General microbiology and science, October 14, 2014

A living review of multivariate techniques, spatial organizations of bacterial genomes, and metabolomics of wetlands, pigs, marine bacteria and free-living humans.

Bioinformatics

* A Guide to Statistical Analysis in Microbial Ecology: a community-focused, living review of multivariate data analyses – Pier Luigi Buttigieg – FEMS Microbiology Ecology

“we present the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): a dynamic, web-based resource providing accessible descriptions of numerous multivariate techniques relevant to microbial ecologists”

Techniques

New approaches to understanding the spatial organization of bacterial genomes – Tung BK Le, Michael T Laub – Current Opinion in Microbiology

“Here, we review the current arsenal of techniques used to query chromosome structure”

Development of Clamping Probe for Rare DNA Detection using Universal Primers – Meyong il Kim – E-FAS Journal

“In this study, we evaluated the efficiency of rare gene detection for two kinds of clamping probes which were successfully utilized for eukaryotic symbiont analysis”

Metabolomics

Microbial community metabolic function in subsurface flow constructed wetlands of different designs – Mark Button – Ecological Engineering

“Microbial community function followed a clear gradient along the flow direction. Metabolic profiles were system specific (horizontal, vertical, and aerated).”

A high fat, high choleststerol diet leads to changes in metabolite patterns in pigs – a metabolomic study – Jianghao Sun – Food Chemistry

“Extracts of plasma, fecal and urine samples from pigs fed high fat or basal regular diets for 11 weeks were analyzed using ultra-high performance liquid chromatography with high-resolution mass spectrometry “

Free-living individuals – as in “not in prison”?
An NMR metabolomics approach reveals a combined-biomarkers model in a wine interventional trial with validation in free-living individuals of the PREDIMED study – Rosa Vázquez-Fresno – Metabolomics

A High-Resolution LC-MS-Based Secondary Metabolite Fingerprint Database of Marine Bacteria – Liang Lu – Nature Scientific Reports

“Till now, 1,430 bacterial strains spanning 168 known species collected from different marine environments were cultured and profiled. “

Viruses and phages

Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses – Eric G. Sakowski – PNAS USA

“We identify ribonucleotide reductase (RNR) genes as superior markers of viral diversity. RNR genes are distributed over a broad range of viruses”

More microbiology

Strength in Diversity – Daniel J. Wolter, Lucas R. Hoffman – Cell Host & Microbe

“In this issue of Cell Host & Microbe, Hammer et al. (2014) show that distinct, slow-growing bacteria have better in vitro and in vivo growth and virulence when cocultured than in isolation. “

The Journal of Infectious Diseases has a special Issue on Polio: The Final Phase of Polio Eradication and Endgame Strategies for the Post-Eradication Era – Journal of Infectious Diseases

Science, publishing, career

Correcting the scientific record: An introduction to retractions – Bonnie Swoger – Scientific American

“Although the system is far from perfect, the retraction process is one of the ways in which the scientific literature corrects itself over time.”

 

Bik’s Picks

When Racism Was a Science – ‘Haunted Files: The Eugenics Record Office’ Recreates a Dark Time in a Laboratory’s Past – Joshua A. Krisch – New York Times

“In its heyday, the office was the premier scientific enterprise at Cold Spring Harbor. There, bigoted scientists applied rudimentary genetics to singling out supposedly superior races and degrading minorities. “

Paul Ryan: Science doesn’t get climate change – Jane C. Timm – MSNBC

“A full 97% of researchers taking a stance on climate change say it’s man-made, as do 97-98% of the most frequently-published climate scientists. But according to Wisconsin Rep. Paul Ryan, they’re all wrong.”

Get fish fry with a side of science at ‘Science of the Supper Club’ this Friday – Lindsay Christians – The Capital Times

“Science is everywhere, even at a Friday night fish fry. That’s the message of a new event this Friday called “Science of Supper Clubs,” part of the four-day Wisconsin Science Festival held at various venues around the state.”

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Microbiome digest, September 23, 2014

I don’t have much time tonight, so I’ll keep it short.

Pregnancy and birth

Homogeneity of the Vaginal Microbiome at the Cervix, Posterior Fornix, and Vaginal Canal in Pregnant Chinese Women – Yi-E Huang- Microbial Ecology

Impact of Feeding and Medical Practices on the Development of Necrotizing Enterocolitis – Brian L. Montenegro, Camilia R. Martin – Current Pediatrics Reports

Human respiratory microbiome

Expanding Our Understanding of Respiratory Microbiota in Cystic Fibrosis – John J. LiPuma – Annals of the American Thoracic Society

Microbiota in the throat and risk factors of laryngeal carcinoma – Hongli Gong – Applied and Environmental Microbiology

Human gut microbiome

Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness – Alexander Zaborin – mBio

The Overarching Influence of the Gut Microbiome on End-Organ Function: The Role of Live Probiotic Cultures – Luis Vitetta – Pharmaceuticals

Excretion of host DNA in feces is associated with risk of Clostridium difficile infection –  Caroline Vincent – Journal of Immunology Research

Animal and in vitro studies of human microbiome

Effect of Oral Administration of Metronidazole or Prednisolone on Fecal Microbiota in Dogs – Hirotaka Igarashi – PLOS ONE

Age and Microenvironment Outweigh Genetic Influence on the Zucker Rat Microbiome
Hannah Lees – PLOS ONE

A comparative evaluation of prebiotic oligosaccharides using in vitro cultures of infant fecal microbiome – J Stiverson – Applied and Environmental Microbiology

Alterations in Ileal Mucosa Bacteria Related to Diet Complexity and Growth Performance in Young Pigs – Crystal L. Levesque – PLOS ONE

Mammal microbiome

Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas), and binturongs (Arctictis binturong) – Erin A. McKenney – Integrative Zoology

Pathogenic Eukaryotes in Gut Microbiota of Western Lowland Gorillas as Revealed by Molecular Survey – Ibrahim Hamad – Scientific Reports

Insect microbiome

Routes of acquisition of the gut microbiota of Apis mellifera – J. Elijah Powell – Applied and Environmental Microbiology

Sponge microbiome

Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality – Fan Zhang – FEMS Microbiology Ecology
http://onlinelibrary.wiley.com/doi/10.1111/1574-6941.12427/abstract

Plant microbiome

Comparison of root system architecture and rhizosphere microbial communities of Balsas teosinte and domesticated corn cultivars – Márton Szoboszlay – Soil Biology and Biochemistry

Micromonospora from nitrogen fixing nodules of alfalfa (Medicago sativa L.). A new promising Plant Probiotic Bacteria – Pilar Martínez-Hidalgo – Scientific Reports

Effects of Clonal Integration on Microbial Community Composition and Processes in the Rhizosphere of the Stoloniferous Herb Glechoma longituba (Nakai) Kuprian – Ningfei Lei – PLOS ONE

Soil type dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce – Susanne Schreiter – FEMS Microbiology Ecology

Soil microbiome

Culturable fungal assemblages growing within Cenococcum sclerotia in forest soils – Keisuke Obase – FEMS Microbiology Ecology

Food microbiology

Dynamic changes of the microbial communities during the preparation of traditional Tibetan Qula cheese – Bei Zhang – Dairy Science & Technology

Metabolomics / Functional metagenomics

Identification of Aminoglycoside and β-Lactam Resistance Genes from within an Infant Gut Functional Metagenomic Library – Fiona Fouhy – PLOS ONE

Mining the Metabiome: Identifying Novel Natural Products from Microbial Communities

Aleksandr Milshteyn, Jessica S. Schneider, Sean F. Brady – Chemistry & Biology

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

Impact of dietary polydextrose fiber on the human gut metabolome – Santosh Lamichhane – Journal of Agricultural and Food Chemistry

Preserving the earth’s microbes for drug discovery in the future – Ranjith N. Kumavath and Satyanarayana S.V – Journal of Microbiology and Microbial Research

Microbial Ecology

PNAS has a special issue this week on Biogeography (with the Panama forest trees paper by Jessica Green): The emergence and promise of functional biogeography – Cyrille Violle – PNAS

Active invasion of bacteria into living fungal cells – Nadine Moebius – eLife

Microbes in the news

Microbiome: You are never alone – John A Goldman – Atlanta Medicine

Seeking the Sweet Spot, from Mouth to Microbiome – David Katz – Huffington Post

New evidence suggests long-term relationships with bacteria begins before we’re born – Norbert Berzog and David Niesel – Galveston County Daily News

MIT Developing Ship-Repairing Bacteria – World Maritime News

Science and publishing

Anonymous peer-review comments may spark legal battle – Kelly Servick – Science

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Non-human microbiome digest, September 15, 2014

Microbiomes of seals, sheep, pigs, raw milk, cheese, rubber, ocean, freshwater, acid mine drainage, deepsea basalt, and insects.

Mammal microbiome

Isolated faecal bacterial communities found for Weddell seals, Leptonychotes weddellii, at White Island, McMurdo Sound, Antarctica – Jonathan C. Banks – Polar Biology

“Here, we used 16S sequences obtained from clone libraries to characterise the faecal microbiota of Weddell seals breeding in McMurdo Sound and at White Island, Antarctica.”

Study of methanogen communities associated with different rumen protozoal populations – Alejandro Belanche – FEMS Microbiology Ecology

“Rumen protozoa were harvested from totally-faunated sheep and six protozoal fractions (plus free-living microbes) were generated by sequential filtration. “

Temporal changes and the effect of subtherapeutic concentrations of antibiotics in the gut microbiota of swine – Devin B. Holman and Martin R. Chénier – 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.”

Development of a phylogenetic microarray for comprehensive analysis of ruminal bacterial communities – M. Kim – Journal of Applied Microbiology

“The utility of the RumenBactArray was tested using fractionated rumen samples obtained from sheep fed two different diets.”

Characterization of the Fecal Microbiota of Pigs before and after Inoculation with “Brachyspira hampsonii” – Matheus O. Costa – PLOS ONE

“Fecal microbiota profiles were generated based on amplification and sequencing of the cpn60 universal target sequence from 89 samples from 18 pigs collected at −8, −5, −3 and 0 days post-inoculation, and at termination.”

Spatial heterogeneity of gut microbiota reveals multiple bacterial communities with distinct characteristics – Hsiao-Pei Lu – Scientific Reports

“We analyzed bacterial communities of six distinct gut sites (the food bolus and mucus layer of the proximal small intestine, cecum and distal large intestine), using wild folivorous flying squirrels.”

Insect microbiome

Dynamics of midgut microflora and dengue virus impact on life history traits in Aedes aegypti – Casey L. Hill – Acta Tropica

“Here we investigated the effects of the midgut microbial environment and dengue infection on several fitness characteristics among three strains of the primary dengue virus vector mosquito Aedes aegypti. “

Anterior Foregut Microbiota of the Glassy-Winged Sharpshooter Explored Using Deep 16S rRNA Gene Sequencing from Individual Insects – Elizabeth E. Rogers – PLOS ONE

Here, a survey of microbiota associated with the GWSS anterior foregut was conducted.”

The bacterial microbiota of Stolotermes ruficeps (Stolotermitidae), a phylogenetically basal termite endemic to New Zealand – Nicola M. Reid – FEMS Microbiology Ecology

“We identified core bacterial taxa involved in gut processes through combined DNA- and RNA (cDNA)-based pyrosequencing analysis of 16S rRNA from five S. ruficeps colonies.”

Sponge and coral microbiome

Molecular diversity of fungal and bacterial communities in the marine sponge Dragmacidon reticulatum – Michel R. Z. Passarini – Journal of Basic Microbiology

“The present work aimed to investigate the diversity of bacteria and filamentous fungi of southern Atlantic Ocean marine sponge Dragmacidon reticulatum using cultivation-independent approaches.”

Host-specific microbial communities in three sympatric North Sea sponges – Mohd Azrul Naim – FEMS Microbiology Ecology

“In this study, we assessed the diversity of the microbial communities hosted by three sympatric sponges living in a semi-enclosed North Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments.”

Plant microbiome

Micro-organisms in latex and natural rubber coagula of Hevea brasiliensis and their impact on rubber composition, structure and properties – M. Salomez – Journal of Applied Microbiology

“This review synthesizes the current knowledge on microbial populations in latex and natural rubber coagula of H. brasiliensis and the changes they induce on the biochemistry and technical properties of natural rubber during maturation.”

Soils, sediments, and rocks microbiomes

A role for biotic filtering in driving phylogenetic clustering in soil bacterial communities – Marta Goberna – Global Ecology and Biogeography

“Here, we used phylogeny-based methods to discern whether the coexistence of evolutionarily related soil bacteria results from abiotic and/or biotic filtering.”

Microbial community composition and in-silico predicted metabolic potential reflect biogeochemical gradients between distinct peatland types – Zuzana Urbanová and Jiří Bárta – FEMS Microbiology Ecology

“..we investigated biogeochemical parameters and microbial community composition in a bog, a fen and two SSF using high throughput barcoded sequencing of the small ribosomal subunit (SSU) variable region V4.”

Deep-biosphere consortium of fungi and prokaryotes in Eocene subseafloor basalts – S. Bengtson – Geobiology

“We report here a consortium of fossilized prokaryotic and eukaryotic micro-organisms, occupying cavities in deep-drilled vesicular basalt from the Emperor Seamounts, Pacific Ocean, 67.5 m below seafloor (mbsf). “

Endolithic bacterial communities in rock coatings from Kärkevagge, Swedish Lapland – Cassandra L. Marnocha – FEMS Microbiology and Ecology

“Using 454 Roche pyrosequencing of the 16S rRNA gene, nine rock coating samples from three different coating mineralogies were sequenced. “

Water microbiome

Spatial and seasonal variation in diversity and structure of microbial biofilms on marine plastics in Northern European waters – Sonja Oberbeckmann – FEMS Microbiology Ecology

“Denaturing gradient gel electrophoresis (DGGE) and sequencing analysis revealed that plastisphere microbial communities on PET fragments varied both with season and location”

Biogeographic patterns in ocean microbes emerge in a neutral agent-based model – Ferdi L. Hellweger – Science

“We quantify the role of neutral processes by simulating division, mutation, and death of 100,000 individual marine bacteria cells with full 1 million–base-pair genomes in a global surface ocean circulation model. “

Microbial gardening in the ocean’s twilight zone: Detritivorous metazoans benefit from fragmenting, rather than ingesting, sinking detritus – Daniel J. Mayor – BioEssays

“Here we speculate that this apparently counterintuitive behaviour is an example of ‘microbial gardening’, a strategy that exploits the enzymatic and biosynthetic capabilities of microorganisms to facilitate the ‘gardener’s’ access to a suite of otherwise unavailable compounds that are essential for metazoan life.”

Diversity and spatiotemporal dynamics of bacterial communities: physicochemical and other drivers along an acid mine drainage – Aurélie Volant – FEMS Microbiology Ecology

“… biodiversity and spatiotemporal distribution of bacterial communities were characterized using T-RFLP fingerprinting and high-throughput sequencing. “

Diversity and activity of marine bacterioplankton during a diatom bloom in the North Sea assessed by total RNA and pyrotag sequencing – Anna Klindworth – Marine Genomics

“In this study we re-analyzed samples from the initial study by total community RNA (metatranscriptomics) and 16S rRNA gene amplicon sequencing.”

Effects of High Hydrostatic Pressure on Coastal Bacterial Community Abundance and Diversity – Angeliki Marietou and Douglas H. Bartlett – Applied and Environmental Microbiology

“Culturable high-pressure-surviving bacteria were obtained and found to be phylogenetically similar to isolates from cold and/or deep-sea environments. “

A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole – Noémie Pascault – FEMS Microbiology Ecology

“Pyrosequencing revealed that bacterial diversity was higher in the river than in the lakes and in previously exposed sites than in pristine sites.”

Food Microbiology

Microbial Ecology Dynamics Reveal a Succession in the Core Microbiota Involved in the Ripening of Pasta Filata Caciocavallo Pugliese Cheese – Ilaria De Pasquale – Applied and Environmental Microbiology

“Pyrosequencing of the 16S rRNA targeting RNA, community-level physiological profiles made with Biolog EcoPlates, proteolysis, and volatile component (VOC) analyses were mainly used to characterize the manufacture and ripening of the pasta filata cheese Caciocavallo Pugliese.”

Tracing the origin of raw milk from farm by using Automated Ribosomal Intergenic Spacer Analysis (ARISA) fingerprinting of microbiota – Maria Feligini – Food Control

“A total of 64 markers within the range 279–756 bp were detected on the thirty-eight bulk milk samples, none of which was common to all the patterns. “

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Non-human microbiome, August 25, 2014

Microbiotas of pigs, two fish species in the same pond, coral-algal associations, hypersaline soil, and marine eukaryotes.

Mammal microbiome

The influence of host’s genetics on the gut microbiota composition in pigs and its links with immunity traits – J. Estellé – Proceedings, 10th World Congress of Genetics Applied to Livestock Production

“A cohort of 60-days old piglets was assessed for fecal microbiota composition by pyrosequencing of the 16S rDNA. “

Fish microbiome

* Do the intestinal microbiotas differ between paddlefish (Polyodon spathala) and bighead carp (Aristichthys nobilis) reared in the same pond? – Xuemei Li – Journal of Applied Microbiology

“After 30-days of rearing the intestinal microbiota of the two fish species were assessed by pyrosequencing of 16S rRNA genes”

Insect microbiome

Microbial Associates of the Vine Mealybug Planococcus ficus (Hemiptera: Pseudococcidae) under Different Rearing Conditions – Lilach Iasur-Kruh – Microbial Ecology

“To examine the possible role of microbial symbionts in virus transmission, the archaeal, bacterial, and fungal microbiota of field and laboratory P. ficus were characterized using molecular and classical microbiological methods. “

Coral microbiome

* The extended phenotypes of marine symbioses: ecological and evolutionary consequences of intraspecific genetic diversity in coral–algal associations – John E. Parkinson and Iliana B. Baums – Frontiers in Microbiology

“Here, we hypothesize that unique combinations of coral and algal individuals yield functional diversity that affects not only the ecology and evolution of the coral holobiont, but associated communities as well. “

Soil microbiome

Salinity-induced differences in soil microbial communities around the hypersaline Lake Urmia – Mohsen Barin – Soil Research

“We tested the hypotheses that salinity reduces microbial biomasses and change the structure of the microbial community.”

Water microbiome

Microbial Community Response to Chlorine Conversion in a Chloraminated Drinking Water Distribution System – Hong Wang – Environmental Science & Technology

“Although high throughput sequencing of 16S rRNA genes revealed a distinct community shift and higher diversity index during the chlorine burn, it steadily returned towards a condition more similar to pre-burn than burn stage.”

Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes – Vera G. Fonseca – Global Ecology and Biogeography

“Here, we ask: (1) if the macroecology of meiobenthic communities is explained mainly by dispersal constraints or by environmental conditions; and (2) if levels of meiofaunal diversity surpass existing estimates based on morphological taxonomy.”

Microbiology of the Built Environment

* A disturbing trend – casual and reckless use of antimicrobial agents in building materials – Jonathan Eisen – MicroBEnet

“So they put in flooring that apparently was impregnated with some sort of antibacterial agent and they have no evidence that it works. “

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Microbiome digest, July 24

Introducing the crAssphage, an 84 bp BLAST from the past, archaea in the Savannah, metabolomics of racehorse microbiome, and X-raying headphones.

Human oral microbiome

Proceedings RoyalMolecular analysis of ancient caries – Marc Simón – Proceedings of the Royal Society, Biological Sciences

“An 84 base pair sequence of the Streptococcus mutans virulence factor, known as dextranase, has been obtained from 10 individuals from the Bronze Age to the Modern Era in Europe and from before and after the colonization in America. “

Human gut microbiome

Nature CommunicationsA highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes – Bas E. Dutilh – Nature Communications

“Here we describe the discovery of a previously unidentified bacteriophage present in the majority of published human faecal metagenomes, which we refer to as crAssphage.”

Gut family SchlossThe dynamics of a family’s gut microbiota reveal variations on a theme – Patrick D Schloss – Microbiome

“Using 16S rRNA gene and metagenomic shotgun sequence data, it was possible to distinguish the family from a cohort of normal individuals living in the same geographic region and to differentiate each family member”

Pregnancy and Birth

Screen Shot 2014-07-24 at 05.53PM, Jul 24An unnecessary cut? – Sky Dylan-Robbins – The New Yorker

“The most common operating-room procedure in the United States is the Cesarean section. “

Animal microbiome

Equine Vet JournalCharacterisation of the faecal metabolome and microbiome of Thoroughbred racehorses – C. J. Proudman – Equine Veterinary Journal

“Faecal metabolome was characterised using thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS), with spectral analysis performed using AMDIS and compared against the NIST database. Taxonomic description of the faecal microbiota was achieved using error-corrected 454 pyrosequencing data from 16S rRNA gene amplicons”

Journal of MicrobiologyPyrosequencing-based analysis of fecal microbial communities in three purebred pig lines – Edward Alain B. Pajarillo – Journal of Microbiology

“Taxon-dependent and -independent analyses were performed to evaluate differences in the fecal bacterial communities and to identify bacterial genera that can be used to discriminate breeds, following high-throughput pyrosequencing of 16S rRNA genes. “

Environmental microbiome

Screen Shot 2014-07-24 at 05.55PM, Jul 24Seasonal Effects in a Lake Sediment Archaeal Community of the Brazilian Savanna – Thiago Rodrigues – Archaea

“Here we describe for the first time the diversity of archaeal communities from freshwater lake sediments of the Cerrado in the dry season and in the transition period between the dry and rainy seasons, when the first rains occur. Gene libraries were constructed, using Archaea-specific primers for the 16S rRNA and amoA genes.”

Screen Shot 2014-07-24 at 05.56PM, Jul 24Spatial patterns and links between microbial community composition and function in cyanobacterial mats – Mohammad A. Al-Najjar – Frontiers in Microbiology

“Similar clustering was found when the community composition of the mats’ cyanobacterial layers were compared by automated ribosomal intergenic spacer analysis, indicating a significant link between the microbial community composition and function. “

MicrobeNetNew Joint Initiative from the Knight and Sogin Labs as a Follow-up to the MoBEDAC Initiative – Embriette Hyde

“By the end of the funded period, standard 16S rRNA and ITS (fungal) analysis pipelines will be developed and made available to the MoBe community, 16S rRNA and ITS databases will be markedly improved, QIIME and VAMPS will be tightly integrated into a new database engine called QiiTA to facilitate analysis by all MoBe researchers, and two major training workshops will be offered. “

Dr. Bik’s PicksDNA

DNA mostly ‘junk?’ Only 8.2 percent of human DNA is ‘functional’, study finds – Science Daily

“This figure is very different from one given in 2012, when some scientists involved in the ENCODE (Encyclopedia of DNA Elements) project stated that 80% of our genome has some biochemical function.”

Screen Shot 2014-07-24 at 05.58PM, Jul 24Sex differences in medicine – BeWell – Stanford University

“A man can be diagnosed with the same disease as a woman, and yet the course the disease takes in each could prove very different. And a treatment which works for one gender may prove ineffective for the other. “

corksIs Climate Change Ruining Wine Corks? – Kelly Dickerson – LiveScience

“Many people may only worry about corks when it’s time to pop the Champagne, but some experts are worried about wine cork quality, which has been mysteriously in decline for almost 20 years.“

Headphone x rayDoc X-Rays His Broken Headphones to Fix Them – Bahar Gholipour – LiveScience

“”Closed fracture of a speaker wire within its rubber/plastic sleeve is a rare headphone injury, usually due to a traction trauma,” Skalski wrote in his report of the case.”

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Human microbiome, July 22

Transcriptome in periodontitis, metabolomic analysis of breath in IBD patients, cystic fibrosis microbiome, and Clostridium difficile.

Human microbiome general

Review: Deciphering the tête-à-tête between the microbiota and the immune system – Neeraj K. Surana and Dennis L. Kasper – Journal of Clinical Investigation

“In this Review, we discuss the current state of knowledge regarding the role of the intestinal microbiota in immunologic development, highlighting mechanistic principles that can guide future work.”

Meeting report: Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013 – Jacques Ravel and many others – Microbiome

“This report summarizes the presentations but also describes what is needed for human microbiome research to move forward and deliver medical translational applications.”

Metabolomics

Metabolomic analysis of breath volatile organic compounds reveals unique breathprints in children with inflammatory bowel disease: a pilot study – N. Patel – Alimentary Pharmacology & Therapeutics

“Exhaled breath was collected and analysed using a selective ion flow tube mass spectroscopy (SIFT-MS) to identify new markers or patterns of IBD.”

Metabolites related to gut bacterial metabolism, peroxisome proliferator-activated receptor-alpha activation, and insulin sensitivity are associated with physical function in functionally-limited older adults – Michael S. Lustgarten – Aging Cell

“Collectively, these data suggest that gut microbial metabolism, PPAR-α activation, and insulin sensitivity may be involved in mechanisms that underlie physical function in functionally-limited older adults.”

Oral microbiome

Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis – Ana E Duran-Pinedo – ISME J

“We report here the in situ genome-wide transcriptome of the subgingival microbiome in six periodontally healthy individuals and seven individuals with periodontitis.”

Respiratory microbiome

Predominant pathogen competition and core microbiota divergence in chronic airway infection – Geraint B Rogers – ISME Journal

“..we analysed 16S rRNA gene pyrosequencing data generated previously from 60 adult bronchiectasis patients, whose airway microbiota was dominated by either P. aeruginosa or H. influenzae.”

Pyrosequencing reveals transient cystic fibrosis lung microbiome changes with intravenous antibiotics – Daniel J. Smith – European Respiratory Journal

“Microbial community profiles were derived through analysis of bacterial-derived 16S ribosomal RNA by pyrosequencing and changes over time were compared.”

Review: Respiratory microbiota: addressing clinical questions, informing clinical practice – Geraint B Rogers – Thorax

“In this article, we set out the key principles underpinning microbiota research in respiratory contexts and provide practical guidance on how best such studies can be designed, executed and interpreted. “

Propionibacterium-Produced Coproporphyrin III Induces Staphylococcus aureus Aggregation and Biofilm Formation – Michael S. Wollenberg – mBio

“We observed that crude extracts of cell-free conditioned medium from Propionibacterium spp. induce S. aureus aggregation in culture. “

Gut microbiome

Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection – Susana Fuentes – ISME Journal

“Global composition and network analysis of the microbiota was performed in faecal samples from nine patients with recurrent CDI. Analyses were performed before and after duodenal donor faeces infusion, and during a follow-up of 10 weeks. The microbiota data were compared with that of the healthy donors. “

Review: Clostridium difficile and the microbiota – Anna M. Seekatz and Vincent B. Young – Journal of Clinical Investigation

“Both human and animal models have demonstrated the importance of the gut microbiota’s capability of providing colonization resistance against C. difficile.”

Vaginal microbiome

Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance – Suleyman Yildirim – ISME Journal

“We conducted comparative analyses of the primate vaginal microbiome using pyrosequencing of the 16S rRNA genes of a phylogenetically broad range of primates to test for factors affecting the diversity of primate vaginal ecosystems. … humans were distinct from other primates in both microbiome composition and diversity.

Semen microbiome

The Semen Microbiome and Its Relationship with Local Immunology and Viral Load in HIV Infection – Cindy M. Liu – PLOS Pathogens

“HIV infection was associated with decreased semen microbiome diversity and richness, which were restored after six months of ART.”

Antibiotic perturbation and microbiome

Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations – Torey Looft – ISME Journal

“In this study, we defined the lumenal and mucosal bacterial communities from the small intestine (ileum) and large intestine (cecum and colon) plus feces, and characterized the effects of in-feed antibiotics (chlortetracycline, sulfamethazine and penicillin (ASP250)) on these communities. “

Impact of Antibiotics on the Intestinal Microbiota and on the Treatment of Shiga-toxin-Producing Escherichia coli and Salmonella Infections – Szych, Jolanta – Current Pharmaceutical Design

“This review evaluates the current literature based on the impact of antibiotics on the intestinal microbiota and the critical role of intestinal bacteria in controlling infection and subsequent clinical disease caused by STEC and Salmonella, and the transmissibility of these important pathogens”

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Non-human microbiome digest, July 3

Parasites, effect of antibiotics in pigs, microbiome of birds, Drosophila, microbiome of plant crops, Hawai’i waters, and bacteria to preserve stone monuments.

Parasites and microbiome

Cooperation and conflict in host manipulation: interactions among macro-parasites and micro-organisms – Frank Cézilly – Frontiers in Microbiology

“Here, we review the empirical evidence in favor of the existence of synergistic or antagonistic interactions between co-occurring parasites, and highlight the neglected role of micro-organisms. “

holobiontHolobiont–Holobiont Interactions: Redefining Host–Parasite Interactions – Nolwenn Marie Dheilly – PLOS Pathogens

“It has been established in different model species that immune system maturation requires the presence of mutualistic bacteria”

Marine mammal microbiome

Screen shot 2014-07-03 at 04.24PM, Jul 03Intestinal helminth fauna of striped dolphins (Stenella coeruleoalba) in the western Mediterranean: No effects of host body length, age and sex – Paula Mateu – Marine Mammal Science

“The intestine of 52 (28 males and 24 females) striped dolphins (Stenella coeruleoalba) from western Mediterranean waters was examined for helminths. Animals were found stranded along the Spanish coasts during the morbillivirus epizootic in 1990.”

Pig microbiome

Screen shot 2014-07-03 at 03.17PM, Jul 03Carbadox has both temporary and lasting effects on the swine gut microbiota – Torey Looft – Frontiers in Microbiology

“Carbadox is an in-feed antibiotic that is widely used in swine production to prevent dysentery and to improve feed efficiency. The goal of this study was to characterize the effects of carbadox and its withdrawal on the swine gut microbiota. ”

Screen shot 2014-07-03 at 03.18PM, Jul 03Learning from agriculture: understanding low-dose antimicrobials as drivers of resistome expansion – Yaqi You – Frontiers in Microbiology

“Unconfined storage or land deposition of a large volume of animal waste causes its wide contact with the environment and drives the expansion of the environmental resistome through mobilome facilitated horizontal genet (sic, EB) transfer. “

Bird microbiome

Screen shot 2014-07-03 at 03.18PM, Jul 03Interspecific variations in the faecal microbiota of Procellariiform seabirds – Meagan L. Dewar – FEMS Microbiology Ecology

“Examining the faecal microbiota of three Procellariiform species (short-tailed shearwater, common diving petrel and fairy prion) provided a unique opportunity to not only characterise the gastrointestinal (GI) microbial composition of seabirds but to also examine the influence of stomach oils on the microbial community.”

Insect microbiome

Drosophila modelTransient adult microbiota, gut homeostasis and longevity: Novel insights from the Drosophila model – Berra Erkosar, Francois Leulier – FEBS Letters

“In the last decade, Drosophila has emerged as a useful model to study host–microbiota interactions, creating an active research field with prolific publications.”

Plant microbiome

Screen shot 2014-07-03 at 03.21PM, Jul 03Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance – Devin Coleman-Derr – Frontiers in Microbiology

“In recent years, studies have attempted to identify microbial symbionts capable of conferring the same stress-tolerance to their plant hosts, and new developments in genomic technologies have greatly facilitated such research. “

Screen shot 2014-07-03 at 03.21PM, Jul 03Convergence in mycorrhizal fungal communities due to drought, plant competition, parasitism, and susceptibility to herbivory: consequences for fungi and host plants – Catherine A. Gehring – Frontiers in Microbiology

“We found that drought and all three of the biotic interactions studied resulted in similar shifts in ectomycorrhizal fungal community composition, demonstrating a convergence of the community towards dominance by a few closely related fungal taxa.”

Screen shot 2014-07-03 at 03.22PM, Jul 03Nitrogen-fixing Rhizobium-legume symbiosis: are polyploidy and host peptide-governed symbiont differentiation general principles of endosymbiosis? – Gergely Maróti- Frontiers in Microbiology

“This review focuses on symbiotic plant cell development and terminal bacteroid differentiation and demonstrates the crucial roles of symbiotic peptides”

Screen shot 2014-07-03 at 03.22PM, Jul 03Disparate origins of Bradyrhizobium symbionts for invasive populations of Cytisus scoparius (Leguminosae) in North America – Kevin Horn – FEMS Microbiology Ecology

“To identify the geographic origin of nodule bacteria associated with invasion of the European legume Cytisus scoparius in the United States, isolates from 15 sites in six states were compared to > 200 Bradyrhizobium strains from indigenous legumes in the U.S., Mexico, Europe (six countries), Morocco, and Australia. “

Food microbiology

Screen shot 2014-07-03 at 03.24PM, Jul 03Weissella confusa: problems with identification of an opportunistic pathogen that has been found in fermented foods and proposed as a probiotic – Marilynn R. Fairfax – Frontiers in Microbiology

“Weissella confusa is found in fermented foods and has been suggested as a probiotic, but also causes sepsis and other serious infections in humans and animals.”

Stone microbiology

Screen shot 2014-07-03 at 03.24PM, Jul 03 1Application of calcifying bacteria for remediation of stones and cultural heritages – Navdeep Kaur Dhami – Frontiers in Microbiology

“The present review emphasizes about different causative agents leading to deterioration and application of microbially induced calcium carbonate precipitation as a novel and potential technology for dealing with these problems. “

Soil microbiology

Screen shot 2014-07-03 at 03.25PM, Jul 03Volatile-mediated interactions between phylogenetically different soil bacteria
Paolina Garbeva – Frontiers in Microbiology

“Here we report that volatile compounds emitted by different soil bacteria can affect the growth, antibiotic production and gene expression of the soil bacterium Pseudomonas fluorescens Pf0–1. “

Screen shot 2014-07-03 at 03.27PM, Jul 03Land-use influences the distribution and activity of high affinity CO-oxidizing bacteria associated to type I-coxL genotype in soil – Liliana Quiza – Frontiers in Microbiology

“The main objective of this study was to assess the impact of land-use and soil properties on coxL gene diversity and identify molecular indicators for the soil uptake of atmospheric CO.”

Screen shot 2014-07-03 at 03.26PM, Jul 03Abundance and community structure of ammonia-oxidizing Archaea and Bacteria in response to fertilization and mowing in a temperate steppe in Inner Mongolia
Yong-Liang Chen – FEMS Microbiology Ecology

“… we investigated the effects of nitrogen (N) and phosphorus (P) fertilization and mowing on the abundance and community compositions of ammonia-oxidizing Bacteria (AOB) and Archaea (AOA) upon early (May) and peak (August) plant growth using quantitative PCR (qPCR), terminal-restriction fragment length polymorphism (T-RFLP), cloning and sequencing. “

Water microbiology

Screen shot 2014-07-03 at 03.27PM, Jul 03Biogeography of planktonic and benthic cyanobacteria in coastal waters of the Big Island, Hawai’i – Samuel D. Chamberlain – FEMS Microbiology Ecology

“To understand the patterns of cyanobacterial biogeography in relation to coastal environmental factors, we examined the diversity of planktonic and benthic cyanobacteria at 12 sites along the west coast of Hawaii’s Big Island.”

Screen shot 2014-07-03 at 03.29PM, Jul 03Rhizosphere heterogeneity shapes abundance and activity of sulfur-oxidizing bacteria in vegetated salt marsh sediments – François Thomas – Frontiers in Microbiology

“We combined next-generation amplicon sequencing of 16S rDNA and rRNA libraries with phylogenetic analyses of marker genes for two S-oxidation pathways (soxB and rdsrAB). Gene and transcript numbers of soxB and rdsrAB phylotypes were quantified simultaneously, using newly designed (RT)-qPCR assays.”

Screen shot 2014-07-03 at 03.28PM, Jul 03Neotropical Andes hot springs harbor diverse and distinct planktonic microbial communities – Luisa Delgado-Serrano – FEMS Microbiology Ecology

“In this study, we describe and compare the planktonic microbial communities present in five high-mountain hot springs with distinct geochemical characteristics, at varying altitudes and geographical locations in the Colombian Andes. “

Screen shot 2014-07-03 at 03.29PM, Jul 03Occurrence and activity of anammox bacteria in surface sediments of the southern North Sea – Nicole J. Bale – FEMS Microbiology Ecology

“The presence of anammox bacteria was established through the detection of specific phosphocholine-monoether ladderane lipids, 16S rRNA gene, and hydrazine synthase (hzsA) genes. “

Screen shot 2014-07-03 at 03.29PM, Jul 03 1Bacterial community structure and dissolved organic matter in repeatedly flooded subsurface karst water pools – Tanja Shabarova – FEMS Microbiology Ecology

“Bacterial diversity, community assembly, and the composition of the dissolved organic matter (DOM) were studied in three temporary subsurface karst pools with different flooding regimes.”

Screen shot 2014-07-03 at 03.30PM, Jul 03Abundance, diversity and seasonal dynamics of predatory bacteria in aquaculture zero discharge systems – Prem P. Kandel – FEMS Microbiology Ecology

“The dynamics of populations belonging to the obligate predators Bdellovibrio and like organisms (BALOs) were analyzed in freshwater and saline ZDS over a 7-month period using QPCR targeting the Bdellovibrionaceae, and the Bacteriovorax and Bacteriolyticum genera in the Bacteriovoracaeae”

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