Non-human microbiome, June 30

Primate vaginal microbiome, birds painting eggs with bacteria, MHC and microbiota in fish, onions and tomato, bacteria on the beach, and (#BacteriaHysteria alert) “fecal veneer on climbing walls”.

Primate microbiome (also see Human digest)

Screen Shot 2014-06-30 at 11.23.32 PMPrimate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance – Suleyman Yildirim – ISME J (uncorrected proof, link to Chapman Research)

“Our results indicated that all primates exhibited host-specific vaginal microbiota and that humans were distinct from other primates in both microbiome composition and extent of diversity”

Bird microbiome

Screen Shot 2014-06-30 at 11.43.49 PMSpecial structures of hoopoe eggshells enhance the adhesion of symbiont-carrying uropygial secretion that increase hatching success – Manuel Martín-Vivaldi – Journal of Animal Ecology

“The findings of specialized crypts on the eggshells of hoopoes, and of video-recorded females smearing secretion containing symbiotic bacteria at a high density onto the eggshells strongly support a link between secretion and bacteria on eggs. “

and:  The Bird That Paints Its Eggs With Bacteria – Ed Yong – National Geographic

“Now, they’ve found evidence that these birds use the same bacteria to protect their young before they’re even born. By filming nesting females, they confirmed that the birds actively paint their eggs with their uropygial secretions.”

Fish microbiology

Screen Shot 2014-06-30 at 11.45.12 PMMajor Histocompatibility Complex class II polymorphism influences gut microbiota composition and diversity – Daniel I. Bolnick – Molecular Ecology

“Here, we show that MHC II polymorphism is associated with among-individual variation in gut microbiota within a single wild vertebrate population of a small fish, the threespine stickleback. “

Insect microbiome

WolbachiaThe Coevolutionary Period of Wolbachia pipientis Infecting Drosophila ananassae and its Impact on the Evolution of the Host Germline Stem Cell Regulating Genes – Jae Young Choi and Charles F. Aquadro – Molecular Biology and Evolution

“Phylogenetic analysis of D. ananassae mitochondrial DNA and W. pipientis DNA sequence diversity revealed the current W. pipientis infection is not recent. In addition, we examined the population genetics and molecular evolution of several Germline Stem Cell (GSC) regulating genes of D. ananassae”

Plant microbiome

Screen Shot 2014-06-30 at 11.43.01 PMIdentification of bacteria pathogenic to or associated with onion (Allium cepa) based on sequence differences in a portion of the conserved gyrase B gene – Jean M. Bonasera – Journal of Microbiological Methods

“We have developed a method for the identification of Gram-negative bacteria, particularly members of the Enterobacteriaceae, based on sequence variation in a portion of the gyrB gene. Thus, we identified, in most cases to species level, over 1000 isolates from onion bulbs and leaves and soil in which onions were grown.”

Occurrence and distribution of tomato seed-borne mycoflora in Saudi Arabia and its correlation with the climatic variables – Abdulaziz A. Al-Askar – Microbial Biotechnology

“One hundred samples of tomato seeds were collected in 2011 and 2012 from tomato-cultivated fields in Saudi Arabia and screened for their seed-borne mycoflora. A total of 30 genera and 57 species of fungi were recovered from the collected seed samples using agar plate and deep-freezing blotter methods. “

WasabiManagement of Meloidogyne incognita on tomato with endophytic bacteria and fresh residue of Wasabia japonica – Guang-Ju Li – Journal of Applied Microbiology

“By in vitro bioassay, 53 NEB strains showing nematicidal efficacies of >50% against J2 of M. incognita were isolated from wasabi. Basing on 16S rRNA gene sequences, these NEB were identified into 18 species of 11 genera.”

Lichen and fungi

Screen Shot 2014-06-30 at 11.46.20 PMA single macrolichen constitutes hundreds of unrecognized species – Robert Lücking – PNAS

“This lichen was long believed to represent a single species, but after revising this number to 16 in two genera (Cora and Corella), here we show that at least 126 phylogenetically and morphologically distinct species are contained within this group, with statistical analysis predicting more than 400. “

Soil, sand, and slurry microbiome

The Ecological Controls on the Prevalence of Candidate Division TM7 in Polar Regions – Tristrom Winsley – Frontiers in Microbiology

“We correlated chemical, physical and biological parameters of each soil with the relative abundance of the two major classes of the phylum to deduce factors that influence the groups’ seemingly ubiquitous nature. “

Review: Present status of effect of microorganisms from sand beach on public
health – Emmanuel Velonakis – Journal of Coastal Life Medicine

“Relatively, recent epidemiological studies in the USA revealed positive correlation between time spent at the beach and gastroenteritis. New parameters such as wind blowing and beach users’ density are also introduced for discussion in association with the sand microbial load”

Crusts slurryMethanotrophs, methanogens, and microbial community structure in livestock slurry surface crusts – Yun-Feng Duan – Journal of Applied Microbiology

“Microbial communities in four crusts from cattle and swine slurries were investigated using DGGE and tag-encoded amplicon pyrosequencing. All crusts had distinct compositions of bacteria and archaea.”

Water microbiology

Biosynthesis of polybrominated aromatic organic compounds by marine bacteria
Vinayak Agarwal – Nature Chemical Biology

“Herein we report the discovery of a conserved biosynthetic gene cluster in marine bacteria responsible for the synthesis of widespread polybrominated aromatic compounds”

Environmental bacteriophages : viruses of microbes in aquatic ecosystems – Télesphore Sime – Ngando – Frontiers in Microbiology

“The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e. phages) in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.”

Built Environment

I really dislike this title …
Screen Shot 2014-06-30 at 11.47.38 PMMicrobial Sequencing Analyses Suggest the Presence of a Fecal Veneer on Indoor Climbing Wall Holds – S. L. Bräuer – Current Microbiology

“In contrast to many other studies of built environments, the majority of microorganisms on holds were most closely related to microbes annotated as being recovered from environmental sources, such as soil, with human skin also representing an important source.”

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Non-human microbiome, June 18

Microbiomes of horses, sheep, chicken, plants in Chili, built environment and rocks.

General microbiomes of animals

Viral Metagenomics on Animals as a Tool for the Detection of Zoonoses Prior to Human Infection? – Sarah Temmam – Int J Mol Sci

“In this review, we summarize our current knowledge of viral diversity within such animals (in particular blood-feeding arthropods, wildlife and domestic animals) using metagenomics and present its possible future application for the surveillance of zoonotic and arboviral diseases.”

Horse microbiome

Screen Shot 2014-06-18 at 9.39.22 PMFaecal Microbiome of the Thoroughbred Racehorse and Its Response to Dietary Amylase Supplementation – Proudman C – Equine Veterinary Journal

Amplicons for the V1-V3 region of the 16S rDNA gene were multiplexed and sequenced on the 454 resulting in ∼25,000 reads per sample. Differences in bacterial community structure were detected by linear discriminant analysis.”

Sheep microbiome

Screen Shot 2014-06-05 at 8.48.40 PMMethane yield phenotypes linked to differential gene expression in the sheep rumen microbiome – Weibing Shi – Genome Research

“Deep metagenomic and metatranscriptomic sequencing demonstrated the presence of methanogens both in the highest and lowest methane-producing sheep, with a similar abundance of methanogens and methanogenesis pathway genes in high and low methane emitters. “

Chicken microbiome

ChickenSpatial heterogeneity and stability of bacterial community in the gastrointestinal tracts of broiler chickens – J. H. Choi – Poultry Science

“Bacterial communities in the different regions of gastrointestinal tract (GIT) of broiler chickens were analyzed by pyrosequencing approach to understand microbial composition and diversity. “

Squid microbiome

SquidThe real threat posed by discover of antibiotic- resistent bacteria found in squid – Robert Lawrence and Patrick Baron, Baltimore – Washington Post

“The Food and Drug Administration can, and should, do more to limit the misuse of antibiotics in the production of food animals, whether terrestrial or aquatic, in order to reduce the risk of accelerating antibiotic resistance.”

Plant microbiome

Bacterial community structure and detection of putative plant growth-promoting rhizobacteria associated with plants grown in Chilean agro-ecosystems and undisturbed ecosystems – Milko A. Jorquera – Biology and Fertility of Soils

“Soil microorganisms with phytase- and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activities are widely studied as plant growth-promoting rhizobacteria (PGPR). Here, we explored the bacterial community structure and occurrence of putative PGPR in plants grown in agro-ecosystems and undisturbed ecosystems from northern, central, and southern Chile.”

Built Environment Microbiome

housesmicroBEnet: Lessons Learned from Building an Interdisciplinary Scientific Community in the Online Sphere – Holly M. Bik, David A. Coil, Jonathan A. Eisen – PLOS Biology

“The microbiology of the Built Environment network (microBEnet: http://www.microbe.net/) was formed as an experiment in interdisciplinary community building, with an overarching goal to facilitate and nurture the development of a new research field: the microbiology of the built environment (MBE). “

Water microbiome

Review: Emerging Strategies and Integrated Systems Microbiology Technologies for Biodiscovery of Marine Bioactive Compounds – Javier Rocha-Martin – Marine Drugs

“Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts.”

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists – María Gomariz – ISME Journal

“Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to >40%), by means of CARD-FISH and DGGE.”

Soil and rock microbiome

Mineral Microniches Control the Diversity of Subsurface Microbial Populations – Aaron A. Jones – Geomicrobiology Journal

“These results suggest that adaptations to specific rocks are retained even when the organism is displaced in time and space from an ancestral rock habitat.”

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Non-human microbiomes, June 6

Today, I am delighted to share my new knowledge on The Ultimate Reader of Dung (TURD), palaeosymbiosis, a scientific journal called “Meat Science”, and that everything tastes better with olive oil and paprika covering.

Insect microbiome

Screen Shot 2014-06-07 at 2.17.11 AMSpotting the differences: probing host/microbiota interactions with a dedicated software tool for the analysis of faecal outputs in Drosophila – Matthew T. Wayland – Journal of Insect Physiology

“To facilitate its use, we present here a free, stand-alone dedicated software tool for the analysis of fly excreta. The Ultimate Reader of Dung (T.U.R.D.) is designed to offer a flexible environment for a wide range of experimental designs, with special attention to automation and high-throughput processing.”

Screen Shot 2014-06-07 at 2.19.09 AMThe gut microbiota of larvae of Rhynchophorus ferrugineus Oliver (Coleoptera: Curculionidae) – Tagliavia M – BMC Microbiology

“The RPW gut microbiota is composed mainly of facultative and obligate anaerobic bacteria with a fermentative metabolism. These bacteria are supposedly responsible for palm tissue fermentation in the tunnels where RPW larvae thrive and might have a key role in the insect nutrition, and other functions that need to be investigated.”

Nematode microbiome

Screen Shot 2014-06-07 at 2.18.06 AMPalaeosymbiosis Revealed by Genomic Fossils of Wolbachia in a Strongyloidean Nematode Georgios Koutsovoulos – PLOS Genetics

“We generated a draft genome sequence for the strongyloidean nematode parasite Dictyocaulus viviparus, the cattle lungworm. In the assembly, we identified nearly 1 Mb of sequence with similarity to Wolbachia. “

Food microbiome

Screen Shot 2014-06-07 at 2.20.26 AMMonitoring of the microbiota profile in nukadoko, a naturally fermented rice bran bed for pickling vegetables – Hiroshi Ono – Journal of Bioscience and Bioengineering

“Nukadoko is a fermented rice bran mash traditionally used for pickling vegetables in Japan. To date, the production of both homemade and commercial nukadoko depends on natural fermentation without using starter cultures. Here, we monitored chemical and microbiological changes in the initial batch fermentation of nukadoko. “

Food MicrobiologyExploitation of Albanian wheat cultivars: characterization of the flours and lactic acid bacteria microbiota, and selection of starters for sourdough fermentation – Luana Nionelli – Food Microbiology

“Type I sourdoughs were prepared through back slopping procedure, and the lactic acid bacteria were typed and identified. Lactobacillus plantarum and Leuconostoc mesenteroides were the predominant species.”

Screen Shot 2014-06-07 at 2.22.09 AMrRNA-based monitoring of the microbiota involved in Fontina PDO cheese production in relation to different stages of cow lactation – Paola Dolci – International Journal of Food Microbiology

“The aim of the present paper was to investigate the bacterial dynamics during Fontina PDO cheese manufacturing and ripening, in relation to the different lactation stages, in order to evaluate a possible correlation between microbiota and phase of lactation. “

Screen Shot 2014-06-07 at 2.27.04 AMAntifungal activity and identification of Lactobacilli, isolated from traditional dairy product “katak” – Rositsa Tropcheva – Anaerobe

“In the present study, four active strains were isolated from traditional fermented curd/yogurt-like product “katak”, produced in Bulgaria from centuries. The new isolates KR3, KR4, KR51 and KR53 were identified by API 50 CH biochemical test and different molecular methods (species-specific PCR, RAPD-PCR and 16S rDNA sequence analysis) as Lactobacillus brevis.”

Screen Shot 2014-06-07 at 2.26.05 AMMicrobiological and physicochemical characterization of dry-cured Halal goat meat. Effect of salting time and addition of olive oil and paprika covering – Sanâa Cherroud – Meat Science

“Molecular analysis proves that staphylococci, especially S. xylosus and S. equorum, were characterized as the most common naturally occurring microbiota. The best manufacturing process would be obtained with a longer salting time and the addition of the olive oil and paprika covering.”

Environmental microbiome

Screen Shot 2014-06-07 at 2.00.39 AMEffects of early-life exposure to allergens and bacteria on recurrent wheeze and atopy in urban children – Susan V. Lynch – The Journal of Allergy and Clinical Immunology

“….first-year exposure to cockroach, mouse, and cat allergens was negatively associated with recurrent wheeze…. House dust microbiome composition is associated with clinical outcomes. 

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