Tag Archives: swine

Non-human microbiome digest, October 2, 2014

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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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Non-human microbiome digest, September 15, 2014

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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, June 23

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What happens with all that triclosan we flush down the drain? Also, baby squirrels, tse-tse flies, pot, and Chinese liquor.

Animal microbiome general 

Two very different papers from the same group, but both are finding that Blautia species are host specific.

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A single genus in the gut microbiome reflects host preference and specificity – A Murat Eren – The ISME Journal

“In our dataset of 57 M sequence reads of the V6 region of the 16S ribosomal RNA gene in samples collected from seven host species, we identified 200 high-resolution taxonomic units within Blautia using oligotyping.” (Humans, cows, swine, deer, chickens)

Screen Shot 2014-06-23 at 11.26.18 PMBlautia and Prevotella sequences distinguish human and animal fecal pollution in Brazil surface waters – Amber M. Koskey – Environmental Microbiology Reports

“We used oligotyping to identify Prevotella and Blautia sequences that can distinguish human fecal contamination. Thirty-five of 61 Blautia oligotypes and 13 of 108 Prevotella oligotypes in humans were specific to or highly abundant (i.e. host-preferred) compared to pig, dog, horse, and cow sources.”

Squirrel microbiome

Screen Shot 2014-06-23 at 11.35.26 PMTemporal Dynamics of the Cecal Gut Microbiota of Juvenile Arctic Ground Squirrels: a Strong Litter Effect across the First Active Season – Timothy J. Stevenson – Applied and Environmental Microbiology  (image courtesy of ego-alterego.com)

“We characterized trends in diversity (454 pyrosequencing), density (flow cytometry), viability (flow cytometry), and metabolism (short-chain fatty acid analysis) of the gut microbial community of juvenile arctic ground squirrels across their first active season at weaning and at 4, 6, 8, and 10 weeks postweaning.”

Insect microbiome

Screen Shot 2014-06-23 at 11.20.33 PMAnalysis of Multiple Tsetse Fly Populations in Uganda Reveals Limited Diversity and Species-Specific Gut Microbiota – Emre Aksoy – Applied and Environmental Microbiology

“We used multiple approaches, including deep sequencing of the V4 hypervariable region of the 16S rRNA gene, 16S rRNA gene clone libraries, and bacterium-specific quantitative PCR (qPCR), to investigate the levels and patterns of gut microbial diversity from a total of 151 individuals.”

Screen Shot 2014-06-23 at 11.22.49 PMMicrobial Population Dynamics in the Hemolymph of Manduca sexta Infected with Xenorhabdus nematophila and the Entomopathogenic Nematode Steinernema carpocapsae – Swati Singh – Applied and Environmental Microbiology

“We show that gut microbes translocate into the hemolymph when the nematode penetrates the insect intestine.”

Screen Shot 2014-06-23 at 11.23.22 PMPurine Biosynthesis, Biofilm Formation, and Persistence of an Insect-Microbe Gut Symbiosis – Jiyeun Kate Kim – Applied and Environmental Microbiology

“When we disrupted purN and purT in the Burkholderia symbiont, the ΔpurN and ΔpurT mutants grew normally, and only the ΔpurT mutant failed to form biofilms. “

Plant microbiome

Plant metabolomics for plant chemical responses to belowground community change by climate change – Sangkyu Park – Journal of Plant Biology

“In this review, we will first summarize recent progress in plant metabolomics methodology and subsequently review recent studies of interactions between plants and soil organisms in relation to climate change issues.”

Bioreactor and sewage microbiology

TriclosanThe Impacts of Triclosan on Anaerobic Community Structures, Function, and Antimicrobial Resistance – Patrick J McNamara – Environmental Science & Technology

“Triclosan amendment caused all of the Bacteria and Archaea communities to structurally diverge from that of the control cultures (based on ARISA).”

Screen Shot 2014-06-23 at 11.24.07 PMShifts in the Microbial Community, Nitrifiers and Denitrifiers in the Biofilm in a Full-scale Rotating Biological Contactor – Xingxing Peng – Environmental Science & Technology

“The objective of this study was to investigate the Microbial community shifts of bacteria, especially nitrifiers and denitrifiers, in the biofilm of two rotating biological contactor (RBC) trains with different running times along the plug flowpath”

Soil microbiology

Screen Shot 2014-06-23 at 11.32.29 PMIdentifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment – Catriona A Macdonald – Environmental Microbiology

“All functional community measures (functions, biogeochemical cycling genes, network association between different taxa) were more strongly affected by invertebrate grazers than rabbits.”

Screen Shot 2014-06-23 at 11.25.34 PMExtensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi – Robert Riley – PNAS

“To test the adequacy of the white/brown-rot categories, we analyzed 33 fungal genomes. Some species lack PODs, and thus resemble brown-rot fungi, but possess the cellulose-degrading apparatus typical of white-rot fungi. “

Food and other consumables microbiology

Screen Shot 2014-06-23 at 11.33.28 PMIf the pot doesn’t worry you, the bacteria might: Food safety a new frontier for legal pot – Kristen Wyatt – The Republic

“In Washington state, where retail sales are expected to begin the week of July 7, regulations call for samples of all marijuana sold for consumption to clear a “microbiological screening,” whether it’s in edible, smokeable or concentrate form.”

Screen Shot 2014-06-23 at 11.34.50 PMStarter Culture Selection for Making Chinese Sesame-Flavored Liquor Based on Microbial Metabolic Activity in Mixed-Culture Fermentation – Qun Wu – Applied and Environmental Microbiology

“To obtain a suitable starter culture for making Chinese sesame-flavored liquor, the yeast and bacterium community structures were investigated during spontaneous and solid-state fermentations of this type of liquor.”

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Non-human microbiome, June 19

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Microbiomes of piggies, chicks, and bread. Yum.

Pig microbiome

Screen Shot 2014-06-19 at 11.04.38 PMCharacterization of the fecal microbiome in different swine groups by high-throughput sequencing – Soo-Je Park – Anaerobe

“High-throughput 16S rRNA gene-based pyrosequencing was used to identify the possible core microorganisms in the gut of swine groups.”

Screen Shot 2014-06-19 at 11.05.40 PMImpact of fibre types on gut microbiota, gut environment and gut function in fattening pigs – H. Chen – Animal Feed Science and Technology

“To be concluded, influences of dietary sources on intestinal microflora and volatile fatty acids seemed to be related to fibre components, which possibly led to the changes in intestinal mucosal digestive physiology and thus affect production parameters of fattening pigs.”

Chicken microbiome

Screen Shot 2014-06-19 at 11.06.06 PMSelection of indigenous lactic acid bacteria to reinforce the intestinal microbiota of newly hatched chicken – Relevance of in vitro and ex vivo methods for strains characterization
Jaime D. Babot – Research in Veterinary Science

“Based on the natural benefits of the indigenous microbiota, lactic acid bacteria (LAB) from poultry origin were isolated from hens and broilers intestine, and their probiotic potential was further studied.”

Food microbiology

Screen Shot 2014-06-19 at 11.06.34 PMQuantitative high-resolution melting PCR analysis for monitoring of fermentation microbiota in sourdough – Xiaoxi B. Lin – International Journal of Food Microbiology

“This study developed two methods based on high-resolution melting curves (HRM) to monitor sourdough microbiota during fermentation and to investigate the effect of cereal substrate on microbial ecology.”

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