Category Archives: Metagenomics & Bioinformatics

June 1, 2015

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Still catching up from my trip abroad – lots of new papers to share, so I will do two blog posts today.

General microbiome

Elucidating microbial codes to distinguish individuals – Allyson L. Byrd and Julia A. Segre – PNAS

Human oral microbiome

Periodontal status and pathogenic bacteria after gastric bypass: a cohort study – Sílvia Helena de Carvalho Sales-Peres – Journal of Clinical Periodontology

Inflammation-associated microbiota in pediatric eosinophilic esophagitis – Alain J Benitez – Microbiome

Global transcription of CRISPR loci in the human oral cavity – Andrew G Lum – BMC Genomics

Oral and Gastric Helicobacter Pylori: Effects and Associations – Nélio Veiga – PLOS ONE

Book Chapter: Obesity and Periodontal Disease – Simon D. Tran – Environmental Metagenomics

Human gut microbiome

Investigation of the Association Between the Fecal Microbiota and Breast Cancer in Postmenopausal Women: a Population-Based Case-Control Pilot Study – James J. Goedert – Journal of the National Cancer Institute

Review: The art of targeting gut microbiota for tackling human obesity – Marisol Aguirre, Koen Venema – Genes and Nutrition

Review article: dietary fibre–microbiota interactions – H. L. Simpson and B. J. Campbell – Alimentary Pharmacology & Therapeutics

Animal and other microbiome models

Evolutionary transition in symbiotic syndromes enabled diversification of phytophagous insects on an imbalanced diet – Sailendharan Sudakaran – ISME Journal

Fecal Microbial Transplant After Ileocolic Resection Reduces Ileitis but Restores Colitis in IL-102/2 Mice – Troy Perry – IBD Journal

Alteration of gut microbiota by vancomycin and bacitracin improves insulin resistance via glucagon-like peptide 1 in diet-induced obesity – Injae Hwang – The FASEB Journal

Pheromone killing of multidrug-resistant Enterococcus faecalis V583 by native commensal strains – Michael S. Gilmore – PNAS

Human Microbiota-Associated Swine: Current Progress and Future Opportunities – Mei Wang and Sharon M. Donovan – ILAR Journal

Animal microbiome

Marked seasonal variation in the wild mouse gut microbiota – Corinne F Maurice – ISME Journal

Evolution of host specialization in gut microbes: the bee gut as a model – Waidan K Kwong – Gut Microbes

Soil microbiome

Soil bacterial diversity patterns and drivers along an elevational gradient on Shennongjia Mountain, China – Yuguang Zhang – Microbial Biotechnology

High resolution dynamics of microbial communities during dissimilatory selenate reduction in an anoxic soil – Ronald Ragudo Navarro – Environmental Science & Technology

Study and assessment of microbial communities in natural and commercial bioleaching – Arevik Vardanyan – Minerals Engineering

Benefactor and allelopathic shrub species have different effects on the soil microbial community along an environmental severity gradient – S. Hortal – Soil Biology and Biochemistry

Evaluation of soil microbial communities as influenced by crude oil pollution – Eucharia Oluchi Nwaichi and Magdalena Frac – African Journal of Biotechnology

Water microbiome

Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management – William Van Bonn – Zoo Biology

Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations – Sergio Pulido-Tamayo – Nucleic Acids Research

Manganese and iron as structuring parameters of microbial communities in Arctic marine sediments from the Baffin Bay – Camelia Algora – FEMS Microbial Ecology

Quantitative analysis of commensal Escherichia coli populations reveals host-specific enterotypes at the intra-species level – Mounira Smati – Microbiology Open

Manganese cycling microbial communities inside deep-sea manganese nodules – Marco Blöthe – Environmental Science & Technology

Effects of Misgurnus anguillicaudatus and Cipangopaludina cathayensis on Pollutant Removal and Microbial Community in Constructed Wetlands – Pengfei Li – Water

Thesis: Evaluating changes in diversity and functional gene abundance of denitrifying microbe communities and nutrient concentrations in runoff following the implementation of low-grade weirs in agricultural drainage systems – Beth Baker – Mississippi State University/ Gradworks

Bioreactor microbiome

Lipid hydrolysis products affect the composition of infant gut microbial communities in vitro – Rikke G. Nejrup – British Journal of Nutrition

Effect of phospholipid on pyrite oxidation and microbial communities under simulated acid mine drainage (AMD) conditions – Andro-Marc Pierre-Louis – Environmental Science & Technology

Antibiotic resistome and its association with bacterial communities during sewage sludge composting – Jianqiang Su – Environmental Science & Technology

Food microbiology

Microbiota dynamics associated with environmental conditions and potential roles of cellulolytic communities in traditional Chinese cereal starter solid-state fermentation – Pan Li- Applied and Environmental Microbiology

Bioinformatics and metagenomics

Note: not metagenomics but Single Locus Sequencing / OTU defining: MICCA: a complete and accurate software for taxonomic profiling of metagenomic data – Davide Albanese – Scientific Reports

An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data: GotCloud – Goo Jun – Genome Research

GITIRBio: A Semantic and Distributed Service OrientedArchitecture for Bioinformatics Pipeline – Luis F. Castillo – Journal of Integrative Bioinformatics

mmnet: an R package for metagenomics systems biology analysis: community-level metabolic network reconstruction – Yang Cao – BioMed Research International

Techniques

How to evaluate PCR assays for the detection of low-level DNA – Frederik Banch Clausen – APMIS
http://onlinelibrary.wiley.com/doi/10.1111/apm.12405/full

A Novel Microbial Source Tracking Microarray for Pathogen Detection and Fecal Source Identification in Environmental Systems – Xiang Li – Environmental Science & Technology

Functional Foods

Programmable probiotics for detection of cancer in urine – Tal Danino – Science Translational Medicine

Microbes in the news

Alterations to the eye microbiome of contact lens wearers may increase infections – Medical News Today

U.S. defense chief monitoring military anthrax investigation – Reuters

Deadly Bacteria Now a Proven Cancer Detector? – Samantha Solomon – Wall Street Daily’

Gut Bacteria Impacts Toddlers’ Behavior, Particularly Boys – Traci Pederson – PsychCentral

Cervicovaginal Bacteria May Increase the risk of HIV Acquisition in Women – University of Kwazulu – Natal

DNA Genotek’s microbiome collection and stabilization blog: Microbiome learnings from the Weizmann Institute – Cindy MacCullough – DNA Genotek

Scientists probe mysterious wave of antelope deaths – Rory Galloway – BBC News

Bacteria may cause Type 2 diabetes – University of Iowa Now

Should we care about fungi? The mycobiome: an emerging field of the human microbiome research – Human Microbiome Club

Hardy bacteria thrive under hot desert rocks – Nola Taylor Redd – Phys.org

Colon Cancer Diagnosis With Lumninescent Bacteria: Modified Probiotics Can Successfully Detect Tumors In Liver – Colon Cancer News Today

Scientists Find Link Between Ocean Bacteria and Atmosphere – Simon Yu – UCSD Guardian

Woman goes blind after cat licks her and transmits rare bacteria that could affect the brain, eyes, heart, and internal organs – Daily Mail

Science, career, and publishing

This poor advice blog post was retracted from Science today, but the internet never forgets.

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May 29, 2015

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General microbiome

Perspective: The trendy microbes – VK Viswanathan – Gut Microbes

Review: Use of the Microbiome in the Practice of Epidemiology: A Primer on -Omic Technologies – Betsy Foxman – American Journal of Epidemiology

Review: Biological warfare: Microorganisms as drivers of host–parasite interactions – Nolwenn M. Dheilly – Infection, Genetics and Evolution

Microbiome of pregnancy and birth

Bacterial communities in neonatal feces are similar to mothers’ placentae – X-D Dong – Canadian Journal of Infectious Diseases and Medical Microbiology

Human oral microbiome

Maturation of Oral Microbiota in Children with or without Dental Caries – Pernilla Lif Holgerson – PLOS ONE

Exploring the variation of oral microbiota in supragingival plaque during and after head-and-neck radiotherapy using pyrosequencing – Li Gao – Archives of Oral Biology

Human genital microbiome

Sensitive Detection of Thirteen Bacterial Vaginosis-Associated Agents Using Multiplex Polymerase Chain Reaction – Natália Malaguti – BioMed Research International

Human gut microbiome

Esophageal Microbiome in Eosinophilic Esophagitis – J. Kirk Harris – PLOS ONE

Pyrosequencing Analysis Reveals Changes in Intestinal Microbiota of Healthy Adults Who Received a Daily Dose of Immunomodulatory Probiotic Strains – Julio Plaza-Díaz – Nutrients

Fecal menaquinone profiles of overweight adults are associated with gut microbiota composition during a gut microbiota–targeted dietary intervention – J Philip Karl – American Journal of Clinical Nutrition

Pouch Inflammation is Associated with a Decrease in Specific Bacterial Taxa – Leah Reshef – Gastroenterology

Human seroreactivity to gut microbiota antigens – Benjamin S. Christmann – Journal of Allergy and Clinical Immunology

Acute cholecystitis associated with infection of Enterobacteriaceae from gut microbiota – Jianjun Liu – Clinical Microbiology and Infection

Letter to the Editor: Mediterranean diet: the missing link between gut microbiota and inflammatory diseases – M Bifulco – European Journal of Clinical Nutrition

Editorial: Fecal Microbiota Transplantation for Ulcerative Colitis: Not Just Yet – Ari M. Grinspan – Gastroenterology

Perspective: Rifaximin, gut microbes and mucosal inflammation: unraveling a complex relationship – Jun Gao – Gut Microbes

Review: Apples and Cardiovascular Health—Is the Gut Microbiota a Core Consideration? – Athanasios Koutsos  – Nutrients

Animal models of microbiome research

Exercise Is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats – Agnieszka Mika – PLOS ONE

Gut microbiota inhibit Asbt-dependent intestinal bile acid reabsorption via Gata4 – Carolien Out – Journal of Hepatology

Animal microbiome

RUMINANT NUTRITION SYMPOSIUM: The impact of the rumen microbiome on nutrition, health, and production – R.A. Kohn – Journal of Animal Science
How to use data on the rumen microbiome to improve our understanding of ruminant nutrition – J.L. Firkins – Journal of Animal Science

Production attributes of Merino sheep genetically divergent for wool growth are reflected in differing rumen microbiotas – I. De Barbieri – Livestock Science

The camel faecal metagenome under different systems of management: phylogenetic and gene-centric Approach – Suchitra S. Dande – Livestock Science

Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences – Cornelia Roder – Molecular Ecology

Early life microbial colonization of the gut and intestinal development differ between genetically divergent broiler lines – Dirkjan Schokker – BMC Genomics

Soil microbiome

Biodegradation kinetic rates of diesel-contaminated sandy soil samples by two different microbial consortia – Alejandro Ledezma-Villanueva – Annals of Microbiology

Temperature sensitivity of soil bacterial community along contrasting warming gradient – Jinfeng Wu – Applied Soil Ecology

Water microbiome

Heavy metals and TPH effects on microbial abundance and diversity in two estuarine areas of the southern-central coast of São Paulo State, Brazil – Aline Bartelochi Pinto – Marine Pollution Bulletin

Food microbiology

Microbial food safety: Potential of DNA extraction methods for use in diagnostic metagenomics – Mathilde H. Josefsen – Journal of Microbiological Methods

Metagenomics

Alarmingly high segregation frequencies of quinolone resistance alleles within human and animal microbiomes are not explained by direct clinical antibiotic exposure – Wesley Field – Genome Biology and Evolution

Bioinformatics

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses – Jennifer Fouquier – PeerJ PrePrints

Microbes in the news

The germ at the scene of the crime – Viviane Richter – Cosmos

Researchers combat bias in next-generation DNA sequencing – Eric Beidel – Phys.org

Microbiome research heralds new era of medical diagnosis – Aaron Krumins – Extreme Tech

Community Microbiomes: Chatting Cat Scat with Kittybiome’s Holly Ganz – Scott Edmunds – BioMedCentral Blog

Pheromones produced by gut bacteria found to kill resistant variants of its own kind – Bob Yirka – Phys.org

500 protesters chant in Santa Barbara as bacteria munch the oil spill – Chriss W. Street – Breitbart

Science, publishing, and career

Career Advice From an Oldish Not-Quite Geezer: You can’t count on your publications and awards to take care of you – Robert J. Sternberg – Chronicle

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May 28, 2015

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Catching up after a couple of days in Paris…

General microbiome

Metagenomics meets time series analysis: unraveling microbial community dynamics – Karoline Faust – Current Opinion in Microbiology

What’s Bugging you and your Diet? – Bryn L Yeomans and Nicholas T Bello – Journal of Food and Nutritional Disorders

Pregnancy and birth microbiome

Comparison of Bacterial Composition in Blood and Placentas Using Conventional and Molecular Methods – Tingtao Chen – Clinical Microbiology: Open Access

Gut microbiome composition is associated with temperament during early childhood – Lisa M. Christian – Brain, Behavior, and Immunity

Human genital microbiome

Cervical Microbiota in Women with Preterm Prelabor Rupture of Membranes – Marian Kacerovsky – PLOS ONE

Re: The vaginal microbiome, vaginal anti-microbial defence mechanisms and the clinical challenge of reducing infection-related preterm birth – C Griffin – BJOG: An International Journal of Obstetrics & Gynaecology
Author’s reply re: The vaginal microbiome, vaginal anti-microbial defence mechanisms and the clinical challenge of reducing infection-related preterm birth – SS Witkin – BJOG: An International Journal of Obstetrics & Gynaecology

Human gut microbiome

Human seroreactivity to gut microbiota antigens – Benjamin S. Christmann – Journal of Allergy and Clinical Immunology

Models of microbiome research

A Role for Gut Microbiota and the Metabolite-Sensing Receptor GPR43 in a Murine Model of Gout – Angélica T. Vieira – Arthritis & Rheumatology

Tumor Grafting Induces Changes of Gut Microbiota in Athymic Nude Mice in the Presence and Absence of Medicinal Gynostemma Saponins – Lei Chen – PLOS ONE

Dynamic vaginal microbiota in pigtail macaques is associated with menstrual cycle and inflammation (MUC9P.753) – Nichole Klatt – The Journal of Immunology

Animal microbiome

Pyrosequencing Characterization of the Microbiota from Atlantic Intertidal Marine Sponges Reveals High Microbial Diversity and the Lack of Co-Occurrence Patterns – Anoop Alex – PLOS ONE

Characterization of the Bacterial Microflora on the Skin of Boreal toads, Anaxyrus (Bufo) boreas boreas, and Columbia Spotted Frogs, Rana luteiventris, in Grand Teton National Park, Wyoming USA – A.M. Hillis – International Journal of Microbiology Research

Soil microbiome

Niche and metabolic principles explain patterns of diversity and distribution: theory and a case study with soil bacterial communities – Jordan G. Okie – The Royal Society – Proceedings B

Book: The Soils of Antarctica – James G. Bockheim

Thesis: Role of Viruses Infecting Bacteria in Subsurface Sediments and Groundwater – Donald Pan – University of Nebraska-Lincoln

Water microbiome

Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria – S. A. Amin – Nature

Towards a better quantitative assessment of the relevance of deep-sea viruses, Bacteria and Archaea in the functioning of the ocean seafloor – R. Danovaro – Aquatic Microbial Ecology

Bioreactor microbiome

Ecological Media Reveal Community Structure Shifts in a Municipal Wastewater Treatment Train – Bergmann RC – Bioremediation & Biodegradation

Extremophile microbiome

Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species – Nur A. Hassan – PNAS

Book: The Soils of Antarctica – James G. Bockheim

Techniques

New Perspectives on Microbial Community Distortion after Whole-Genome Amplification – Alexander J. Probst – PLOS ONE

Human Bacterial and Fungal Amplicon Collection and Processing for Sequencing – Julia Oh – Bio-Protocol

Deconstructing the Polymerase Chain Reaction: Understanding and Correcting Bias Associated with Primer Degeneracies and Primer-Template Mismatches – Stefan J. Green – PLOS ONE

Microbial Ecology

Community quorum sensing signalling and quenching: microbial granular biofilm assembly – Chuan Hao Tan – NPJ Biofilms and Microbiomes

Theoretical analysis of the cost of antagonistic activity for aquatic bacteria in oligotrophic environments – Eneas Aguirre-von-Wobeser – Frontiers in Microbiology

More microbiology

Instrumentation: The mystery of the microscope in mud – Brian J. Ford – Nature

Antibiotic alternatives rev up bacterial arms race: From predatory microbes to toxic metals, nature is inspiring new ways to treat infections – Sara Reardon – Nature

Bioinformatics and Metagenomics

obitools: a unix-inspired software package for DNA metabarcoding – Frédéric Boyer – Molecular Ecology Resources

GenoLIB: a database of biological parts derived from a library of common plasmid features – Neil R. Adames – Nucleic Acids Research

PhD Thesis: Scalable Parallel Methods for Analyzing Metagenomics Data at Extreme Scale – Jeffrey A. Daily – Washington State University

Book Chapter: Lessons Learned from Simulated Metagenomic Datasets – Germán Bonilla-Rosso – Encyclopedia of Metagenomics

Review: Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology – Lisa Ufarté – Frontiers in Microbiology

Microbes in the news

The microbial world at our feet – Richard Burn – Society for General Microbiology

‘Bacteria Whisperer’ Bonnie Bassler reveals the secret lives of bacteria in Vancouver – CBC News

Google Ventures: These eight life sciences techs are the most promising – and worthy of investment – Meghana Keshavan – MedCityNews

Fast food versus the African diet, the bacteria battle waged in your gut – Carina Storrs – CNN

Toddler temperament could be influenced by different types of gut bacteria – Science Daily

Is Your Nervous System Being Hacked by Bacteria in Your Gut? – Gaia Vince – Gizmodo

Bacteria appears to help bats fight deadly white-nose syndrome – Mary Beth Griggs – Popular Science

Invisible helpers of the sea: Marine bacteria boost growth of tiny ocean algae – Phys.org

Some like it hot: Extremophile bacteria could be key to solving nuclear problems – Seaes Manchester

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May 23, 2015

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Human vaginal microbiome

Vaginal Biofilm: Much Ado About Nothing, or a New Therapeutic Challenge? – Jack D. Sobel – Clinical Infectious Diseases

Human respiratory microbiome

Correlation between Either Cupriavidus or Porphyromonas and Primary Pulmonary Tuberculosis Found by Analysing the Microbiota in Patients’ Bronchoalveolar Lavage Fluid – Yuhua Zhou – PLOS ONE

Human gut microbiome

Temporal and technical variability of human gut metagenomes – Anita Y Voigt – Genome Biology

Gut metabolites and bacterial community networks during a pilot intervention study with flaxseeds in healthy adult men – Ilias Lagkouvardos – Molecular Nutrition & Food Research

Fecal Microbiota in Pediatric Inflammatory Bowel Disease and Its Relation to Inflammation – Kaija-Leena Kolho – American Journal of Gastroenterology

The impact of ciprofloxacin and clindamycin administration on Gram-negative bacteria isolated from healthy volunteers and characterizing the resistance genes they harbour – Roderick M. Card – Antimicrobial Agents and Chemotherapy

Review: The Role of the Microbiome in Mental Health: A Psychoneuroimmunologic Perspective – Kelly Brogan – Alternative and Complementary Therapies

Review: Dysbiosis and Immune Dysregulation in Outer Space – Jorge L. Cervantes – International Reviews of Immunology

Models of microbiome research

Effects of two whole-grain barley varieties on caecal SCFA, gut microbiota and plasma inflammatory markers in rats consuming low- and high-fat diets – Yadong Zhong – British Journal of Nutrition

Animal microbiome

Dogs: Characterization of Microbial Dysbiosis and Metabolomic Changes in Dogs with Acute Diarrhea – BC Guard – PLOS ONE

Coral: Productivity links morphology, symbiont specificity and bleaching in the evolution of Caribbean octocoral symbioses – David M Baker – ISME Journal

Plant and soil microbiome

Quantitative assessment of the differential impacts of arbuscular and ectomycorrhiza on soil carbon cycling – Nadejda A. Soudzilovskaia – New Phytologist

Soil pH and biome are both key determinants of soil archaeal community structure –
Binu M. Tripathi – Soil Biology and Biochemistry

Solarization makes a great impact on the abundance and composition of microbial communities in soil – Kazunori Yokoe – Soil Science and Plant Nutrition

The relationship between successional vascular plant assemblages and associated microbial communities on coal mine spoil heaps – G. Woźniak – Community Ecology

Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover – Yuting Liang – ISME Journal

Differential acquisition of amino acid and peptide enantiomers within microbial community groups and its implications for carbon and nitrogen cycling in soil – R.C.I. Broughton – Soil Biology and Biochemistry

Molecular mechanisms underlying the close association between soil Burkholderia and fungi – Nejc Stopnisek – ISME Journal

Water microbiome

Editorial: Computational eco‐systems biology in Tara Oceans: translating data into knowledge – Shinichi Sunagawa – Molecular Systems Biology

Editorial: The making of Tara Oceans: funding blue skies research for our Blue Planet – Eric Karsenti – Molecular Systems Biology

Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes – Jacob A Cram – ISME Journal

Air microbiome

Characterization of active and total fungal communities in the atmosphere over the Amazon rainforest – A. M. Womack – Biogeosciences Discuss

Bioreactor microbiology

Palygorskite changes heavy metal bioavailability and microbial functional diversity in sewage sludge composting – Siying Liu – Environmental Technology

Evaluation of System Performance and Microbial Communities of a Bioaugmented Anaerobic Membrane Bioreactor Treating Pharmaceutical Wastewater – Kok Kwang Ng – Water Research

Bioinformatics and Metagenomics

Read Mapping on de Bruijn graph – Antoine Limasset and Pierre Peterlongo – arXiv

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation – Roie Levy – BMC Bioinformatics

Consortium of the ‘bichlorophyllous’ cyanobacterium Prochlorothrix hollandica and chemoheterotrophic partner bacteria: culture and metagenome based description – Natalia Velichko – Environmental Microbiology Reports

A new approach for detecting fungal and oomycete plant pathogens in next generation sequencing metagenome data utilising electronic probes – Andres Espindola – International Journal of Data Mining and Bioinformatics

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity – Yan He – Microbiome

Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries – Kathy N Lam – Microbiome

Metabolomics

Using community metabolomics as a new approach to discriminate marine microbial particulate organic matter in the western English Channel – Carole A. Llewellyn – Progress in Oceanography

Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat – Xueju Lin – ISME Journal

Phages, viruses, CRISPRs

Computational Detection of CRISPR/crRNA Targets – Ambarish Biswas – CRISPR Methods in Molecular Biology

Creation and Analysis of a Virome: Using CRISPR Spacers – Michelle Davison – CRISPR Methods in Molecular Biology

More microbes

Not open access, alas. van Leeuwenhoek microscopes—where are they now? – Lesley A. Robertson – FEMS Microbiology Letters

Microbes in the news

Headline from 2030: Is your space commute making you sick? Microbiomes undergo weird changes in space – Alexandra Ossola – Popular Science

Leaf bacteria fertilize trees, researchers claim – Elizabeth Pennisi – Science

The bugs within us – Hordes of bacteria live inside animals, affecting their health, food choices and mating – Roberta Kwok – Student Science

Report from the 1st Annual Translational Microbiome Conference: Moving from lab to clinic: Microbiome on the move – Taconic Insights

Recent Built Environment Microbiology papers – Elisabeth Bik – MicroBE.net

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May 20, 2015

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Human wound microbiome

Biochemical Association of Metabolic Profile and Microbiome in Chronic Pressure Ulcer Wounds – Mary Cloud B. Ammons – PLOS ONE

Human gut microbiome

Development and Validation of a Biomarker for Diarrhea-Predominant Irritable Bowel Syndrome in Human Subjects – Mark Pimentel – PLOS ONE

Editorial: Microbiota key to diet-associated risk of colon cancer – Nature Reviews Microbiology

Microbiome models

Antibiotics in Early Life Alter the Gut Microbiome and Increase Disease Incidence in a Spontaneous Mouse Model of Autoimmune Insulin-Dependent Diabetes – Sophie Candon – PLOS ONE

Changes in Gut Microbiota in Rats Fed a High Fat Diet Correlate with Obesity-Associated Metabolic Parameters – Virginie Lecomte – PLOS ONE

Gut Microbiota Dynamics during Dietary Shift in Eastern African Cichlid Fishes – Laura Baldo – PLOS ONE

Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant – Dongming Liu – Microbial Biotechnology

Animal microbiome

The Fecal Microbiome in Cats with Diarrhea – Jan S. Suchodolski – PLOS ONE

Plant and soil microbiome

Effect of crop management and sample year on abundance of soil bacterial communities in organic and conventional cropping systems – C.H. Orr – Journal of Applied Microbiology

Water microbiome

Characterization of the relative importance of human- and infrastructure-associated bacteria in grey water: a case study – S.P. Keely – Journal of Applied Microbiology

Techniques

PCR-Based Multiple Species Cell Counting for In Vitro Mixed Culture – Ruijie Huang – PLOS ONE

Bioinformatics

FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data – Takeru Uchiyama – PLOS ONE

Microbes in the news

Manipulating the Microbiome Produces Hope, but Uneven Results – Monica J. Smith – Gastroenterology & Endoscopy News

In America, is our food, in fact, too clean? – Kate Murphy – Herald Tribune

Study reveals intestinal bacteria succession during recovery from cholera in Bangladesh – Eureka Alert

Targeting Antibiotic-Resistant Bacteria with CRISPR and Phages – Anna Azvolinsky – The Scientist

Marine Bacteria Can Control Chemistry of Sea Spray Ejected into Atmosphere – SciNews

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May 19, 2015

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Two papers today on the microbiome of the Giant Panda – it’s not good at digesting bamboo!

Microbiome of pregnancy and birth

Bacterial community structure associated with elective cesarean section versus vaginal delivery in Chinese newborns – Liu D, et al. – J Pediatr Gastroenterol Nutr

The microbiota at multiple body sites during pregnancy in a rural Tanzanian population and the effects of Moringa supplemented probiotic yogurt – Jordan E. Bisanz – Applied and Environmental Microbiology

Review: Gut microbiome and immunity: possible role in sudden infant death syndrome (SIDS) – Paul N. Goldwater – Frontiers in Immunology

Human oral microbiome

Microbiome Profiles in Periodontitis in Relation to Host and Disease Characteristics
Bo-Young Hong – PLOS ONE

Review: The human saliva proteome: overview and emerging methods for characterization
Timothy J. Griffin – SPIE Proceedings

Human gut microbiome

Deviations in human gut microbiota: a novel diagnostic test for determining dysbiosis in patients with IBS or IBD – C. Casén – Alimentary Pharmacology and Therapeutics

Schisandra chinensis fruit modulates the gut microbiota composition in association with metabolic markers in obese women : a randomized, double-blind placebo controlled study – Mi-young Song – Nutrition Research

Gut Microbial Succession Follows Acute Secretory Diarrhea in Humans – Lawrence A. David – mBio

Food Fight: Our gut microbes are no fans of junk food – Laura Beil – Science News

Human vaginal microbiome

Review: Antimicrobial and immune modulatory effects of lactic acid and short chain fatty acids produced by vaginal microbiota associated with eubiosis and bacterial vaginosis – Muriel Aldunate – Frontiers in Physiology

Microbiome models

Composition and function of the undernourished neonatal mouse intestinal microbiome – Geoffrey A. Preidis – The Journal of Nutritional Biochemistry

Maternal microbiota regulate glucocorticoids levels and placental development in mice – Maha Al-Asmakh – Endocrine Abstracts

Different Dynamic Patterns of β-Lactams, Quinolones, Glycopeptides and Macrolides on Mouse Gut Microbial Diversity – Jia Yin – PLOS ONE

Relationships Between Diet-Related Changes in the Gut Microbiome and Cognitive Flexibility – K.R. Magnusson – Neuroscience

Physiological variability in volatile organic compounds (VOCs) in exhaled breath and released from faeces due to nutrition- and somatic growth in a standardized caprine animal model – Sina Fischer – Journal of Breath Research

Animal microbiome

The Bamboo-Eating Giant Panda Harbors a Carnivore-Like Gut Microbiota, with Excessive Seasonal Variations – Zhengsheng Xue – mBio

The evolution of the gut microbiota in the giant and the red pandas – Ying Li – Scientific Reports

Patterns of Gut Bacterial Colonization in Three Primate Species – Erin A. McKenney – PLOS ONE

Skin bacteria provide early protection for newly metamorphosed southern leopard frogs (Rana sphenocephala) against the frog-killing fungus, Batrachochytrium dendrobatidis
Whitney M. Holden – Biological Conservation

Plant and Soil microbiome

Bacterial and Fungal Communities in a Degraded Ombrotrophic Peatland Undergoing Natural and Managed Re-Vegetation – David R. Elliott – PLOS ONE

Response of soil, leaf endosphere and phyllosphere bacterial communities to elevated CO2 and soil temperature in a rice paddy – Gaidi Ren – Plant and Soil

Patterns in Species Persistence and Biomass Production in Soil Microcosms Recovering from a Disturbance Reject a Neutral Hypothesis for Bacterial Community Assembly
Fen-Guo Zhang – PLOS ONE

Time-dependent effect of graphene on the structure, abundance and function of the soil bacterial community – Wenjie Ren – Journal of Hazardous Materials

Patterns in Wetland Microbial Community Composition and Functional Gene Repertoire Associated with Methane Emissions – Shaomei He – mBio

Nano titania aided clustering and adhesion of beneficial bacteria to plant roots to enhance crop growth and stress management – G. M. Palmqvist – Scientific Reports

Review: Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant-microbiome interactions – J. M. Barea – Journal of soil science and plant nutrition

Water microbiome

The influence of land-use, nutrients, and geography on microbial communities and fecal indicator abundance at Lake Michigan beaches – Danielle D. Cloutier – Applied and Environmental Microbiology

Microbial responses to changes in flow status in temporary headwater streams: a cross-system comparison – Catherine M. Febria – Frontiers in Microbiology

Built environment microbiome

Distribution and population structure characteristics of microorganisms in urban sewage system – Yanchen Liu – Applied Microbiology and Biotechnology

Extremophile microbiome

Microbial Community in High Arsenic Shallow Groundwater Aquifers in Hetao Basin of Inner Mongolia, China – Ping Li – PLOS ONE

Microbial diversity in engineered haloalkaline environments shaped by shared geochemical drivers observed in natural analogues – Talitha C. Santini – Applied and Environmental Microbiology

Metagenomic characterization of biodiversity in the extremely arid desert soils of Kazakhstan – O. V. Kutovaya – Eurasian Soil Science

Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil – Yendi E. Navarro-Noya – Archaea

Food microbiology

An Integrated Metagenomics/Metaproteomics Investigation of the Microbial Communities and Enzymes in Solid-state Fermentation of Pu-erh tea – Ming Zhao – Scientific Reports

Review: Foodomics in microbiological investigations – Yong-Jiang Xu – Current Opinion in Food Science

Metagenomics and Bioinformatics

Review: Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies – Anastasis Oulas – Bioinformatics and Biology Insights

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods – Jullien M. Flynn – Ecology and Evolution

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities? – Emily A. Brown – Ecology and Evolution

Sharing is caring – Claudio Nunes-Alves – Nature Reviews Microbiology

Microbes in the news

Kitty Kickstarter: See the Microbes That Live in Your Cat – Becky Oskin – Live Science

Eden unveils The Human Microbiome this week – West Briton

Bodyguards for precious seeds—without chemical mace – Phys.org

Panda poop reveals they’re bad at digesting bamboo – Laura Geggel – CBS News

Giant Panda Microbiome Ill-Suited for Bamboo Diet, Study Finds – Genome Web

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May 18, 2015

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(Shorter posts this week because of international travel)

Events

Digestive Disease Week (DDW), May 16-19, Washington DC: Video: Hot topics at DDW 2015 include microbiome, new HCV treatments  –

Bioinformatics

phylogeo: an R package for geographic analysis and visualization of microbiome data -Zachary Charlop-Powers – Bioinformatics

Microbes in the news

Oddly Microbial: Honey Bee Gut Microbiomes — Queen vs. Workers –  Marcia Stone – Small Things Considered

Incredible ‘bioconcrete’ can heal itself thanks to limestone-producing bacteria – Brad Reed – BGR

NASA Hopes to Rely on Algae and Bacteria for Oxygen Production on Mars – Rachel K Wentz – Science Times

How Bacteria Break Through The Blood-Brain Barrier – Science 2.0

Ever wondered how milk becomes cheese? – Howard J. Bennett – Washington Post

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May 15, 2015

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Human skin microbiome

Pilot Study on Novel Skin Care Method by Augmentation with Staphylococcus epidermidis, an Autologous Skin Microbe – A Blinded Randomized Clinical Trial – Yuichi Nodake – Journal of Dermatological Science

Human gut microbiome

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota – Simone Rampelli – Current Biology

Deviations in human gut microbiota: a novel diagnostic test for determining dysbiosis in patients with IBS or IBD – C. Casén – Alimentary Pharmacology & Therapeutics

Intestinal Blautia is associated with reduced death from graft-versus-host disease – Robert R. Jenq – Biology of Blood and Marrow Transplantation

Pubmed link only: The coeliac stomach: gastritis in patients with coeliac disease – B. Lebwohl – Alimentary Pharmacology & Therapeutics

DGGE: Schisandra chinensis fruit modulates the gut microbiota composition in association with metabolic markers in obese women : a randomized, double-blind placebo controlled study – Mi-young Song – Nutrition Research

Review: Gut microbes, immunity, and spondyloarthritis – Matthew L. Stoll – Clinical Immunology

Microbiome models

Relationships Between Diet-Related Changes in the Gut Microbiome And Cognitive Flexibility – K.R. Magnusson – Neuroscience

Animal microbiome

Aphids: Genetic characterisation of new host-specialised biotypes and novel associations with bacterial symbionts in the pea aphid complex – Jean Peccoud – Insect Conservation and Diversity

Review: The Multi-Tasking Gut Epithelium of Insects – Jia-Hsin Huang – Insect Biochemistry and Molecular Biology

Plant and soil microbiome

On small soil beetles: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics – Carmelo Andújar – Molecular Ecology

Changes in soil nutrient content and bacterial community after 12 years of organic amendment application to a vineyard – M. E. Calleja-Cervantes – European Journal of Soil Science

Built Environment microbiology

Self-healing bio-concrete uses bacteria to repair itself – Anthony Cuthbertson – International Business Times

Bioreactor microbiology

Rare taxa have potential to make metabolic contributions in enhanced biological phosphorus removal ecosystems – Christopher E. Lawson – Environmental Microbiology

Bioinformatics

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods – Jullien M. Flynn -Ecology and Evolution

More microbiology

Editorial: Sifting out virulent bacteria – Naomi Attar – Nature Reviews Microbiology

Review: Dust Devil: The Life and Times of the Fungus That Causes Valley Fever – Eric R. G. Lewis – PLOS Pathogens

Microbes in the news

Decode your kitty’s microbiome – participate in some Cat-izen science – Alexandra Ossola –
Popular science

BacteriaHysteria

Faecal matter on plane tray tables, unwashed blankets… and 80 million bacteria on suitcases: The dirty secrets of air travel revealed – John Hutchinson – Daily Mail

Science, publishing, and career

“Reframing my track record undoubtedly helped. Here’s how I did it.” Accounting for career breaks – Emily Nicholson – Science

Bik’s Picks

Denver Zoo Penguins Go ‘Extinct’ For Endangered Species Day – CBS Denver

A Simple Hand-Grip Test Could Predict Your Risk For Heart Disease And Death – Anna Almendrala – Huffington Post

An astronaut’s surprisingly helpful guide to pooping in space – Elahe Izadi – Washington Post

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May 12, 2015

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Microbiome of pregnancy and birth

Metagenomic Analysis of Milk of Healthy and Mastitis-Suffering Women – Esther Jiménez – Journal of Human Lactation

Human oral microbiome

Abstract: Changes In The Oral Microbiome Of HIV-Infected Individuals May Alter Nitrogen Metabolism And The Enterosalivary Circulation Of Nitrate – Carl D. Koch – Am J Respir Crit Care Med

Human respiratory microbiome

Conference abstracts in Am J Respir Crit Care Med:

Human gut microbiome

Metabolism Links Bacterial Biofilms and Colon Carcinogenesis – Caroline H. Johnson – Cell Metabolism

Review: The gut microbiome: What do we know? – Francisco Guarner – Clinical Liver Disease

Review: A model for the role of gut bacteria in the development of autoimmunity for type 1 diabetes – Austin G. Davis-Richardson – Diabetologia

Functional foods

Review: A breakthrough in probiotics: Clostridium butyricum regulates gut homeostasis and anti-inflammatory response in inflammatory bowel disease – Takanori Kanai – Journal of Gastroenterology

Animal models of microbiome research

Phylum Level Change in the Cecal and Fecal Gut Communities of Rats Fed Diets Containing Different Fermentable Substrates Supports a Role for Nitrogen as a Factor Contributing to Community Structure – Martin Kalmokoff – Nutrients

Animal microbiome

Variation in koala microbiomes within and between individuals: effect of body region and captivity status – Niccoló Alfano – Scientific Reports

Plants and soil microbiome

Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota – Mizue Naito – PNAS

Transcriptome diversity among rice root types during asymbiosis and interaction with arbuscular mycorrhizal fungi – Caroline Gutjahr – PNAS
Reintroduction of locally extinct vertebrates impacts arid soil fungal communities –
Laurence J. Clarke – Molecular Ecology

Compartmentalized and contrasted response of ectomycorrhizal and soil fungal communities of Scots pine forests along elevation gradients in France and Spain
Ana Rincón – Environmental Microbiology

Impact of tropical lowland rainforest conversion into rubber and oil palm plantations on soil microbial communities – Valentyna Krashevska – Biology and Fertility of Soils

Masters Thesis: The establishment of apple orchards as temperate forest garden systems and their impact on indigenous bacterial and fungal population abundance in Southern Ontario, Canada – Paul Wartman – University of Guelph, Canada

Review: Plant growth promoting rhizobacteria and sustainable agriculture: A review –
Muhammad Arslan Ashraf – African Journal of Microbiology Research

Water microbiome

Organic and inorganic composition and microbiology of produced waters from Pennsylvania shale gas wells – Denise M. Akob – Applied Geochemistry

Perspective: Using dispersants after oil spills: impacts on the composition and activity of microbial communities – Sara Kleindienst – Nature Reviews Microbiology

Not sure if these are small enough (20-500 um) to be classified as microbes: Metagenetic tools for the census of marine meiofaunal biodiversity: An overview – Laura Carugati – Marine Genomics

Extremophile microbiome

Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes – Naseer Sangwan – Environmental Microbiology Reports

Comparison of Archaeal and Bacterial Diversity in Methane Seep Carbonate Nodules and Host Sediments, Eel River Basin and Hydrate Ridge, USA – Olivia U. Mason – Microbial Ecology

Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species – Nur A. Hasan – PNAS

Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time – Cody S. Sheik – Frontiers in Microbiology

Built environment microbiome

Forensic analysis of the microbiome of phones and shoes – Simon Lax – Microbiome

The Actinobacterial Colonization of Etruscan Paintings – Marta Diaz-Herraiz – Scientific Reports

Food microbiology

Molecular Analysis of Skin Bacterial Assemblages from Codfish and Pollock after Dry-Salted Fish Production – Natalia Pegoraro

Viruses and phages

Infection of phytoplankton by aerosolized marine viruses – Shlomit Sharoni – PNAS

Archaea

The two-domain tree of life is linked to a new root for the Archaea – Kasie Raymann – PNAS

Review: Archaeal Lineages within the Human Microbiome: Absent, Rare or Elusive?
Hans-Peter Horz – Life

Review: The interplay between nucleoid organization and transcription in archaeal genomes – Eveline Peeters – Nature Reviews Microbiology

Metagenomics and bioinformatics

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data – Kathrin P. Aßhauer – Bioinformatics

ProtPhylo: identification of protein–phenotype and protein–protein functional associations via phylogenetic profiling – Yiming Cheng – Nucleic Acids Research

IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data – Adrian Baez-Ortega – Bioinformatics

Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors – Mark B. Smith – mBio

Manuscript: Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant – Andreas Bremges

Review: The integration of sequencing and bioinformatics in metagenomics – Firouz Abbasian – Reviews in Environmental Science and Bio/Technology

Book Chapter: Protocols and Methods for the in Silico Reconstruction of the Origin and Evolution of Metabolic Pathways – Luana Presta – Briefs in Molecular Science 2015

Book Chapter: Molecular Screening of Azurin-Like Anticancer Bacteriocins from Human Gut Microflora Using Bioinformatics – Van Duy Nguyen – Advanced Computational Methods for Knowledge Engineering

Other microbial papers of interest

Bacterial Swarms Recruit Cargo Bacteria To Pave the Way in Toxic Environments – Alin Finkelshtein – mBio

Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association – Gloria Torres-Cortés – PNAS

Perspective: Resilience vs. historical contingency in microbial responses to environmental change – Christine V. Hawkes – Ecology Letters

A tortoise–hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria – Joshua R. Nahum – PNAS

Microbes in the news
Can The Microbes You Leave Behind Be Used to Identify You? – Ed Yong – National Geographic

Forbidden Data: Wyoming wants to conceal the fact that many of its streams are contaminated by E. coli bacteria – Slate

UGSG looks at microbiology, chemistry of Pa. fracked wells – Bob Downing – Ohio.com

Chinese breast milk discovery strengthens case for probiotics in infant formula: Chr Hansen – By Mark Astley – Dairy Reporter

Researchers find metabolic link between bacterial ‘biofilms’, colon cancer – Medical Xpress

Accessing the Hidden Kingdom: Fungal ITS Reference Sequences – NCBI Insights
#BacteriaHysteria

Germ City: Bacteria thriving at the makeup counter: 30% of used makeup samples in stores contain bacteria – PIX11

Tests found bacteria on popular single-serve coffeemakers – Your Central Valley

Bik’s Picks

De novo synthesis of a sunscreen compound in vertebrates – Andrew R Osborn – eLIFE

Chemical messages in 170-year-old champagne bottles from the Baltic Sea: Revealing tastes from the past – Philippe Jeandet – PNAS

Unraveling ancient Egypt’s animal mummy mystery: Roughly a third of the animal mummies examined were completely empty – Michael E. Miller – Washington Post

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May 11, 2015

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General microbiome / Microbial ecology

Microbiomes raise privacy concerns: DNA from microbes living on the human body can be used to identify individuals – Ewen Callaway – Nature

Identifying personal microbiomes using metagenomic codes – Eric A. Franzosa – PNAS USA

Unraveling interactions in microbial communities – from co-cultures to microbiomes – Justin Tan – Journal of Microbiology

Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach – Román Zapién-Campos – Frontiers in Microbiology

Human oral microbiome

Hospitalisation impacts on oral hygiene: an audit of oral hygiene in a metropolitan health service – Rachael Danckert – Scandinavian Journal of Caring Sciences

DGGE: Dynamic Shifts in the Oral Microbiome during Radiotherapy – Tine De Ryck – Clinical Research in Infectious Diseases

Effects of Source- versus Household Contamination of Tubewell Water on Child Diarrhea in Rural Bangladesh: A Randomized Controlled Trial – Ayse Ercumen – PLOS ONE

Human vaginal microbiome

Review: Biofilms: An Underappreciated Mechanism of Treatment Failure and Recurrence in Vaginal Infections – Christina A. Muzny – Clinical Infectious Diseases

Human gut microbiome

Editorial: The Gut Microbiota Strikes Again – Debra D. Poutsiaka – Clinical Infectious Diseases
Belongs to:
Acute Gastrointestinal Graft-vs-Host Disease Is Associated With Increased Enteric Bacterial Bloodstream Infection Density in Pediatric Allogeneic Hematopoietic Cell Transplant Recipients – Anya Levinson – Clinical Infectious Diseases

Review: Exploring the role of environmental enteropathy in malnutrition, infant development and oral vaccine response – Allissia A. Gilmartin , William A. Petri – Philosophical Transactions B

Review: Role of the gastrointestinal ecosystem in the development of type 1 diabetes – Joseph G Daft – Pediatric Diabetes

Plant and soil microbiome

Ectomycorrhizal fungal communities coinvading with Pinaceae host plants in Argentina: Gringos bajo el bosque – Jeremy Hayward – New Phytologist

Atmospheric N Deposition Alters Connectance, but not Functional Potential Among Saprotrophic Bacterial Communities – Zachary B. Freedman – Molecular Ecology

Rhizospheric changes of fungal and bacterial communities in relation to soil health of multi-generation apple orchards – F. Caputo – Biological Control

Permafrost microbial community traits and functional diversity indicate low activity at in situ thaw temperatures – Jessica G. Ernakovich – Soil Biology and Biochemistry

Switchgrass Biochar Effects on Plant Biomass and Microbial Dynamics in Two Soils from Different Regions – Charlene N. Kelly – Pedosphere

Water microbiome

Melting glacier impacts community structure of Bacteria, Archaea and Fungi in a Chilean Patagonia fjord – Marcelo H. Gutiérrez – Environmental Microbiology

Evaluation of water sampling methodologies for amplicon-based characterization of bacterial community structure – Christopher Staley – Journal of Microbiological Methods

Thesis: Bacterial Community Structure and Petroleum Hydrocarbon Degradation in the Baltic Sea – Anna Reunamo – University of Turku

Phages and viruses

Editorial: A CRISPR sense of self – Naomi Attar – Nature Reviews Microbiology

Bioinformatics and metagenomes

Nucleotide 9-mers Characterize the Type II Diabetic Gut Metagenome – Balazs Szalkai – ArXiv

CS-SCORE: Rapid identification and removal of human genome contaminants from metagenomic datasets – Mohammed Monzoorul Haque – Genomics

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters – Tilmann Weber – Nucleic Acids Research

Review: Alignment of Next-Generation Sequencing Reads – Knut Reinert – Annual Review of Genomics and Human Genetics

Metabolic dependencies drive species co-occurrence in diverse microbial communities – Aleksej Zelezniak – PNAS USA

Functional Foods

Probiotics can improve the clinical outcomes of hepatic encephalopathy: An update meta-analysis – Li-Na Zhao – Clinics and Research in Hepatology and Gastroenterology

Microbes in the news

How Germs Might Shape the Future of Architecture – Vicky Gan – City Lab

FDA digging into hand cleaners in hospitals – Jonathan Eisen – MicroBEnet

Essay: The Fight Against the Fight Against the Fight Against Bacteria – Daniel Yin – University of Oxford

Freshman Biology, Creativity, and Extra Credit… – Mark O. Martin – MicrobesRule

You Asked: Should I Use Antibacterial Soap? – Markham Heid – Time
About Tim Spector book “The Diet Myth”: Fast food kills gut bacteria that can keep you slim, study finds – Daniel Costa-Roberts

About the Sonnenburgs’ book “The Good Gut”: To be healthy, take care of your microbiome – Kate Allen – The Start

Should you put yogurt on your face? The benefits of probiotics go beyond improved digestion – Victoria Dawson Hoff – Elle Beauty

My Archaea, My Brother – Genome Web

“This Idle No More movement is like bacteria, it has grown a life of its own all across this nation,” – RCMP apologizes for Idle No More ‘bacteria’ comparison – APTN

Calls for global database on bacteria contained in food – Channel News Asia

Antibiotic-Resistant Typhoid Spreading Abroad – Dennis Thompson – WebMD

“You may not want to eat lunch with Misty Bever”: Intestinal fortitude: There’s an illness lurking that causes chronic, debilitating pain. The cure, however, comes from deep within.– Dan England – The Tribune

Bik’s Picks

Mars sunsets are beautiful — and blue, NASA photo shows – Matthew T. Hall – UT San Diego

What do these new alien photos reveal about Roswell UFO crash – Sam Catherman – State Column

Google says its self-driving cars have had 11 crashes – Chris Woodyard – USA Today

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