mercury News

Based on a 2006 paper: This Weed Takes Out Other Plants by Attacking Their “Gut Bacteria” – Esther Inglis-Arkell – Gizmodo

Bacteria Hysteria

Could your child’s teddy give them a stomach bug? Wash youngsters’ favourite toys… and other tips to keep your family lurgy-free this Christmas – The Sun

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December 12, 2015

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Events

3rd Microbiome R&D and Business Collaboration Forum: Europe, 11-12 April, 2016, London

Pregnancy and birth

Study protocol (no data yet): Intestinal microbiota composition after antibiotic treatment in early life: the INCA study – N. B. M. M. Rutten – BMC Pediatrics

Review: The very low birth weight infant microbiome and childhood health – Maureen W. Groer – Birth Defects Research Part C: Embryo Today: Reviews

Review: Development of the infant intestinal microbiome: A bird’s eye view of a complex process – Sharon B. Meropol – – Birth Defects Research Part C: Embryo Today: Reviews

Review: Microbial programming of health and disease starts during fetal life – Petya T. Koleva – Birth Defects Research Part C: Embryo Today: Reviews

Human gut microbiome

Review: Gut microbiota in health and disease: an overview focused on metabolic inflammation – R. Nagpal – Beneficial Microbes

Animal models

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

Water microbiome

Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre – Jessica A Bryant – ISME Journal

Bioprospecting around Arctic islands: Marine bacteria as rich source of biocatalysts
– Concetta De Santi – Journal of Basic Microbiology

Built environment microbiology

Review: Microlayer enrichment in natural treatment systems: linking the surface microlayer to urban water quality – Megan A. Rippy – Wiley Interdisciplinary Reviews: Water

Food microbiology

Dynamics and Diversity of Microbial Community Succession of Surimi During Fermentation with Next-Generation Sequencing – Dandan Zhao – Journal of Food Safety

Infection microbiology

Making the Leap from Research Laboratory to Clinic: Challenges and Opportunities for Next-Generation Sequencing in Infectious Disease Diagnostics – Brittany Goldberg – mBio

Microbes in the news

Scientist who injected himself with 3.5 million year old bacteria ‘feels fine’ – Brittany A. Roston – Slash Gear

Kim Kardashian Has a Cold: Health issues are the new frontier in celebrity PR – Ruth Graham – Slate

Biotech startup will mine the gut for drugs affecting human behavior – Ike Swetlitz – STAT news

Functions of global ocean microbiome key to understanding environmental changes: Mary Ann Moran – University of Georgia / EurekAlert

Foodstuffs: N.H. Sauerkraut Maker Rides the Microbiome Wave Into Tom Brady’s Pantry (Maybe) – Sam Evans-Brown – NHPR

Kickstarter project: Snotbot, custom-built drones that hover in the air above a surfacing whale and collect the blow (or snot) exhaled from its lungs – Kickstarter
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