Non-human microbiome digest, October 27, 2014

Microbiomes of camels, cheetahs, jackals, birds and reptiles, limpets, corals, plant roots, soils, and sea water.

Animal microbiome

* In-depth diversity analysis of the bacterial community resident in the camel rumen – Javad Gharechahi – Systematic and Applied Microbiology

“In this study, 16S rRNA gene amplicon pyrosequencing was applied in order to explore the structure of the bacterial community inhabiting the camel rumen.”

Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level – Sebastian Menke – Frontiers in Microbiology

“Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas).”

Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia – Marius Vital – ISME Journal

“We investigated the butyrate-producing community in hindgut-fermenting Mammalia (n=38), Aves (n=8) and Reptilia (n=8) using a gene-targeted pyrosequencing approach of the terminal genes of the main butyrate-synthesis pathways”

Decadal changes in common reef coral populations and their associations with algal symbionts (Symbiodinium spp.) – Timothy R. McClanahan – Marine Ecology

“Decadal populations changes in four coral taxa and their patterns of association with algal symbionts (Symbiodinium spp. – 10 years of sampling) were examined on Kenyan back reefs over a period of climatic disturbances (1991−2009). “

Metaphylogenomic and Potential Functionality of the Limpet Patella pellucida’s Gastrointestinal Tract Microbiome – Magda Dudek – International Journal of Molecular Sciences

“This study investigated the microbial diversity associated with the digestive tract of the seaweed grazing marine limpet Patella pellucida.”

Plant microbiome

* Distinct root-associated bacterial communities on three wild plant species growing in a common field – Kristin Aleklett – PeerJ Preprints

“We sampled endophytic and epiphytic bacteria in root tissues from a population of a wild, clonal plant… as well as two neighboring plant species … to determine if plant species hosted unique root microbiota”

The fungal leaf endophyte Paraconiothyrium variabile specifically metabolizes the host-plant metabolome for its own benefit – Yuan Tian – Phytochemistry

“..we have investigated the action of the endophytic fungus Paraconiothyrium variabile, isolated from the leaves of Cephalotaxus harringtonia, on the secondary metabolome of the host-plant. “

Soil microbiome

Late winter under ice pelagic microbial communities in the high Arctic Ocean and the impact of short-term exposure to elevated CO2 levels – Adam Monier – Frontiers in Microbiology

“Phylogenetic diversity was greater in the attached fraction compared to the free-living fraction in situ, in the controls and in the treatments.”

The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys – Catarina M. Magalhães – Frontiers in Microbiology

“Here we showed that AOB and AOA amoA gene diversity was generally low; only four AOA and three AOB operational taxonomic units (OTUs) were identified from a total of 420 AOA and AOB amoA clones.”

Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils – Akihiro Koyama – Frontiers in Microbiology

“Fertilization significantly altered overall bacterial community composition and reduced evenness, to a greater degree in organic than mineral soils, and in the 1989 compared to the 2006 site.”

Effect of volatile organic compounds absorbed to fresh biochar on survival of Bacillus mucilaginosus and structure of soil microbial communities – Daquan Sun – Journal of Soils and Sediments

“The structure of a soil microbial community incubated in biochar was examined via denaturing gradient gel electrophoresis (DGGE). “

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community – Uli Klümper – ISME Journal

“We identified transfer to many different recipients belonging to 11 different bacterial phyla. “

Water microbiome

Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities – Chris L Dupont – ISME Journal

“Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses.”

Aerobic methanotrophic communities at the Red Sea brine-seawater interface – Rehab Z. Abdallah – Frontiers in Microbiology

“The current study analyzed the aerobic free–living methane-oxidizing bacterial communities that potentially contribute to methane oxidation at the brine-seawater interfaces of the three aforementioned brine pools, using metagenomic pyrosequencing, 16S rRNA pyrotags and pmoA library constructs. “

Bacterial community structure is indicative of chemical inputs in the Upper Mississippi River – Christopher Staley – Frontiers in Microbiology

“Bacterial communities were characterized by Illumina sequencing of the V6 region of 16S rDNA and compared to >40 chemical and nutrient concentrations. “

Semiconductor Sequencing Reveals the Diversity of Bacterial Communities in an Amazonian Reservoir – Diego Assis das Graças – Aquatic Science and Technology

“In this study, we used a next-generation sequencing platform, the Ion Torrent Personal Genome Machine, and employed a barcode library to investigate the bacterial diversity along a 70-m deep water column in the proximity of the dam. “

Seasonal changes of microbial communities in two shallow peat bog lakes – Sylwia Lew – Folia Microbiologica

“We investigated the seasonal dynamics of the microbial community in two small peat bog lakes, Kuźnik Olsowy and Kuźnik Bagienny, located in western Poland.”

Bioreactor microbiome

Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response – Igor Y Oshkin – ISME Journal

“We report observations on the dynamics of bacterial communities in response to methane stimulus in laboratory microcosm incubations prepared with lake sediment samples.”

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Microbiome digest, October 21, 2014

Human oral microbiome

Abstract 4834: Microbiome in Oral Epithelial Dysplasia and Squamous Cell Carcinoma
Deepak Saxena – Cancer Research

“PCR amplicons targeting V3-V5 region of 16S rRNA gene were sequenced by 454 pyrosequencing. “

Human respiratory microbiome

Microbial Communities in the Upper Respiratory Tract of Patients with Asthma and Chronic Obstructive Pulmonary Disease – HeeKuk Park – PLOS ONE

“To account for the qualitative and quantitative diversity of the 16S rRNA gene in the oropharynx, the microbiomes of 18 asthma patients, 17 COPD patients, and 12 normal individuals were assessed using a high-throughput next-generation sequencing analysis.”

Human gut microbiome

Decreased bacterial diversity characterizes an altered gut microbiota in psoriatic arthritis and resembles dysbiosis of inflammatory bowel disease – Jose U. Scher – Arthritis & Rheumatology

“High-throughput 16S rRNA pyrosequencing was utilized to compare community composition of gut microbiota in PsA patients, subjects with psoriasis of the skin and healthy, matched-controls. “

Pregnancy and birth

The Salivary Scavenger and Agglutinin in Early Life: Diverse Roles in Amniotic Fluid and in the Infant Intestine – Martin Parnov Reichhardt – Journal of Immunology

“The present study revealed that SALSA was present in the amniotic fluid (AF) and exceptionally enriched in both meconium and feces of infants. “

Animal microbiome

* Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts – Kevin D. Kohl – FEMS Microbiology Ecology

“We used 16S rRNA sequencing to document changes in colonic and cecal microbiomes of animals representing five classes of vertebrates at four time points through prolonged fasting: tilapia, toads, geckos, quail, and mice. “

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (HMA, LMA) and seawater – Kristina Bayer – FEMS Microbiology Ecology

“By use of GeoChip, altogether 20,273 probes encoding for 627 functional genes and representing 16 gene categories were identified”

Natural volcanic CO2 seeps reveal future trajectories for host–microbial associations in corals and sponges – Kathleen M Morrow – ISME Journal

“The corals Acropora millepora and Porites cylindrica were less abundant and hosted significantly different microbial communities at the CO2 seep than at nearby control sites <500 m away.”
Plant microbiome

Phylogenetic conservatism in plant-soil feedback and its implications for plant abundance – Brian L. Anacke – Ecology Letters

“We conclude that soil biota influence the abundance of close plant relatives in nature.”

Bioreactor microbiome

Influence of Acidic pH on Hydrogen and Acetate Production by an Electrosynthetic Microbiome – Edward V. LaBelle – PLOS ONE

“Production of hydrogen and organic compounds by an electrosynthetic microbiome using electrodes and carbon dioxide as sole electron donor and carbon source, respectively, was examined after exposure to acidic pH (~5). “

Metagenomics / Transcriptomics / Bioinformatics

Census-based rapid and accurate metagenome taxonomic profiling – Amirhossein Shamsaddini – BMC Genomics

“We have developed a robust subsampling-based algorithm implemented in a tool called CensuScope meant to take a ‘sneak peak’ into the population distribution and estimate taxonomic composition as if a census was taken of the metagenomic landscape. “

Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation – Andrew Toseland – BMC Genomics

“To investigate the effect of such techniques on the annotation of metatranscriptome data we assess two commonly employed methods: clustering and de-novo assembly. To do this, we also developed an approach to simulate 454 and Illumina metatranscriptome data sets with varying degrees of taxonomic diversity. “

Microbial Ecology

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review – Hyun-Seob Song – Processes

“In this article, we provide an overview of mathematical tools that include not only current mainstream approaches, but also less traditional approaches that, in our opinion, can be potentially useful. “

A phylogenetic perspective on species diversity, β-diversity, and biogeography for the microbial world – Albert Barberán† and Emilio O. Casamayor – Molecular Ecology

“We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high altitude lakes district dataset to describe phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition.”

Distance-Decay and Taxa-Area Relationships for Bacteria, Archaea and Methanogenic Archaea in a Tropical Lake Sediment – Davi Pedroni Barreto – PLOS ONE

“The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA.”

More microbiology

From Denise Monack’s lab: Role of disease-associated tolerance in infectious superspreaders – Smita Gopinath – PNAS USA

“Using a mouse model of Salmonella infection, we show that levels of Salmonella are equivalent between antibiotic-treated superspreader and nonsuperspreader hosts; however, superspreader hosts are uniquely able to tolerate antibiotic treatment, unlike nonsuperspreader hosts. “

*Also see:  Antibiotics may help Salmonella spread in infected animals, scientists learn – Stanford Medicine News

Spatial organization of bacterial chromosomes – Xindan Wang, David Z Rudner – Current Opinion in Microbiology

“Here, we summarize these different patterns highlighting similarities and differences and discuss the protein factors that help establish and maintain them.”

Bacterial healers: Microbes can redeem themselves to fight disease – Susan Gaidos – Science News

“It’s just a matter of time before bacterial-based treatments become a routine part of a doctor’s toolkit, says microbiologist Robert Britton of the Baylor College of Medicine in Houston, who is studying the relationship between microbes and human health. “

Techniques

Rapid fingerprinting of methanogenic communities by high-resolution melting analysis – Jaai Kim, Changsoo Lee – Bioresource Technology

“The new method produced robust community clustering and ordination results comparable to the results from the commonly used denaturing gradient gel electrophoresis (DGGE) performed in parallel.”

Microbes in the news

Our unique ‘microbial aura’ travels with us wherever we go – Science Friday – PRI

“Unless you lived exactly the same life as me, you would not have the same microbiome. You are, in essence, microbially unique,” explains Jack Gilbert

We’re making a Microbiome Documentary Series and could use your Help – Jamie – Reddit

“My name’s Jamie and I’m part of a team trying to crowdfund a documentary series on the human microbiome titled: ‘Redefining Human’.”

Building houses with bacteria – Euronews

“Houses of the future could be partially built with bacteria. It sounds like science fiction but researchers involved in an EU-backed project in Madrid are working towards making this a concrete reality.”

Bik’s Picks

The Role of Surface Chemistry in Adhesion and Wetting of Gecko Toe Pads – Ila Badge – Scientific Reports

“As expected, under wet conditions, adhesion on a hydrophilic surface (glass) was lower than that on a hydrophobic surface (alkyl-silane monolayer on glass).”

Scientists prepare for an 8-month mission to Mars – on Earth soil- BetaWired

“There’s a new experiment commencing in Hawaii, and the results will help NASA better prepare its astronauts for a lengthy mission to Mars.”

White rhino subspecies is down to one breeding male – Andrea James – BoingBoing

“Sad news from Kenya: the northern white rhino subspecies is down to one breeding male with the death of Suni this month. Only six remain.”

Scientists restore hearing in noise-deafened mice, pointing way to new therapies – ScienceDirect

“Scientists have restored the hearing of mice partly deafened by noise, using advanced tools to boost the production of a key protein in their ears.”

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Microbiome digest, October 17, 2014

Resistance one year after antibiotic treatment, skin microbiome in atopic dermatitis, bacterial 16S rRNA load in the lungs, the rat oral microbiome, and microbes in cheese. And an exciting new discovery by Stanford scientists. Have a great weekend!

 

Multiple site human microbiome

Development of antimicrobial resistance in the normal anaerobic microbiota during one year after administration of clindamycin or ciprofloxacin – Mamun-Ur Rashid – Anaerobe

“Clindamycin or ciprofloxacin or placebo was given for 10 days in three groups. Skin, nasal, saliva, faeces sampling at day -1 and 11, 1, 2, 4 and 12 months.“

Shared microbiome in gums and the lung in an outpatient population – Patrick R. Schmidlin – Journal of Infection

“PCR to determine four periopathogens and seven less pathogenic species in both the periodontal pocket and bronchial protected specimen brush was used. “

Human skin microbiome

* Review: Role of the skin microbiome in atopic dermatitis – Alexander Salava and Antti Lauerma – Clinical and Translational Allergy

“Molecular genetics have dramatically changed our vision of the micro-organisms colonizing the human skin and recently well-documented changes in the skin microbiome in atopic dermatitis have become evident.”

Human respiratory microbiome

* The effect of long-term macrolide treatment on respiratory microbiota composition in non-cystic fibrosis bronchiectasis: an analysis from the randomised, double-blind, placebo-controlled BLESS trial – Geraint B Rogers – The Lancet Respiratory Medicine

“Microbiota composition was determined by 16S rRNA gene sequencing of sputum samples from participants in the BLESS trial”

A Comparison between Droplet Digital and Quantitative PCR in the Analysis of Bacterial 16S Load in Lung Tissue Samples from Control and COPD GOLD 2 – Marc A. Sze – PLOS ONE

“qPCR and ddPCR were performed on these samples using primers spanning the V2 region on the 16S rRNA gene along with negative controls. Total 16S counts were compared between the two methods.”

Human gut microbiome

* With pictures! Fecal microbiota transplantation: A ‘How-To’ guide for nurses – Sharyn Leis – Collegian

“However, to date, much of the literature addresses the procedure from a physician’s point of view, and can therefore be lacking in practical detail. As nurses are often the ‘unsung heroes’ of the procedure, it is timely to address the subject from a nursing perspective.”

The Intestinal Microbiota and Microenvironment in Liver – Hong-Di Ma- Autoimmunity Reviews

“But the interplay between the intestinal tract and the liver may explain the increased association with autoimmune liver diseases and inflammatory bowel diseases. “

Alterations of gut barrier and gut microbiota in food restriction, food deprivation and protein-energy wasting – L. Genton – Clinical Nutrition

“This review… highlights the complex interactions between the components of gut barrier in depleted states due to food deprivation, food restriction and protein energy wasting and shows that these interactions are multidirectional”

Application of next-generation sequencing to study ascitic microbiome in cirrhotic patients with or without spontaneous bacterial peritonitis – Ye Feng- Journal of Microbiology, Immunology and Infection

“Both the 16S polymerase chain reaction approach and the whole genome shotgun approach were adopted for the next-generation sequencing technology. “

Chronic ethanol consumption alters intestinal microbiota impairing immune function – T. Barr – Alcohol

The gastrointestinal microbiome – functional interference between stomach and intestine – Loris R. Lopetuso – Best Practice & Research Clinical Gastroenterology

“This review focuses and speculates on the possible interactions between gastric microorganisms and intestinal microbiota and on the consequences of this interplay in modulating gut health.”

Animal models of microbiome research

Can Pre-Weaning Modulation of Intestinal Microbiota by Oligosaccharides or Amoxicillin Program Adult One in Rats? – Fanny B. Morel – Nutrition

“As revealed by a targeted qPCR approach, programming of adult intestinal microbiota seems to vary according to the nature of the pre-weaning microbiotal modulator.”

Animal microbiome

* Characterization of the rat oral microbiome and the effects of dietary nitrate – Embriette R. Hyde – Free Radical Biology and Medicine

“Demonstrates the utility of using metagenomics techniques to characterize the healthy rat tongue microbiome and to compare it to the healthy human tongue microbiome.”

Soil microbiome

High-Level Diversity of Tailed Phages, Eukaryote-Associated Viruses, and Virophage-Like Elements in the Metaviromes of Antarctic Soils – Olivier Zablocki – Applied and Environmental Microbiology

“The metaviromes of two distinct Antarctic hyperarid desert soil communities have been characterized.”

Food microbiology

Microbial communities involved in Kashar cheese ripening – Oğuz Aydemir – Food Microbiology

“The molecular classification and identification of 594 LAB isolates during Kashar cheese ripening were performed through (GTG)5–PCR fingerprinting of their genomic DNA followed by verification of the (GTG)5–PCR clusters obtained after numerical analysis through 16S rRNA gene sequencing of representative isolates. “

Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food)
Cristina Riquelme – International Journal of Food Microbiology

“Pyrosequencing of tagged amplicons of the V3–V4 regions of the 16S rDNA and Operational Taxonomic Unit-based (OTU-based) analysis were applied to obtain an overall idea of the microbiota in Pico cheese and to elucidate possible differences between cheese-makers (A, B and C) and maturation times.”

Metagenomics/Bioinformatics

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models – Matthew N. Benedict – PLOS Computational Biology

“Here we develop an approach for applying genomic information to predict alternative functions for genes and estimate their likelihoods from sequence homology. “

Microbes in the news

‘Critical Conversation’ to focus on human microbiome – Sue Wuetcher – UB Reporter, University at Buffalo

“David Relman, the Thomas C. and Joan M. Merigan Professor and professor of microbiology and immunology at the Stanford University School of Medicine, will speak on “Your Inner Self: The Human Microbiome in Health and Disease””

 

Bik’s Weekend Picks

Want to Ace That Test? Get the Right Kind of Sleep – Benedict Carey – New York Times

“Scientists now argue that a primary purpose of sleep is learning consolidation, separating the signal from the noise and flagging what is most valuable.”

‘Human face of science’: Researchers dance to raise funds for cancer study – RT.com

“Biomedicine scientists in Barcelona have released a music clip aimed at raising funds for medical research, as well as promoting their profession’s “human face.” The video’s release comes amid low levels of public interest in science throughout Spain.”

In science, popularity breeds unreliability – Tom Siegfried – Science News

“In recent decades, pressure to publish and seek publicity has distorted the scientific enterprise. Scientists need grants. Getting published raises the likelihood of getting those grants. “

Satire: Scientists Discover Two New Kinds Of Bird Poop – The Allium

“Scientists at Stanford University have revealed that they have discovered two new species of bird poop that defy classification. These are the first new species of poop that have been discovered in thirty five years. The findings have been reported this week in the journal Nature.”

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Microbiome digest, October 16, 2014

Lung microbiome and pneumonia, bacterial vaginosis, microbiome and jetlag, cardiovascular consequences of gut dysbiosis, bacteria in locust guts and cropland in China, and how to earn some $$$ with your poop.

Human respiratory microbiome

Single-Molecule Long-Read 16S Sequencing To Characterize the Lung Microbiome from Mechanically Ventilated Patients with Suspected Pneumonia – Ian Toma – Journal of Clinical Microbiology

“The present study used NGS of essentially full-length PCR-amplified 16S ribosomal DNA from the bronchial aspirates of intubated patients with suspected pneumonia.”

Human vaginal microbiome

Recent progress in understanding the epidemiology of bacterial vaginosis – Kenyon, Chris R.; Osbak, Kara – Current Opinion in Obstetrics & Gynecology

“Bacterial vaginosis epidemiology has been transformed by new theoretical insights and methodologies, such as molecular sequencing. We summarize the progress made in these domains.”

Human gut microbiome

Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis – Christoph A. Thaiss – Cell

“Consequently, jet-lag-induced dysbiosis in both mice and humans promotes glucose intolerance and obesity that are transferrable to germ-free mice upon fecal transplantation.”

Far from the Eyes, Close to the Heart: Dysbiosis of Gut Microbiota and Cardiovascular Consequences – Matteo Serino – Current Cardiology Reports

“Here, we report evidence from the literature, as well as a few controversial reports, regarding the putative role of gut microbiota dysbiosis-induced cardiovascular diseases”

Insect microbiome

Cellulolytic activity and structure of symbiotic bacteria in locust guts – L-J Su – Genetics and Molecular Research

“The diversity of gut symbiotic bacteria was studied using denaturing gradient gel electrophoresis (DGGE). “

Soil microbiome

Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China – Zhen Zhen – PLOS ONE

“Denaturing gradient electrophoresis (DGGE) fingerprinting analysis showed that the structure and composition of bacterial and fungi communities in the six fertilizer treatments varied at different levels. “

Water microbiome

Substratum-Associated Microbiota – Furey, Paula C.; Liess, Antonia – Water Environment Research

“In this review of the 2013 literature, advances in laboratory, field, and assessment methods are highlighted as are updates in taxonomy and systematics.”

More microbiology

Commensally sourced antibiotics – Cláudio Nunes-Alves – Nature Reviews Microbiology

Donia et al. have carried out the first systematic screen of biosynthetic gene clusters (BGCs) in the healthy human microbiota and found that BGCs for the thiopeptide class of antibiotics are widely distributed.”

First aid kit for cholera – Andrea Du Toit – Nature Reviews Microbiology

“In a new study, Gordon and colleagues examined the role of the human gut microbiota in V. cholerae infection and showed that one of its members, Ruminococcus obeum, decreases the expression of V. cholerae virulence factors to limit colonization.”

Microbes in the news

* A Poop Bank in Massachusetts Will Pay You $40 Every Day – Chelsea Rice – Boston.com

“All you have to do is visit OpenBiome, launched in 2012 as the only independent nonprofit stool bank in the country.”

Study reveals rats in NYC carry variety of infectious bacteria – Larry McShane – New York Daily News

“The first-of-its-kind study showed the rodents carrying an average of two bacteria capable of causing gastrointestinal problems for humans and the Seoul hantavirus, which causes a potentially life-threatening fever and kidney failure.”

* New Genes = New Archaea? – Molly Sharlach – The Scientist

“The study, published today (October 15) in Nature, also suggests that genetic transfers from bacteria to archaea are at least five times more common than from archaea to bacteria.”

Bik’s Picks

“Epicenters” of resilience – Mary Lou Zoback – Science

“The 25th anniversary of the magnitude (M) 6.9 Loma Prieta earthquake that struck the San Francisco Bay Area on 17 October 1989 is a fitting time to examine what progress has been made in increasing community resilience to minimize seismic risk. “

Cells’ powerhouses were once energy parasites: Study upends current theories of how mitochondria began – Science Daily

“Parasitic bacteria were the first cousins of the mitochondria that power cells in animals and plants — and first acted as energy parasites in those cells before becoming beneficial, according to a new study”

How Did We Become a Society Suspicious of Science? – Keith M. Parsons – Huffington Post

“But something has been lost. Fifty years ago science was king. Science had respect; it was bigger than ideology. No longer. “

 

Biology Week: Bio-bodies Bake Off Public Vote – Physiological Society

“In the lead up to biology week we set you a challenge! We wanted you to celebrate the science of life by creating your own physiology bakes, and you didn’t let us down! ”

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Microbiome digest, October 15, 2014

A seminar this Friday with Pat Schloss, but without HMP girl, aspartame and gut microbiome in a rat model, bacteria in arsenic contaminated soil, and inter-kingdom horizontal gene transfer.

Human oral microbiome

General Immune Status and Oral Microbiology in Patients with Different Forms of Periodontitis and Healthy Control Subjects – Jana Schmidt – PLOS ONE

“Subgingival plaque samples were taken from each individual and immediately cultivated for microbiological examination.”

Pregnancy and birth

* 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

“Ascending bacterial infection is implicated in about 40–50% of preterm births. “

Animal models of microbiome research

* Low-Dose Aspartame Consumption Differentially Affects Gut Microbiota-Host Metabolic Interactions in the Diet-Induced Obese Rat – Marie S. A. Palmnäs – PLOS ONE

“Serum metabolomics analysis revealed aspartame to be rapidly metabolized and to be associated with elevations in the short chain fatty acid propionate, a bacterial end product and highly gluconeogenic substrate, potentially explaining its negative affects on insulin tolerance. “

Effect of dietary supplementation with resveratrol on nutrient digestibility, methanogenesis and ruminal microbial flora in sheep – T. Ma – Journal of Animal Physiology and Animal Nutrition

“Two experiments were conducted to evaluate the effect of resveratrol on methanogenesis and microbial flora in Dorper × thin-tailed Han cross-bred ewes. “

Soil microbiome

Changing precipitation pattern alters soil microbial community response to wet-up under a Mediterranean-type climate – Romain L Barnard – ISME Journal

“Here, we investigated the effects of extending winter rainfall into the normally dry summer period on soil microbial response to a controlled rewetting event”

Surface binding and intracellular uptake of arsenic in bacteria isolated from arsenic contaminated site – Neha Vishnoi, Sonal Dixit, D.P. Singh – Ecological Engineering

“The present study deals with the surface binding and uptake of arsenic (As) in two bacterial strains (Bacillus subtilis and Paenibacillus macerans) isolated from the As contaminated soil.”

Water microbiome

Effects of ecological engineered oxygenation on the bacterial community structure in an anoxic fjord in western Sweden – Michael Forth – ISME Journal

“We used molecular ecologic methods to study changes in bacterial community structure in response to the oxygenation in the Byfjord. “

Food microbiology

Assessment of the bacterial and fungal diversity in home-made yoghurts of Xinjiang, China by pyrosequencing – Haiyan Xu – Journal of the Science of Food and Agriculture

“The bacterial and fungal community diversity in 22 home-made yoghurt samples was analyzed by pyrosequencing. “

CRISPRs, phages, viruses

In Hopes Of Fixing Faulty Genes, One Scientist Starts With The Basics – Joe Palca – NPR Morning Edition

“That’s certainly true for Jennifer Doudna. She hasn’t won a Nobel Prize, but many are whispering that she’s in line to win one for her work on something called CRISPR/Cas9 — a tool for editing genes.”

Bioinformatics and metagenomics

* Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria – Alejandro Caro-Quintero and Konstantinos T Konstantinidis – ISME Journal

“Here, we devised a novel bioinformatic pipeline, which minimized the effect of over-representation of specific taxa in the available databases and other limitations of homology-based approaches by analyzing genomes in standardized triplets, to quantify gene exchange between bacterial genomes representing different phyla. “

* Origins of major archaeal clades correspond to gene acquisitions from bacteria
Shijulal Nelson-Sathi – Nature

“To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes.”

Evidence of Carbon Fixation Pathway in a Bacterium from Candidate Phylum SBR1093 Revealed with Genomic Analysis – Zhiping Wang – PLOS ONE

“A phylogenetic analysis based on the 16S rRNA gene reveals that the phylotypes within candidate phylum SBR1093 are primarily clustered into 5 clades with a shallow branching pattern. “

Metagenomic Approach Reveals Variation of Microbes with Arsenic and Antimony Metabolism Genes from Highly Contaminated Soil – Jinming Luo – PLOS ONE

“Metagenomic analysis revealed that microbes from 18 phyla were present in the 5 samples of soil contaminated with high As and Sb.”

More microbiology

* The Phylogeny of Everything, the Origin of Eukaryotes, and the Rules of Taxonomy: Death to Archaea, Bacteria, and Eucarya! Long live Archaebacteria, Eubacteria, Eukaryota, and Prokaryota! – Judge Starling

“The molecular revelation based on orthologous ribosomal RNA sequences that prokaryotes are separable into two basic taxa—archaebacteria and eubacteria, and that these two taxa are approximately equidistant from eukaryotes, prompted Woese et al. (1990) to come up with a tripartite taxonomy of all life forms.”

Adhesion as a weapon in microbial competition – Jonas Schluter – ISME Journal

“We test the predictions of our model using the enteric pathogen Vibrio cholerae, which produces an extracellular matrix important for biofilm formation. “

Microbes in the news:

* Google Hangout on Friday: MicroSeminar: A new way of doing conferences – Pat Schloss

“You will not see HMP Girl, no quotes of specious statistics, no mention of obscure disease, and no venturing into the weeds of bioinformatics. I will be describing unpublished experiments from the lab where we have taken various sources of microorganisms and used them to colonize mice that lack their own microbiota.”

‘Grapes of Wrath’: Stomping out grape disease one vineyard at a time – Phys.org

“A Rochester Institute of Technology scientist and an RIT alumnus are close to completing the genetic blueprint, or microbiome, of grape crown gall tumor disease—the bane of vineyards worldwide. ”

Redefining Human: The Microbiome Documentary Series – Root House Studio – Kickstarter

“We know science documentaries can be painfully boring, so Redefining Human will use a variety of new techniques to turn this complex science into an informative and entertaining documentary series.”

What’s in my microbiome? – Richard Sprague

“To find out what’s in my microbiome now, I bought a $400 kit from the San Francisco company uBiome. “

Science, publishing and career

* Rise of the Rest: The Growing Impact of Non-Elite Journals – Anurag Acharya – Google / Arxiv

“Our analysis indicates that the number of top-1000 papers published in non-elite journals for the representative subject category went from 149 in 1995 to 245 in 2013, a growth of 64%.”

Review rewards – Welcome efforts are being made to recognize academics who give up their time to peer review – Nature Editorial

“A welcome movement is under way to publicly register and recognize the hitherto invisible efforts of referees.”

Overqualified or underqualified? – Carrie Arnold – Science

“As unemployment stretched from weeks into months, Milstein decided that her Ph.D. was working against her. “

 

Satire: Facebook Offers To Freeze Female Employee’s Newborn Children – The Onion

“Women deserve to have the option to postpone motherhood until they feel fully prepared, which is why Facebook will also cover the cryonic facility’s annual maintenance costs for as many years as our employees feel they need. “

Bik’s Picks

360-Degree View of the Tomato – Anna Azvolinsky – The Scientist

“Researchers have sequenced 360 varieties of the tomato plant to create a comprehensive map of the evolution of the fruit from its wild form to the modern varieties. “

Extinct giant kangaroos didn’t hop, they walked – Andy Coghlan – New Scientist

“They had faces like rabbits and some were 2 metres tall. But now it seems that an extinct giant kangaroo didn’t hop – it walked.“

 

Chimpanzees have favorite ‘tool set’ for hunting staple food of army ants – Science Daily

“New research shows that chimpanzees search for the right tools from a key plant species when preparing to ‘ant dip’ — a crafty technique enabling them to feast on army ants without getting bitten. “

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Non-human microbiome digest, October 14, 2014

Diatoms in aquatic animals, bacteria in agaves and soybeans, and bacteria in artificial soil.

Animal microbiome

Diatoms in cytologic specimens of aquatic animals – Part I, fecal samples – Nicole StacyDiatoms in cytologic specimens of aquatic animals – Part II, dermal, respiratory, and gastric samples – Nicole Stacy – Veterinary Clinical Pathology

“Diatoms are a common finding in cytologic samples of aquatic animals…and it is necessary to differentiate these microbiota from parasite ova or protozoa.”

Impacts of large-bodied crustaceans on the microbial loop – Krystyna Kalinowska – Hydrobiologia

“Three alien crustacean species (Daphnia pulex, Simocephalus vetulus and Macrocyclops albidus) were collected from the regional species pool and added to mesocosms that were filled with water from a eutrophic lake “

Bacterial Community Composition of Three Candidate Insect Vectors of Palm Phytoplasma (Texas Phoenix Palm Decline and Lethal Yellowing) –  Christopher M. Powell – Current Microbiology

“Individuals from each species were subjected to 16S bacterial community sequencing using the Roche 454 platform, providing new information regarding the previously unexplored bacterial communities present in putative vectors.”

Plant microbiome

Diazotrophic potential among bacterial communities associated with wild and cultivated agaves – Damaris Desgarennes – FEMS Microbiology Ecology

“Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA-DGGE fingerprinting and sequencing.”

Spatio temporal influence of isoflavonoids on bacterial diversity in the soybean rhizosphere – Laura J White – Molecular Plant-Microbe Interactions

“We silenced the biosynthesis of isoflavonoids, a major component of soybean rhizodeposits, using RNA interference in hairy root composite plants, and examined changes in rhizosphere bacteriome diversity.”

Soil microbiome

Artificial soil studies reveal domain-specific preferences of microorganisms for the colonisation of different soil minerals and particles size fractions – Michael Hemkemeyer – FEMS Microbiology Ecology

“this study demonstrates that the mineral composition and the particle size fractions have specific and different selective effects on the three domains”

Improving soil bacterial taxa–area relationships assessment using DNA meta-barcoding – S Terrat – Heredity

“Our objectives in this study were to compare DNA fingerprinting and meta-barcoding approaches for evaluating soil bacterial TAR and the determinism of soil bacterial community assembly on a broad scale. “

The role of stochasticity differs in the assembly of soil- and root-associated fungal communities – Sarah Beck – Soil Biology and Biochemistry

“The importance of spatial and environmental factors in shaping fungal beta diversity was determined over a 500 km transect.”

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Microbiome digest, October 8, 2014

Blogging from our yearly retreat in Santa Cruz, California: Rethinking Enterotypes, Wolbachia phylogenomics,  hydrothermal vents, and the influence of salamanders on soil microbiome.

Human Microbiome General

Genes & cells: Body microbes make useful molecules: Human microbiome produces thousands of drug candidates – Tina Hesman Saey – Science News

Human Gut Microbiome

Rethinking “Enterotypes” – Dan Knights – Cell Host and Microbe

“However, as discussed here, several different methods of collapsing enterotype variation into a few discrete clusters suggest that enterotype distribution is continuous and can vary widely within an individual.”

Fecal Bacterial Community Changes Associated with Isoflavone Metabolites in Postmenopausal Women after Soy Bar Consumption – Cindy H. Nakatsu – PLOS ONE

“Using DGGE profiles of PCR amplified 16S rRNA genes (V3 region) to compare microbial communities in fecal samples collected one week before and one week during soy supplementation revealed significant differences (ANOSIM p<0.03) before and after soy supplementation in all subjects. “

Insect microbiome

Phylogenomic analyses uncover origin and spread of the Wolbachia pandemic – Michael Gerth  – Nature Communications

“Here we present the first comprehensive phylogenomic analysis of Wolbachia supergroup relationships based on new whole-genome-shotgun data.”

Coral microbiome

Comparing Bacterial Community Composition of Healthy and Dark Spot-Affected Siderastrea siderea in Florida and the Caribbean – Christina A. Kellogg – PLOS ONE

“Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. “

Soil Microbiome

Summer temperature increase has distinct effects on the ectomycorrhizal fungal communities of moist tussock and dry tundra in Arctic Alaska – Luis N. Morgado – Global Change Biology

“We used Ion Torrent sequencing of the rDNA internal transcribed spacer 2 (ITS2) region to compare ECM fungal communities in plots with and without long-term experimental warming in both dry and moist tussock tundra.”

A metagenomics-based approach to the top-down effect on the detritivore food web: a salamanders influence on fungal communities within a deciduous forest – Donald M. Walker – Ecology and Evolution

“From each sample, DNA was extracted, fungal-specific amplification performed, and 454 pyrosequencing was used to sequence the nuclear ribosomal internal transcribed spacer (ITS2) region and partial ribosomal large subunit (LSU).”

Water microbiome

Evolutionary Strategies of Viruses, Bacteria and Archaea in Hydrothermal Vent Ecosystems Revealed through Metagenomics – Rika E Anderson – PLOS ONE

“Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, “

Metabolomics

Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine – Brianna B. Williams – -Cell Host and Microbe

“Using a combination of genetics, biochemistry, and crystallography, we identify and characterize two phylogenetically distinct enzymes found in the human microbiome that decarboxylate tryptophan to form the β-arylamine neurotransmitter

Techniques

Selective Microbial Genomic DNA Isolation Using Restriction Endonucleases – Helen E. Barnes – PLOS ONE

“Using synthetic genome mixtures, we demonstrate 80% recovery of Escherichia coli genomic DNA even when only femtogram quantities are spiked into 10 µg of human DNA background.”

 More Microbiology

Pseudomonas aeruginosa eradicates Staphylococcus aureus by manipulating the host immunity – Erwan Pernet – Nature Communications

“Our results indicate that a bacterium can eradicate another bacterium by manipulating the host immunity.”

Preparation and evaluation of low-calorie functional ice cream containing inulin, lactulose and Bifidobacterium lactis  – Majid Hashemi- International Journal of Dairy Technology

“This study was aimed to investigate the effects of replacing 5% fat and sugar by inulin and lactulose, respectively, on the survival of Bifidobacterium lactis and physicochemical and sensorial characteristics of the ice cream. “

Microbes in the News

Second Genome, Mayo Clinic team up to explore the microbiome – Stephanie M. Lee – SF Gate

“Second Genome will identify up to eight conditions in which the microbiome potentially plays a role, and the Mayo Clinic will provide human clinical samples for patients with those diseases.”

 Oral health affects overall health – PhillyTrib

“The evidence shows that an infection from periodontitis, or gum disease, can put you at risk for other serious conditions like heart disease, stroke and more.”

Safety Bees: Bacteria From Bees Used To Fight Infections – The Ledger

 “A group of 13 lactic-acid bacteria found in fresh honey from the honey stomach of bees could be the key to bringing an old folk remedy into modern science”

Bik’s Picks  

How dinosaurs divided their meals at the Jurassic dinner table – Science Daily

“How the largest animals to have ever walked on Earth fed, and how this allowed them to live alongside one another in prehistoric ecosystems, is the subject of new research.”

Imitation, Genetic Lineages, and Time Influenced the Morphological Evolution of the Violin – Daniel H. Chitwood – PLOS ONE

“Here, I provide an analysis of morphological evolution in the violin family, sampling the body shapes of over 9,000 instruments over 400 years of history.”

Cat Watch 2014: What’s it like being a cat? – BBC

“Cats are at a crucial point in their evolutionary journey as they transform from solitary hunters to domestic pets, a study by the BBC and the Royal Veterinary College has revealed.”
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Non-human microbiome digest, October 7, 2014

Weaning piglets, fungus-farming termites, mosquito larval stages, antibiotic resistant bacteria in soil after fertilization, and biogeography of marine microbiomes.

Mammal microbiome

Assessment of fecal bacterial diversity among healthy piglets during the weaning transition – Edward Alain B. Pajarillo – Journal of General and Applied Microbiology

“This study describes the fecal microbial shifts of healthy piglets during the weaning transition using barcoded pyrosequencing of the prokaryotic 16S rRNA gene.”

Insect microbiome

Complementary symbiont contributions to plant decomposition in a fungus-farming termite – Michael Poulsen – PNAS USA

“We analyzed the genomic potential for biomass decomposition in a farming termite, its fungal symbiont, and its bacterial gut communities. “

Composition of Anopheles coluzzii and Anopheles gambiae microbiota from larval to adult stages – Geoffrey Gimonneau – Infection, Genetics and Evolution

“We characterized bacterial communities from aquatic habitats, at surface microlayer and subsurface water levels, to freshly emerge adult mosquitoes using multiplexed 16S rRNA gene pyrosequencing”

Soil microbiome

From the Handelsman lab: Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization – Nikolina Udikovic-Kolic – PNAS USA

“In this study, we found that dairy cow manure amendment enhanced the proliferation of resident antibiotic-resistant bacteria and genes encoding β-lactamases in soil even though the cows from which the manure was derived had not been treated with antibiotics. “

Niche-Partitioning of Edaphic Microbial Communities in the Namib Desert Gravel Plain Fairy Circles – Jean-Baptiste Ramond – PLOS ONE

“T-RFLP fingerprinting of the bacterial (16S rRNA gene) and fungal (ITS region) communities, in parallel with two-way crossed ANOSIM, showed that FC communities were significantly different to those of external control vegetated soil”

Temporal Changes in Soil Bacterial Diversity and Humic Substances Degradation in Subarctic Tundra Soil – Ha Ju Park – Microbial Ecology

“Culture-independent microbial community analysis showed that during the microcosm experiments, the relative abundance of phyla Proteobacteria (bacteria) and Euryarchaeota (archaea) largely increased, indicating their involvement in HS degradation. “

Water microbiome

Distinct patterns of marine bacterial communities in the South and North Pacific Oceans – Sung-Suk Suh – Journal of Microbiology

“In this study, 16S rRNA gene tag pyrosequencing was used to investigate change in bacterial community structure between summer and winter water masses from Gosung Bay in the South Sea of Korea and Chuuk in Micronesia, located in the North and South Pacific Oceans, respectively.”

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Non-human microbiome digest, October 6, 2014

Microbiomes of cats with diabetes, vaginas of ewes and cows, chickens, hoopoes, Drosophila, sponges, plants, and subways.

Mammal Microbiome

* Faecal Microbiota of Cats with Insulin-Treated Diabetes Mellitus – Erin T. Bell – PLOS ONE

“Faecal samples were collected from insulin-treated diabetic and non-diabetic cats, and Illumina sequencing of the 16S rRNA gene and quantitative PCR were performed on each sample. “

Characterization of the vaginal microbiota of ewes and cows reveals a unique microbiota with low levels of lactobacilli and near-neutral pH – JD Swartz, M Lachman, K Westveer, T O’Neill, T Geary – Frontiers in Veterinary Science

“We amplified and sequenced the V3-V4 region of the 16S ribosomal RNA contents yielding a total of 907,667 high-quality reads. “

Avian microbiome

The chicken gastrointestinal microbiome – Brian B. Oakley – FEMS Microbiology Letters

“In this mini-review, we provide an overview of the current state of knowledge of the chicken GI microbiome focusing on spatial and temporal variability, the presence and importance of human pathogens, the influence of the microbiota on the immune system, and the importance of the microbiome for poultry nutrition.”

Environmental Factors Shape the Community of Symbionts in the Hoopoe Uropygial Gland More than Genetic Factors – Magdalena Ruiz-Rodríguez – Applied and Environmental Microbiology

“By disentangling the diversity of bacterial strains from the uropygium of hoopoes (Upupa epops) due to genetic relatedness or to a common environment, we explored the importance of horizontal (from the environment) and vertical (from parents) acquisition of antimicrobial-producing symbionts in this species.”

Insect Microbiome

Metagenome-Wide Association of Microbial Determinants of Host Phenotype in Drosophila melanogaster – John M. Chaston – mBio

“Monoassociation with bacteria that ectopically expressed a predicted oxidoreductase or gluconate dehydrogenase conferred reduced Drosophila TAG contents relative to the TAG contents in empty vector controls.”

Invertebrate microbiome

* Microbial Communities and Bioactive Compounds in Marine Sponges of the Family Irciniidae—A Review – Cristiane C. P. Hardoim and Rodrigo Costa – Marine Drugs

“The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. “

Plant microbiome

Microbial genome-enabled insights into plant–microorganism interactions – David Guttman, Alice C. McHardy & Paul Schulze-Lefert – Nature Reviews Genetics

“… culture-independent community profiling methods, coupled with metagenomic and metatranscriptomic studies, have provided the first insights into the emerging field of research on plant-associated microbial communities.”

Soil microbiome

Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland – Antje Gittel – Frontiers in Microbiology

“We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities.”

Water microbiome

Illuminating Microbial Dark Matter in Meromictic Sakinaw Lake – Esther A. Gies – Applied and Environmental Microbiology

“Here we describe diversity, abundance, and cooccurrence patterns of uncultivated microbial communities inhabiting the permanently stratified waters of meromictic Sakinaw Lake, British Columbia, Canada, using 454 sequencing of the small-subunit rRNA gene with three-domain resolution.”

Microbiome of the built environment

* Indoor-Air Microbiome in an Urban Subway Network: Diversity and Dynamics – Marcus H. Y. Leung – Applied and Environmental Microbiology

“Overall, subway lines harbored different phylogenetic communities based on α- and β-diversity comparisons, and closer inspection suggests that each community within a line is dependent on architectural characteristics, nearby outdoor microbiomes, and connectedness with other lines. “

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Non-human microbiome digest, October 2, 2014

Microbiomes of mares with colic, corals and ascidians, bacteria in plant seeds, ciprofloxacin in compost, and yeast in Turkish sausages.

Mammal microbiome

Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods – Timothy J. Snelling – PLOS ONE

“Sequences mapping to rumen 16S rRNA and mcrA gene references were extracted from Illumina metagenome data.“

* Temporal changes and the effect of subtherapeutic concentrations of antibiotics in the gut microbiota of swine – Devin B. Holman – FEMS Microbiology Ecology

“In this study, the effect of two antibiotics on the swine gut microbiota over a 19-week monitoring period was investigated using Illumina-based sequencing. “

Changes in the faecal microbiota of mares precede the development of postpartum colic
J. S. Weese – Equine Veterinary Journal

“Next generation sequencing of the V4 region of the 16S rRNA gene was performed on samples from 13 mares that developed colic, 13 mares that did not display colic, and 5 non-pregnant controls.”

Bird microbiome

Correlations between changes in intestinal microbiota composition and performance parameters in broiler chickens – L. A. Rubio – Journal of Animal Physiology and Animal Nutrition

“The composition of the intestinal microbiota was analysed by qPCR at different points of the intestinal tract, and a number of nutritional parameters were also determined.”

Insect microbiomes

Differential Genome Evolution Between Companion Symbionts in an Insect-Bacterial Symbiosis – Gordon M. Bennett – mBio

“To understand how symbiont genome degeneration proceeds, we compared the genomes of symbionts in two leafhopper species”

Metagenome-Wide Association of Microbial Determinants of Host Phenotype in Drosophila melanogaster – John M. Chaston – mBio

“.. we measured two microbiota-responsive host traits, development time and triglyceride (TAG) content, in Drosophila melanogaster flies monoassociated with each of 41 bacterial strains.”

Invertebrate microbiome

Quorum Sensing Signal Production and Microbial Interactions in a Polymicrobial Disease of Corals and the Coral Surface Mucopolysaccharide Layer – Beth L. Zimmer – PLOS ONE

“These findings demonstrate for the first time that AHLs are present in an active coral disease.”

The secret to a successful relationship: lasting chemistry between ascidians and their symbiotic bacteria – Eric W. Schmidt – Invertebrate Biology

Plant microbiome

Plants prepackage beneficial microbes in their seeds – Phys.org

“The researchers, from the University of Notre Dame, presented their findings today at the 5th ASM Conference on Beneficial Microbes.”

Cave microbiome

* Mycobiome of the Bat White Nose Syndrome Affected Caves and Mines Reveals Diversity of Fungi and Local Adaptation by the Fungal Pathogen Pseudogymnoascus (Geomyces) destructans – Tao Zhang – PLOS ONE

“This study was conducted in 2010–2011 in New York and Vermont using 90 samples from four mines and two caves situated within the epicenter of WNS. “

Soil and sediment microbiome

Differential distribution and abundance of diazotrophic bacterial communities across different soil niches using a gene-targeted clone library approach – Basit Yousuf – FEMS Microbiology Letters

“Differential occurrence of diazotrophs was studied by the nifH gene-targeted clone library approach.”

Spatiotemporal Analysis of Bacterial Diversity in Sediments of Sundarbans Using Parallel 16S rRNA Gene Tag Sequencing – Pijush Basak – Microbial Ecology

“The total sediment DNA was extracted and subjected to the 16S rRNA gene pyrosequencing, which resulted in 117 Mbp of data from three experimental stations. “

Ciprofloxacin residues in municipal biosolids compost do not selectively enrich populations of resistant bacteria – Caitlin P. Youngquist – Applied and Environmental Microbiology

“Regression analysis showed that growth of the susceptible strain of E. coli can be reduced given a sufficiently high concentration of ciprofloxacin (P<0.007), a result that is consistent with adsorption being the primary mechanism of sequestration. “

Biogeographic patterns in below-ground diversity in New York City’s Central Park are similar to those observed globally – Kelly S. Ramirez – Proceedings of the Royal Society B

“Here, we present an assessment of soil biodiversity and biogeographic patterns across Central Park in New York City that spanned all three domains of life, demonstrating that even an urban, managed system harbours large amounts of undescribed soil biodiversity.”

Water microbiome

Abundance and Dynamics of Antibiotic Resistance Genes and Integrons in Lake Sediment Microcosms – Björn Berglund – PLOS ONE

“Resistance genes sulI and ermB were quantified in the microcosm sediments with mean abundances 5 and 15 gene copies/106 16S rRNA gene copies, respectively. “

Microbial composition of the activated sludge of Moscow wastewater treatment plants
A. Yu. Kallistova – Microbiology

“FISH investigation revealed that aerobic sludge were eubacterial communities; the metabolically active archaea contributed insignificantly.”

Phytoplankton, bacterioplankton and virioplankton structure and function across the southern Great Barrier Reef shelf – Daniel M. Alongi – Journal of Marine Systems

“Phytoplankton, bacteria and virus dynamics are driven by across-shelf changes in water chemistry and hydrography.”

Food microbiology

Pulque production from fermented agave sap as a dietary supplement in Prehispanic Mesoamerica – Marisol Correa-Ascencio – PNAS

“A novel bacterial lipid biomarker approach is reported, which provides a new means of documenting the consumption of bacterially fermented alcoholic beverages in antiquity worldwide.”

Biodiversity of Yeast Mycobiota in “Sucuk,” a Traditional Turkish Fermented Dry Sausage: Phenotypic and Genotypic Identification, Functional and Technological Properties – Ismet Ozturk, and Osman Sagdic – Journal of Food Science

“The yeast isolates were determined as genotypic using 2 different polymerase chain reaction (PCR) methods (rep-PCR and RAPD-PCR).”

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