Category Archives: Transcriptomics Proteomics

February 4, 2016

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A late digest today – Meetings and lab work kept me busy all day! Review about gut microbiota and malnutrition, Helicobacter infection affects local microbiome, salinity tolerance in corals, rhizosphere reviews, microbial mats in Shark Bay, and missing CRISPR regions in major bacterial lineages.

Jobs

Assistant, Associate or Senior Editor (Microbiology and Infectious Disease), Nature Communications, London, New York or Shanghai

Bioinformatics Scientist, Microbiome – Synthetic Genomics, Inc. – La Jolla CA

Pregnancy and birth
Routine Amoxicillin for Uncomplicated Severe Acute Malnutrition in Children – Sheila Isanaka – New England Journal of Medicine

Review: The case in favour of probiotics before, during and after pregnancy: insights from the first 1,500 days – G. Reid – Beneficial Microbes

Review: Development of the Neonatal Intestinal Microbiome and Its Association With Necrotizing Enterocolitis – Timothy G. Elgin – Clinical Therapeutics

Human oral microbiome

Interesting choice of  journal: Periodontitis induced by Porphyromonas gingivalis drives periodontal microbiota dysbiosis and insulin resistance via an impaired adaptive immune response – Vincent Blasco-Baque

Non-oral gram-negative facultative rods in chronic periodontitis microbiota – Arie J. van Winkelhoff – Microbial Pathogenesis

Microbial profiles at baseline and not the use of antibiotics determine the clinical outcome of the treatment of chronic periodontitis – S. Bizzarro – Scientific Reports

Human respiratory microbiome

Effect of Advanced HIV Infection on the Respiratory Microbiome – Homer L Twigg III – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

The emerging view of Firmicutes as key fibre degraders in the human gut – David Berry – Environmental Microbiology

Review: Gut Microbiota and Malnutrition – Matthieu Million – Microbial Pathogenesis

Review: Diet, Microbiota, And Dysbiosis: A ‘Recipe’ For Colorectal Cancer – Kishore Vipperla – Food & Function

Review: Microbiota, Immunity and the Liver – T. Vaikunthanathan – Immunology Letters

Animal and other models of microbiome research

Alterations of the Ileal and Colonic Mucosal Microbiota in Canine Chronic Enteropathies – Eric Cassmann – PLOS ONE

In a Neonatal Piglet Model of Intestinal Failure, Administration of Antibiotics and Lack of Enteral Nutrition Have a Greater Impact on Intestinal Microflora Than Surgical Resection Alone – Crystal L. Levesque – Journal of Parenteral & Enteral Nutrition

Development of the Chick Microbiome: How Early Exposure Influences Future Microbial Diversity – Anne L. Ballou – Frontiers in Veterinary Science

Gastric Helicobacter pylori Infection Affects Local and Distant Microbial Populations and Host Responses – Sabine Kienesberger – Cell Reports

Salmonella enterica Serovar Typhimurium Exploits Inflammation to Modify Swine Intestinal Microbiota – Rosanna Drumo – Frontiers in Cellular and Infection Microbiology

Changes in intestinal microflora of Caenorhabditis elegans following Bacillus nematocida B16 infection – Qiuhong Niu – Scientific Reports

Chitosan lowers body weight through intestinal microbiota and reduces IL-17 expression via mTOR signalling – Dingfu Xiao – Journal of Functional Foods

The effect of agave fructan products on the activity and composition of the microbiota determined in a dynamic in vitro model of the human proximal large intestine – Marjorie E. Koenen – Journal of Functional Foods

Animal microbiome

Long-term salinity tolerance is accompanied by major restructuring of the coral bacterial microbiome – Till Röthig – Molecular Ecology

High-throughput sequencing reveals the core gut microbiome of Bar-headed goose (Anser indicus) in different wintering areas in Tibet – Wen Wang – Microbiology Open

Plant, root, and soil microbiome

Spatial Distribution of Fungal Communities in an Arable Soil – Julia Moll – PLOS ONE

Soil Nitrogen Status Modifies Rice Root Response to Nematode-Bacteria Interactions in the Rhizosphere – Yanhong Cheng – PLOS ONE

Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria – Paul C. A. Wintermans – Plant Molecular Biology

Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition – Cheng Wang – Biotechnology for Biofuels

Microbial Profiling of a Suppressiveness-Induced Agricultural Soil Amended with Composted Almond Shells – Carmen Vida – Frontiers in Microbiology

Editorial: How does the tree root microbiome assemble? Influence of ectomycorrhizal species on Pinus sylvestris root bacterial communities – Aurélie Deveau – Environmental Microbiology

Lots of reviews on the plant rhizosphere in Trends in Plant Science: 

Review: Impact of Bacterial–Fungal Interactions on the Colonization of the Endosphere – Leonard S. van Overbeek – Trends in Plant Science

Review: Signaling in the Rhizosphere – Vittorio Venturi – Trends in Plant Science

Review: Root–Root Interactions: Towards A Rhizosphere Framework – Liesje Mommer – Trends in Plant Science

Review: Metabolomics in the Rhizosphere: Tapping into Belowground Chemical Communication – Nicole M. van Dam – Trends in Plant Science

Opinion: Mannitol in Plants, Fungi, and Plant–Fungal Interactions
Takshay K. Patel – Trends in Plant Science

Water and extremophile microbiome

Evolution of Chemical Characteristics of Technosols in an Afforested Coal Mine Dump over a 20-year Period – Ivana M. Rivas-Pérez – Land Degradation and Development

Microbial mats: New multi-scale perspectives on the stromatolites of Shark Bay, Western Australia – E. P. Suosaari – Scientific Reports

Spatial isolation and environmental factors drive distinct bacterial and archaeal communities in different types of petroleum reservoirs in China – Peike Gao – Scientific Reports

Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea) – Christina Pavloudi – Marine Genomics

Microbial diversity in European alpine permafrost and active layers – Beat Frey – FEMS Microbiology Ecology

Nutrient and metal pollution of the eastern Gulf of Finland coastline: Sediments, macroalgae, microbiota – Yulia Gubelit – Science of the Total Environment

Food microbiology

Unraveling the Enzymatic Basis of Wine “Flavorome”: A Phylo-Functional Study of Wine Related Yeast Species – Ignacio Belda – Frontiers in Microbiology

Developmental Peculiarities and Seed-Borne Endophytes in Quinoa: Omnipresent, Robust Bacilli Contribute to Plant Fitness – Andrea Pitzschke – Frontiers in Microbiology

Viruses, phages, and CRISPRs

Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems – David Burstein – Nature Communications

High-Throughput Isolation of Giant Viruses in Liquid Medium Using Automated Flow Cytometry and Fluorescence Staining – Jacques Y. B. Khalil – Frontiers in Microbiology

Review: Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems – Mart Krupovic – Current Opinion in Microbiology

Techniques

Assessing the impact of long term frozen storage of faecal samples on protein concentration and protease activity – Laura S. Morris – Journal of Microbiological Methods

More microbiology

Elie Metchnikoff, the Man and the Myth – Gordon S. – Journal of Innate Immunology

Microbes in the news

What Your Low-Fiber Diet Does to Your Health – Mandy Oaklander – Time

Your beard doesn’t contain poop, but it could help develop new antibiotics – Sarah Kaplan – The Washington Post

Modern microbial ecosystems provide window to early life on Earth. UM Rosenstiel School-led team reveals new details on modern-day stromatolites – Science Daily

Two Santa Clara University Students Confirmed with Meningitis – ABC7

USDA Imposes Stricter Limit On Salmonella Bacteria In Poultry Products – NPR Morning Edition

Young scientists present intriguing and surprising research – Kristen Browning-Blas – Colorado State University

Meet the CEO of Europe’s Leading Microbiome Biotech, Pierre Belichard of Enterome – Labiotech

Podcast: As Arctic Permafrost Thaws, Microbes Kick Into Action – with Janet Jansson – Science Friday

Podcast: Bear Gut Microbes Help Prep Hibernation – Karen Hopkin – Scientific American

Podcast: The Good Side of Viruses – Medical Discovery News
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February 2, 2016, second edition

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Updated status of the microbial census, bacteria in the nasopharynx, deodorant and armpit microbiome, lichen microbiome, fungi on decomposing forest materials, and metagenomics cover the amplicon gaps. So many papers I had to do a second installment today!

Events and jobs

Microbiology and bioinformatics positions at Whole Biome in San Francisco. Wearing hoodies encouraged.

General microbiome

The status of the microbial census: an update – Patrick D Schloss – BioRxiv

Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes – Kevin R Theis – BioRxiv

Human oral microbiome

Interactions between Streptococcus oralis, Actinomyces oris, and Candida albicans in the development of multispecies oral microbial biofilms on salivary pellicle – Indira M.G. Cavalcanti – Molecular Oral Microbiology

Human respiratory microbiome

Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure – Wouter A. A. de Steenhuijsen Piters – mBio 

Human skin microbiome

The effect of habitual and experimental antiperspirant and deodorant product use on the armpit microbiome – Julie Urban – PeerJ

Skin microbiome surveys are strongly influenced by experimental design – Jacquelyn S. Meisel – Journal of Investigative Dermatology

Unique features of a global human ectoparasite identified through sequencing of the bed bug genome – Joshua B. Benoit – Nature Communications

Human vaginal microbiome

Hormonal Contraceptive Effects on the Vaginal Milieu: Microbiota and Immunity – Jessica Tarleton – Current Obstetrics and Gynecology Reports

Human gut microbiome

Sex differences in the gut microbiome–brain axis across the lifespan – Eldin Jašarević – Philosophical Transactions of the Royal Society B

Very poor English and presentation, does not look peer reviewed: Preliminary analysis showed country-specific gut resistome based on 1267 feces samples – Zhenyu Yang – Gene

Confusing study design and interpretations: Gut Microbiota Linked to Sexual Preference and HIV Infection – Marc Noguera-Julian – EBioMedicine

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

Review: Microbiota and arthritis: correlations or cause? – Bravo-Blas, Alberto – Current Opinion in Rheumatology

Perspective: Gut microbiota in 2015: Prevotella in the gut: choose carefully – Ruth E. Ley – Nature Reviews Gastroenterology & Hepatology

Editorial: PPIs alter gut microbiota composition – Nature Reviews Gastroenterology & Hepatology

Review: Samples and techniques highlighting the links between obesity and microbiota –
Emmanouil Angelakis – Microbial Pathogenesis

Animal models of microbiome

Bidirectional interactions between indomethacin and the murine intestinal microbiota – Xue Liang – eLife

 

Mixed feelings about this study that killed turtles to look at effect of probiotics on their shells: Dietary Probiotics Affect Gastrointestinal Microbiota, Histological Structure and Shell Mineralization in Turtles – Mateusz Rawski – PLOS ONE

Animal microbiome

The Role of the Microbial Environment in Drosophila Post-Embryonic Development –
Maura Strigini – Developmental & Comparative Immunology

Plant, root, and soil microbiome

Review about lichen bacterial microbiome: Understanding microbial multi-species symbioses – Ines A. Aschenbrenner – Frontiers in Microbiology

Dead fungal mycelium in forest soil represents a decomposition hotspot and a habitat for a specific microbial community – Vendula Brabcová – New Phytologist

Litter decomposition, residue chemistry and microbial community structure under two subtropical forest plantations: A reciprocal litter transplant study –
Zongming He – Applied Soil Ecology

Disentangling nematode-bacteria interactions using a modular soil model system and biochemical markers – Michael Ackermann – Nematology

Using native trees and cacti to improve soil potential nitrogen fixation during long-term restoration of arid lands – Nguyen E. Lopez-Lozano – Plant and Soil

Warming and nitrogen deposition are interactive in shaping surface soil microbial communities near the alpine timberline zone on the eastern Qinghai–Tibet Plateau, southwestern China – Qinli Xiong – Applied Soil Ecology

Short-term effects of mechanical drainage on fungal and bacterial community structure in a managed grassland soil – B.J. Fay – Applied Soil Ecology

Water and extremophile microbiome

Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin – Frederick Dowell – Frontiers in Microbiology

Bioreactor and crude oil microbiology

Illumina MiSeq sequencing reveals the key microorganisms involved in partial nitritation followed by simultaneous sludge fermentation, denitrification and anammox process – Bo Wang – Bioresource Technology

Microbial communities of light crude from Nigeria and potential for in situ biodegradation, souring, and corrosion – Okoro Chuma Conlette – Petroleum Science and Technology

Built environment microbiome

Rhinitis, Ocular, Throat and Dermal Symptoms, Headache and Tiredness among Students in Schools from Johor Bahru, Malaysia: Associations with Fungal DNA and Mycotoxins in Classroom Dust – Dan Norbäck – PLOS ONE

Bioinformatics and metagenomics

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity – Emiley A. Eloe-Fadrosh – Nature Microbiology

Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples – Jennifer J. Barb – PLOS ONE

Optimization of alignment-based methods for taxonomic binning of metagenomics reads – Magali Jaillard – Bioinformatics

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes – John A Lees – BioRxiv

Proteomics

Review: Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria – Keding Cheng – Proteomics – Clinical Applications

Microbes in the news

Study shows maternal diet alters the breast milk microbiome and microbial gene content – EurekAlert

Deodorant And Antiperspirant Alter The Skin Microbiome, But Researchers Can’t Be Sure Of Long-Term Effects – Stephanie Castillo – Medical Daily

Beard bacteria could lead to new antibiotics – Matthew Stock – Reuters

Science, publishing, and career

“Those who can, publish. Those who can’t, blog.” Jingmai O’Connor – Current Biology

Chill out about Jingmai O’Connor’s criticism of bloggers – Jeremy Fox – Dynamic Ecology

Paul Knoepfler: Stem cell scientist finds his ‘niche’ in blogging – Karen Weintraub – STAT News

How to (not) write a microbiome grant, part I

How to (not) write a microbiome grant, part II. A deeper dive on preliminary data – David Baltrus – My Chrobial Romance

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January 14, 2016

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Sorry for a late post today – I had a lot of meetings. Here is what I found:

Gut microbiota shaped via fecal microRNA, the microgenderome, dysbiosis in Vitiligo skin lesions, metatranscriptomics, and an 18th century Yersinia pestis.

General microbiome

Perspective: Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease – Niv Zmora – Cell Host & Microbe

The Human Microbiome: Opportunities for Dynamics, Systems, and Control
(based on the IFAC blog post Translate or Die) – Travis E. Gibson – Submitted to ACC 2016

Human skin microbiome

Microbial community profiling shows dysbiosis in the lesional skin of Vitiligo subjects – Parul Ganju – Scientific Reports

Human oral microbiome

Diversity and homogeneity of oral microbiota in healthy Korean pre-school children using pyrosequencing – Soo Eon Lee – Acta Odontologica Scandinavica

Short-term effects of povidone iodine and sodium fluoride therapy on plaque levels and microbiome diversity – C Reilly – Oral Diseases

Commentary: A new association for the oral metagenome – Nicholas S Jakubovics – Oral Diseases

Human vaginal microbiome

Review: Vaginal microbiota and microbiome:- Role in health and disease – Dr Amit A. Rangari – Indian Journal of Basic and Applied Medical Research;

Human gut microbiome

Support for the Microgenderome: Associations in a Human Clinical Population – Amy Wallis – Scientific Reports

Impact of increasing fruit and vegetables and flavonoid intake on the human gut microbiota – Annett Klinder – Food & Function

Colonization potential to reconstitute a microbe community in patients detected early after fecal microbe transplant for recurrent C. difficile – Ranjit Kumar – BMC Microbiology

Review: The microbiome and its implications in intestinal transplantation – Kroemer, Alexander – Current Opinion in Organ Transplantation

Animal models

Genetic and Metabolic Signals during Acute Enteric Bacterial Infection Alter the Microbiota and Drive Progression to Chronic Inflammatory Disease – Karishma Kamdar – Cell Host & Microbe

The Host Shapes the Gut Microbiota via Fecal MicroRNA – Shirong Liu – Cell Host & Microbe

Animal microbiome

The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica – Ngare Wilkinson – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

Culturable endophytic bacterial communities associated with field grown soybean – Karla Bianca de Almeida Lopes – Journal of Applied Microbiology

Historical precipitation predictably alters the shape and magnitude of microbial functional response to soil moisture – Colin Averill – Global Change Biology

Water and waste microbiome

Development of new host-specific Bacteroides qPCRs for the identification of fecal contamination sources in water – Marta Gómez-Doñate – Microbiology Open

Bacterial diversity in oil-polluted marine coastal sediments – Alejandro Acosta-González – Current Opinion in Biotechnology

Spatial and temporal variability of bacterial communities in high alpine water spring sediments – Alfonso Esposito – Research in Microbiology

Biogeochemical, Isotopic and Bacterial Distributions Trace Oceanic Abyssal Circulation – Angelo Rubino – PLOS ONE

Metagenomics, metatranscriptomics, and bioinformatics

Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus – Kirsten I Bos – BioRxiv

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality – Yue Jiang – BMC Microbiome Journal

Viral metagenomics and blood safety – V. Sauvage – Transfusion Clinique et Biologique

Microbes in the news

Does our Microbiome Control Us or Do We Control It? – Dina Fine Maron – Scientific American

Your gut’s trick for controlling the bacteria that live in it – New Scientist

Mammals shape their microbiome to prevent disease – Science Codex

Low-Fiber Diets Cause Waves of Extinction in the Gut – Ed Yong – The Atlantic

Bad diets today can alter our great-great-grandkids’ biology – Katherine Ellen Foley – Quartz

Thoughtful and balanced comparison: mothur and QIIME – Pat Schloss – Mothur blog

Modifying the structure of wood alters plant microbiome – Science Daily

Gut Microbiome Similar in Formula- and Combination-Fed Babies – Troy Brown – MedScape

Eglin medical group first to find bacteria unseen in humans: Borrelia turicatae – Ilka Cole – US Air Force

Protecting the infant microbiome – Kathryn Kos – Examiner

Microbiology and art

Sunshine and microbiology inspire Reading artist’s work – Francesca Perryman – Get Reading

Science, publishing, and career

Re: Your Recent Email to Your Professor: Students who use emojis in their emails and write “heeeeelp!” in the subject line don’t necessarily know better.  – Paul T. Corrigan and Cameron Hunt McNabb – Inside Higher Education

ORCID: Publishers embrace scheme to end name confusion – John Bohannon – Science

Give teachers a physics test from a woman and they’ll give her worse grades – John Timmer – Ars Technica

Astronomy’s snowballing sexual harassment scandal picks up even more cases – Rachel Feltman – Washington Post

Bik’s Picks

Inside the Eye: Nature’s Most Exquisite Creation – Ed Yong – National Geographic
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January 13, 2016

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Frozen vs fresh stool transplants, the primate skin microbiome, diet-induced extinctions, bacteria in breast milk from low income Mexican-American moms, and engineered poplar tree endosphere.

Events

Tapping the Human Microbiome (Kavli Hangout) – Tuesday, Jan. 19, 1:30 pm EST, with Janet Jansson, Rob Knight, and Jeff Miller

Pregnancy and birth microbiome

Bacterial microbiome of breast milk and child saliva from low-income Mexican-American women and children – Veronica Davé – Pediatric Research

Human vaginal microbiome

Review: Biotherapeutic agents and vaginal health – F. H. Al-Ghazzewi – Journal of Applied Microbiology

Human gut microbiome

Frozen vs Fresh Fecal Microbiota Transplantation and Clinical Resolution of Diarrhea in Patients With Recurrent Clostridium difficile Infection – Christine H. Lee – JAMA

Small Intestine Bacterial Overgrowth and Environmental Enteropathy in Bangladeshi Children – Jeffrey R. Donowitz – mBio

Animal and bioreactor models

Diet-induced extinctions in the gut microbiota compound over generations – Erica D. Sonnenburg – Nature

Intestinal epithelial TLR4 signaling affects epithelial function, colonic microbiota and promotes risk for transmissible colitis – Rishu Dheer – Infection and Immunity

Modulation of the human gut microbiota by dietary fibres occurs at the species level – Wing Sun Faith Chung – BMC Biology

Animal microbiome

Diversity and evolution of the primate skin microbiome – Sarah E. Council – Proceedings of the Royal Society B

Host-associated coral reef microbes respond to the cumulative pressures of ocean warming and ocean acidification – N. S. Webster – Scientific Reports

Plant, root, and soil microbiome

Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome – Bram Beckers – PNAS

Invariant community structure of soil bacteria in subtropical coniferous and broadleaved forests – Xiaoli Wang – Scientific Reports

Food microbiology

Seasonal and Growth-Dependent Dynamics of Bacterial Community in Radish Sprouts – Hiroshi Asakura – Journal of Food Safety

Bacterial dynamics and metabolite changes in solid-state acetic acid fermentation of Shanxi aged vinegar – Sha Li – Applied Microbiology and Biotechnology

Transcriptomics

Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline – Mark Davids – PLOS ONE

Metagenomics and bioinformatics

Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome – Dingchen Li – Biology Direct

Microbes in the news

DNA Genotek’s microbiome collection and stabilization blog – Lisa Gamwell – The Microbiome Snapshot

Human trials will test freeze-dried poop pills as a weight-loss treatment – David Nield – Science Alert

What is Zika virus? Interview with Derek Gatherer – Microbe Post

E. coli Slinky: Revealed: the awful anchor that lets urinary tract infections take hold – Josh Barney – University of Virginia

Bik’s Picks

Estimation of a Killer Whale (Orcinus orca) Population’s Diet Using Sequencing Analysis of DNA from Feces – Michael J. Ford – PLOS ONE

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December 26, 2015

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Gut microbiota of patients with and without abdominal bloating, probiotics to help with academic stress, and a copper gradient near a Canadian mine.

Pregnancy and birth

Review: The microbiome and childhood diseases: Focus on brain-gut axis –
Siobhain M. O’ Mahony – Birth Defects Research Part C: Embryo Today: Reviews

Human respiratory tract microbiome

Microbiological and Molecular Identification of Bacterial Species Isolated from Nasal and Oropharyngeal mucosa of Fuel Workers in Riyadh, Saudi Arabia – Suaad S. AlWakeel – Saudi Journal of Biological Sciences

Human gut microbiome

Molecular Characterization of the Intestinal Microbiota in Patients With and Without Abdominal Bloating – Tamar Ringel-Kulka – American Journal of Physiology

Microbiome models

Choline Diet and Its Gut Microbe–Derived Metabolite, Trimethylamine N-Oxide, Exacerbate Pressure Overload–Induced Heart Failure – Chelsea L. Organ – Circulation: Heart Failure

Bidirectional interactions between indomethacin and the murine intestinal microbiota
Xue Liang

A simple coculture system shows mutualism between anaerobic faecalibacteria and epithelial Caco-2 cells – Mehdi Sadaghian Sadabad – Scientific Reports

Animal microbiome

Metagenomic assessment of the functional potential of the rumen microbiome in Holstein dairy cows – Dipti W. Pitta – Anaerobe

Age-Related Shifts in Bacterial Diversity in a Reef Coral – Alex D. Williams – PLOS ONE

Microbial composition of biofilms associated with lithifying rubble of Acropora palmata branches – Yislem Beltrán – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Comparisons of diazotrophic communities in native and agricultural desert ecosystems reveal plants as important drivers in diversity – Martina Köberl – FEMS Microbiology Ecology

Locally adapted arbuscular mycorrhizal fungi improve vigor and resistance to herbivory of native prairie plant species – Elizabeth L. Middleton – Ecosphere

Root Exudation by Aphid Leaf Infestation Recruits Root-associated Paenibacillus spp. to Lead Plant Insect Susceptibility – Bora Kim – Journal of Microbiology and Biotechnology

Effects of the allelochemical coumarin on plants and soil microbial community – E. Niro – Soil Biology and Biochemistry

Water and waste microbiome

Microbiome analysis across a natural copper gradient at a proposed Northern Canadian mine site – Thea Van Rossum – Frontiers in Environmental Science

Evaluation of Community-Level Physiological Profiling for Monitoring Microbial Community Function in Aquaculture Ponds – Gerald L. Kurten – North American Journal of Aquaculture

Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages – David H. Case – mBio

Microbial colonisation and litter decomposition in a Cerrado stream are limited by low dissolved nutrient concentrations – Adriana O. Medeiros – Limnetica

Diversity, community structure, and bioremediation potential of mercury-resistant marine bacteria of estuarine and coastal environments of Odisha, India – Hirak R. Dash – Environmental Science and Pollution Research

Review: Microbial Surface Colonization and Biofilm Development in Marine Environments – Hongyue Dang – Microbiology and Molecular Biology Reviews

Bioinformatics and metagenomics

Effect of k-tuple length on sample-comparison with high-throughput sequencing data – Ying Wang – Biochemical and Biophysical Research Communications

Unifying view of stem–loop hairpin RNA as origin of current and ancient parasitic and non-parasitic RNAs, including in giant viruses – Hervé Seligmann – Current Opinion in Microbiology

Alignment behaviors of short peptides provide a roadmap for functional profiling of metagenomic data – Rohita Sinha – BMC Genomics

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis – Phelim Bradley – Nature Communications

Proteomics

Review: The challenge of metaproteomic analysis in human samples – Jonathan M Blackburn – Expert Review of Proteomics

Functional foods

Fermented milk containing Lactobacillus casei strain Shirota prevents the onset of physical symptoms in medical students under academic examination stress – A. Kato-Kataoka – Beneficial Microbes

Microbes in the news

Topical Mupirocin Changes Sinus Microbiome – Interview with Tara F. Carr – Medical Research

Is This Snowy Wonderland Or The World Inside A Petri Dish? – Meredith Rizzo – NPR

End of the year lists

From Blood Rain to Green Poo: 10 Weirdest Science Stories of 2015 – Elizabeth Palermo – Live Science

The Altmetric Top 100 Research Papers 2015 – Altmetric
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December 2, 2015

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General microbiome

Microbiology: Microbiome studies need local leaders – Victor S. Pylro – Nature

Human skin microbiome

Conclusions not strongly supported by data: Chitosan Coated Textiles May Improve Atopic Dermatitis Severity by Modulating Skin Staphylococcal Profile: A Randomized Controlled Trial – Cristina Lopes – PLOS ONE

Human respiratory microbiome

Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome – Robert A Quinn – The ISME Journal

Perspective: In the name of ventilator-associated pneumonia prevention: lung microbiota blown away by colistin! – Saad Nseir – European Respiratory Journal

Human gut microbiome

Better link than yesterday: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota – Kristoffer Forslund – Nature

Animal microbiome

Human Staphylococcus aureus lineages among Zoological Park residents in
Greece – E. Drougka – Open Veterinary Journal

Fecal Bacterial Composition of the Endangered Yangtze Finless Porpoises Living Under Captive and Semi-natural Conditions – Xiaoling Wan – Current Microbiology

Plant, root, and soil microbiome

Commentary: Microbiomes: Curating communities from plants – Gwyn A. Beattie – Nature

Better link than yesterday: Functional overlap of the Arabidopsis leaf and root microbiota – Yang Bai – Nature

Bioinformatics and metagenomics

A New Approach for Scalable Analysis of Microbial Communities – Ehsaneddin Asgari – ArXiv

Microbial ecology

Networks of energetic and metabolic interactions define dynamics in microbial communities – Mallory Embree

Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria – João Barroso-Batista – Nature Communications

Social dynamics within decomposer communities lead to nitrogen retention and organic matter build-up in soils – Christina Kaiser – Nature Communications

Proteomics

Enhancing Metaproteomics – The value of models and defined environmental microbial systems – Florian-Alexander Herbst – Proteomics

Infection microbiology

Nature Supplement: Expanding the role of diagnostic and prognostic tools for infectious diseases in resource-poor settings – Azra C. Ghani – Nature

Microbes in the news

Bacteriophage therapy: an alternative to antibiotics? An interview with Professor Martha Clokie – April Cashin-Garbutt – News Medical

Friends for Life: How Good Bugs Keep You Healthy (Op-Ed) – Jeremy Taylor – LiveScience

Science, publishing, and career

How to build a better PhD: There are too many PhD students for too few academic jobs — but with imagination, the problem could be solved – Julie Gould – Nature

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November 12, 2015

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Gut microbiome and definition of self, symbionts of corals and algae, and microbial geobiology of space exploration. And – yeah! – my Twitter account made it to a “Top 100 Twitter Influencers Working in Life Sciences” list. My Twitter handle is @MicrobiomDigest.

Human gut microbiome

Extensive T-cell epitope repertoire sharing among human proteome, gastrointestinal microbiome, and pathogenic bacteria: implications for the definition of self –
Robert D. Bremel – Frontiers in Immunology

Gut microbiota and diet in patients with different glucose tolerance – Lilit Vanikovna Egshatyan – Endocrine Connections

Review: Alcoholic Liver Disease: The Gut Microbiome and Liver Cross Talk – Phillipp Hartmann – Alcoholism: Clinical and Experimental Research

Review: Linking Microbiota to Human Diseases: A Systems Biology Perspective – Hao Wu – Trends in Endocrinology & Metabolism

Review: Gut microbiota and host metabolism in liver cirrhosis – Makoto Usami – World Journal of Gastroenterology

Infection and cancer microbiology

Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis – Samuel A. Shelburne – PLOS ONE

Animal microbiome

Open Access: Stable and sporadic symbiotic communities of coral and algal holobionts – Eric R. Hester – The ISME Journal

Plant, root, and soil biology

Past water management affected GHG production and microbial community pattern in Italian rice paddy soils – A. Lagomarsino – Soil Biology and Biochemistry

Elemental stoichiometry indicates predominant influence of potassium and phosphorus limitation on arbuscular mycorrhizal symbiosis in acidic soil at high altitude –
Mohammad Haneef Khan – Journal of Plant Physiology

Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach – P. Bhattacharyya – Science of The Total Environment

Food microbiology

Monitoring of spoilage and determination of microbial communities based on 16S rRNA gene sequence analysis of whole sea bream stored at various temperatures – Foteini F. Parlapani – LWT – Food Science and Technology

Variation in fungal microbiome (mycobiome) and aflatoxin in stored in-shell peanuts at four different areas of China – Ning Ding – Frontiers in Microbiology

Waste microbiology

Characterization of successional changes in bacterial community composition during bioremediation of used motor oil-contaminated soil in a boreal climate – Lijuan Yan – Science of the Total Environment

Space microbiology

An ESA Roadmap for Geobiology in Space Exploration – Claire R Cousins – Acta Astronautica

Transcriptomics

Protocol: Prokaryotic Metatranscriptomics – Danilo Pérez-Pantoja – Springer Protocols Handbooks

Microbes in the news

Story behind the paper: Porphyrobacter mercurialis, a new species found by #citizenscience and then sent to the #iss – David Coil – MicroBEnet

Getting a flu shot every year? More may not be better – Helen Branswell – STAT news

Dangerous liaison: Bacteria, viruses in league – Bruce Goldman – Stanford Medicine News

Filamentous Bacteriophage Promote Biofilm Assembly and Function – Patrick R. Secor – Cell Host & Microbe

Intestinal Pathogens Change the Microbiome, Cause E. Coli To “Bloom” – Interview with Shannon D. Manning – Medical Research

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October 6, 2015

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Human gut microbiome

Intersections between Microbiome and Heart Failure: Revisiting the Gut Hypothesis –
Yuji Nagatomo – Journal of Cardiac Failure

Phenolic compounds from red wine and coffee are associated with specific intestinal microorganisms in allergic subjects – Adriana Cuervo – Food and Function

Review: The Human Microbiota: Composition, Functions, and Therapeutic Potential – Rick Conrad, Alexander V. Vlassov – Medical Science Review

Models of microbiome research

Inflammation-associated alterations to the intestinal microbiota reduce colonization resistance against non-typhoidal Salmonella during concurrent malaria parasite infection – Jason P. Mooney – Scientific Reports

Protocols for the Use of Gut Models to Study the Potential Contribution of the Gut Microbiota to Human Nutrition Through the Production of Short-Chain Fatty Acids –
Andrew J McBain – Springer Protocols Handbooks

Salami? Cecum microbial communities from steers differing in feed efficiency – P. R. Myer – Journal of Animal Science

Animal microbiome

Dholes are a species of wild dog: First report on the bacterial diversity in the distal gut of dholes (Cuon alpinus) by using 16S rRNA gene sequences analysis – Lei Chen – Journal of Applied Genetics

Plant, root, and soil microbiome

Diversity of fungi associated with plants growing in geothermal ecosystems and evaluation of their capacities to enhance thermotolerance of host plants – Wen-Na Zhou – Journal of Plant Interactions

Forage crops alter soil bacterial and fungal communities in an apple orchard – Sijun Qin – Acta Agriculturae Scandinavica, Section B — Soil & Plant Science

Bacterial communities estimated by pyrosequencing in the soils of chinampa, a traditional sustainable agro-ecosystem in Mexico – Salvador Embarcadero-Jiménez – Journal of Soils and Sediments

Water microbiome

Bacterial diversity and community composition from seasurface to subseafloor – Emily A Walsh – The ISME Journal

Modelling the effects of hydrodynamic regimes on microbial communities within fluvial biofilms: combining deterministic and stochastic processes – Yi Li – Environmental Science & Technology

A new tool for long-term studies of POM-bacteria interactions: overcoming the century-old Bottle Effect – Danny Ionescu – Scientific Reports

Book chapter: Protistan Diversity in Environmental Molecular Surveys – Ramon Massana – Marine Protists

Book chapter: Diversity of Microbial Eukaryotes in Deep Sea Chemosynthetic Ecosystems Illuminated by Molecular Techniques – Kiyotaka Takishita – Marine Protists

Extremophile microbiome

Metagenomic and metatranscriptomic analyses of Lake Vostok accretion ice – Yury M. Shtarkman – Bowling Green State University

Metabolic networks, proteomics

Gastrointestinal symptoms and altered intestinal permeability induced by combat-training are associated with distinct metabotypic changes – Lee Cheng Phua – Journal of Proteome Research

Review: Roles of Indole as an Interspecies and Interkingdom Signaling Molecule – Jin-Hyung Lee – Trends in Microbiology

Bioinformatics and metagenomics

Comparison of three clustering approaches for detecting novel environmental microbial diversity – Dominik Forster – PeerJ Preprints

MG-RAST, a Metagenomics Service for the Analysis of Microbial Community Structure and Function – Elizabeth M. Glass, Folker Meyer – Springer Protocols Handbook

Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering – Oscar Franzén – Microbiome

Techniques

An extended single-index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq illumina platforms – Hooman Derakhshani – Journal of Basic Microbiology

More microbiology

This paper contains large amounts of plagiarism and confusing images, but here it is: Microbial Forensics in Legal Medicine – Pankaj Shrivastava – SAS Journal of Medicine

Microbes in the news

Georgia State Researcher Gets $1.35 Million to Study Effects of Common Food Additive on Body – Georgia State University
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September 30, 2015

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Gut virome in infants, metabolome of Mediterranean diet, zebrafish gut assembly, antibiotic use and psoriasis risk, Roseobacter proteomics, and MetaPhlAn2.

Pregnancy and birth

The gut virome and bacterial microbiome—the early years – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Early life dynamics of the human gut virome and bacterial microbiome in infants –
Efrem S Lim – Nature Medicine

Human oral microbiome

Functional biomarkers for chronic periodontitis and insights into the roles of Prevotella nigrescens and Fusobacterium nucleatum; a metatranscriptome analysis – Szymon P Szafrański – NPJ Biofilms and Microbiomes

Urease and Dental Plaque Microbial Profiles in Children – Evangelia Morou-Bermudez – PLOS ONE

High prevalence of colonization of oral cavity by respiratory pathogens in frail older patients with oropharyngeal dysphagia – O. Ortega – Neurogastroenterology & Motility

Periodontal-disease-associated biofilm: A reservoir for pathogens of medical importance – Ana Paula Vieira Colombo – Microbial Pathogenesis

Human gut microbiome

High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome – Francesca De Fillippis – Gut

Review: Clinical and Pathophysiological Consequences of Alterations in the Microbiome in Cirrhosis – Jane Macnaughtan – American Journal of Gastroenterology

Animal models

Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut – Sandi Wong – mBio

Antibiotics in neonatal life increase murine susceptibility to experimental psoriasis –
Peter Zanvit – Nature Communications

Plant, root, and soil microbiome

Plant diversity shapes microbe-rhizosphere effects on P mobilisation from organic matter in soil – Nina Hacker – Ecology Letters

Oily waste containing natural radionuclides: does it cause stimulation or inhibition of soil bacterial community? – Polina Galitskaya – Journal of Plant Nutrition and Soil Science

Plant diversity shapes microbe-rhizosphere effects on P mobilisation from organic matter in soil – Nina Hacker – Ecology Letters

Water microbiome

Proteomics of the Roseobacter clade, a window to the marine microbiology landscape – Joseph A. Christie-Oleza – Proteomics

Extremophile microbiome

Perspective: The discovery of Antarctic RNA viruses: a new game changer – Ricardo Cavicchioli – Molecular Ecology

Metagenomics and bioinformatics

MetaPhlAn2 for enhanced metagenomic taxonomic profiling – Duy Tin Truong – Nature Methods

Metabolomics, proteomics

An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products – Chad W. Johnston – Nature Communications

Proteomics of the Roseobacter clade, a window to the marine microbiology landscape – Joseph A. Christie-Oleza – Proteomics

CRISPRs

Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR proteins – Joseph Bondy-Denomy – Nature

Review: CRISPR-Cas immunity in prokaryotes – Luciano A. Marraffini – Nature

Microbes in the news

Study Links Skin Microbiome to Infections – Skin Inc

Ancient ‘Superman’ microbe’s ability to withstand damage to its DNA could be key to unlocking cancer cure, Chinese scientists say – Stephen Chen – South China Morning Post

Another Frontier in Microbiome Research: Preterm Birth – Julie A. Jacob – JAMA

Science, publishing, and career

A taxonomy of authorship roles – Credit Casrai

Bik’s Picks

What if everyone lived to 100? – Georgina Peters – London Business School Review

Gene-Edited “Micropigs” to Be Sold as Pets: The institute in Shenzhen, China, that creates the pigs quoted an initial price tag of $1,600 – David Cyranoski – Scientific American / Nature

1500-Year-Old Mosaic Map Found – Rossella Lorenzi – Discovery

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August 25, 2015

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Microbiome of Polish Cemetery soil, microbiome and risk of Plasmodium infection, interactions between mouse gut microbiota, host Genetics and diet, and the microbiome of air at three different heights.

The microbiome of death

Microbiological Analysis of Necrosols Collected from Urban Cemeteries in Poland – Ireneusz Całkosiński – BioMed Research International

Book: Carrion Ecology, Evolution, and Their Applications – M. Eric Benbow – CRC Press

Pregnancy and birth

Review: Rate of establishing the gut microbiota in infancy has consequences for future health – Shaillay Dogra – Gut Microbes

Editorial with disturbing title: Can establishment of human microbiome be customized after birth with local traditions of first feed and intimate kissing? – Sarman Singh – Journal of Laboratory Physicians

Human oral microbiome

Alterations of the Subgingival Microbiota in Pediatric Crohn’s Disease Studied Longitudinally in Discovery and Validation Cohorts – Judith Kelsen – Inflammatory Bowel Diseases

Review: Human microbiome: From the bathroom to the bedside – Stephen Malnick, Ehud Melzer – World J Gastrointest Pathophysiol

Human gut microbiota / transcriptomics

Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection – Shibu Yooseph – BMC Genomics

Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota – Guanhui Bao – Frontiers in Microbiology

The Fecal Virome of Children with Hand, Foot, and Mouth Disease that Tested PCR Negative for Pathogenic Enteroviruses – Piyada Linsuwanon – PLOS ONE

Review: Gut microbiota and allogeneic transplantation – Weilin Wang – Journal of Translational Medicine

Animal models

Interactions between Gut Microbiota, Host Genetics and Diet Modulate the Predisposition to Obesity and Metabolic Syndrome – Siegfried Ussar – Cell Metabolism

Physical Activity Differentially Affects the Cecal Microbiota of Ovariectomized Female Rats Selectively Bred for High and Low Aerobic Capacity – Tzu-Wen Liu – PLOS ONE

Animal microbiome

Isolation of oxalotrophic bacteria associated with Varroa destructor mites – M. Maddaloni – Letters in Applied Microbiology

Diversity of bacterial communities in the midgut of Bactrocera cucurbitae (Diptera: Tephritidae) populations and their potential use as attractants – Ashok B. Hadapad – Pest Management Science

Midgut bacterial communities in the giant Asian honeybee (Apisdorsata) across four developmental stages: a comparative study – Prakaimuk Saraithong – Insect Science

Bacterial communities associated with four ctenophore genera from the German Bight (North Sea) – Wenjin Hao – FEMS Microbial Ecology

Plant, root, and soil microbiome
(also see study above filed under Microbiome of Death)

The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon – Wei H. Xu – Frontiers in Microbiology

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

Molecular characterization of microbial communities in the rhizosphere soils and roots of diseased and healthy Panax notoginseng – Zhaoxiang Wu – Antonie van Leeuwenhoek

The diversity changes of soil microbial communities stimulated by climate, soil type and vegetation type analyzed via a functional gene array – Fu Chen – World Journal of Microbiology and Biotechnology

Water microbiome

Carbon fixation by basalt-hosted microbial communities – Beth N. Orcutt – Frontiers in Microbiology

Annual dynamics of North Sea bacterioplankton: Seasonal variability superimposes short-term variation – Judith Lucas – Microbiology Ecology

Ecology and Distribution of Thaumarchaea in the Deep Hypolimnion of Lake Maggiore –
Manuela Coci – Archaea

Viral and grazer regulation of prokaryotic growth efficiency in temperate freshwater pelagic environments – A.S. Pradeep Ram – FEMS Microbiology Ecology

Air / built environment microbiome

Vertical distribution of airborne bacterial communities in an Asian-dust downwind area, Noto Peninsula – Teruya Maki – Atmospheric Environment

Microbiological consequences of indoor composting – Alexandre Naegele – Indoor Air

Extremophiles

Response of the rare biosphere to environmental stressors in a highly diverse ecosystem (Zodletone spring, OK, USA) – Suzanne Coveley – PeerJ

Food microbiology

Wine fermentation microbiome: a landscape from different Portuguese wine appellations – Cátia Pinto – Frontiers in Microbiology

Difference of microbial community stressed in artificial pit muds for Luzhou-flavour liquor brewing revealed by multiphase culture-independent technology – Liqiang Zhang – Journal of Applied Microbiology

Monitoring of Yeast Communities and Volatile Flavor Changes During Traditional Korean Soy Sauce Fermentation – Young-Ran Song – Journal of Food Science

Bioreactor microbiology

Microbial community in a hydrogenotrophic denitrification reactor based on pyrosequencing – Hongyu Wang – Applied Microbiology and Biotechnology

Techniques and other microbiology

Application of iChip to Grow “Uncultivable” Microorganisms and its Impact on Antibiotic Discovery – Rinzhin T. Sherpa – Journal of Pharmacy & Pharmaceutical Sciences

Cultivating the uncultured: growing the recalcitrant cluster-2 Frankia strains – Maher Gtari – Scientific Reports

Isolation of Genetically Tractable Most-Wanted Bacteria by Metaparental Mating – Páraic Ó Cuív – Scientific Reports

Burkholderia bacteria infectiously induce the proto-farming symbiosis of Dictyostelium amoebae and food bacteria – Susanne DiSalvo – PNAS

Science, publishing, and career

A call to arms for women in science – Women’s Agenda
Microbes in the news

The Bacteria That Turn Amoebas Into Farmers – Ed Yong – National Geographic

Testers find twice as many ‘superbugs’ in conventional hamburger as organic ones – Lena H. Sun – Washington Post

Humans carry more antibiotic-resistant bacteria than animals they work with – Medical Xpress
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