Non-human microbiome, June 19

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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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 microbiome, June 13

MRSA in cats and dogs, metabolomics on cow rumen, bacteria in soil, sewage and sea water, and how to get rid of invasive species.

Mammal microbiome

Screen Shot 2014-06-13 at 11.26.20 PMCarriage of methicillin-resistant staphylococci by healthy companion animals in the US – J.A. Davis – Letters in Applied Microbiology

“In this study, 276 healthy dogs and cats from veterinary clinics were tested for the presence of antimicrobial-resistant Staphylococcus spp. Isolates were tested for antimicrobial susceptibility and the presence of select resistance genes, and typed using Pulsed-Field Gel Electrophoresis (PFGE).”

Screen Shot 2014-06-13 at 11.29.33 PMMetabolomics analysis reveals large effect of roughage types on rumen microbial metabolic profile in dairy cows – S. Zhao – Letters in Applied Microbiology

“ Rumen fluid was sampled from each cow through a ruminal cannula at 0630 and 1030 h, and the mixed ruminal fluid from 3 day in each cow was analysed using nuclear magnetic resonance (NMR) spectroscopy. A multivariate analysis revealed a significant difference between the ruminal metabolome of the CS and MF groups at both time points. “

Soil microbes

Screen Shot 2014-06-13 at 11.30.13 PMDiversity and activity of sulphur-oxidizing bacteria and sulphate-reducing bacteria in landfill cover soils – F.F. Xia – Letters in Applied Microbiology

“In this study, two landfills with or without landfill gas collection and utilization system were investigated to characterize the role of biotic and abiotic factors affecting diversity and activity of SOB and SRB in the landfill cover soils.”

Water microbes

Screen Shot 2014-06-13 at 11.30.55 PMEvaluation of Bacteroides fragilis GB-124 bacteriophages as novel human-associated faecal indicators in the United States – B.R. McMinn – Letters in Applied Microbiology

“Animal faecal samples (>250) from 14 different species were tested for the presence of the three phage groups. GB-124 phages were consistently detected in sewage (10–102 PFU ml−1), but not in animal faeces.”

Letters in applied microbiologyArcobacter spp. isolated from untreated domestic effluent – J.Y. Merga – Letters in Applied Microbiology

“Arcobacter butzleri and Arcobacter cryaerophilus were isolated from samples of raw untreated domestic sewage influent from nine separate wastewater treatment facilities in Cheshire, UK. This is the first report of Arcobacter spp. from sewage in the UK and suggests that Arcobacter spp. may be present in the human community.”

Sunset beachMarine bacteria could help treat human diseases – Mohamed Hassan – The New Zealand Herald

“New Zealand will take part in the first simultaneous sampling of all the world’s oceans as part of “Micro B3 Ocean Sampling Day” on June 20. The project, at 150 sites worldwide, is spearheaded by Germany’s Jacobs University and the University of Oxford in the UK, and will include researchers from the universities of Auckland and Otago.”

zebra musselBacteria could help kill zebra mussels – Associated Press

“State agricultural officials are reviewing a request from the U.S. Geological Survey to experiment with a bacteria to kill zebra mussels in a northern Wisconsin lake.”

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Non-human microbiomes, June 9

Phages in cow dung, genome of a bumble-bee symbiont, and the microbiome of beach sand.

Mammal microbiomes

Screen shot 2014-06-09 at 02.43PM, Jun 09Differing Populations of Endemic Bacteriophages in Cattle Shedding High and Low Numbers of Escherichia coli O157:H7 Bacteria in Feces – J. Hallewell – Applied and Environmental Microbiology

“Based on genome size estimated by pulsed-field gel electrophoresis and morphology determined by transmission electron microscopy, T4- and O1-like phages of Myoviridae and T1-like phage of Siphoviridae were isolated. “

Insect microbiomes

Screen shot 2014-06-09 at 02.59PM, Jun 09Genomic Features of a Bumble Bee Symbiont Reflect Its Host Environment – Vincent G. Martinson – Applied and Environmental Microbiology

“Here, we report the genome of one gammaproteobacterial member of the gut microbiota, for which we propose the name “Candidatus Schmidhempelia bombi,” that was inadvertently sequenced alongside the genome of its host, the bumble bee, Bombus impatiens.”

Plant microbiomes

Screen shot 2014-06-09 at 02.52PM, Jun 09In Situ Evaluation of Paenibacillus alvei in Reducing Carriage of Salmonella enterica Serovar Newport on Whole Tomato Plants – Sarah Allard – Applied and Environmental Microbiology

“Long-term intervention measures to reduce Salmonella prevalence on tomatoes remain elusive for growing and postharvest environments. A naturally occurring bacterium identified by 16S rRNA gene sequencing as Paenibacillus alvei was isolated epiphytically from plants native to the Virginia Eastern Shore tomato-growing region. “

Screen shot 2014-06-09 at 03.20PM, Jun 09Streptomyces sp. strain PGPA39 alleviates salt stress and promotes growth of ‘Micro Tom’ tomato plants – Sasikumar Arunachalam Palaniyandi – Journal of Applied Microbiology

“A significant increase in plant biomass and chlorophyll content, and a reduction in leaf proline content were observed in PGPA39-inoculated tomato plants under salt stress compared to control and salt stressed non-inoculated plants.”

Screen shot 2014-06-09 at 02.54PM, Jun 09Microscopy, Culture, and Quantitative Real-Time PCR Examination Confirm Internalization of Mycobacteria in Plants – M. Kaevska – Applied and Environmental Microbiology

” The substrate into which plants were seeded was previously contaminated with different strains of Mycobacterium avium (108to 1010 cells/g of soil) and feces from animals with paratuberculosis. We detected M.avium subsp. aviumhominissuis, and paratuberculosis in the stems and leaves of the plants by both culture and real-time quantitative PCR. “

Environmental microbiomes

Screen shot 2014-06-09 at 02.40PM, Jun 09

Soil and groundwater microbiomes

Use of Silicate Minerals for pH Control during Reductive Dechlorination of Chloroethenes in Batch Cultures of Different Microbial Consortia  – Elsa Lacroix – Applied and Environmental Microbiology

“The consortia showed significant differences in sensitivities toward acidic pH for the different dechlorination steps. Molecular analysis indicated that Dehalococcoides spp. that were present in all consortia were the most pH-sensitive organohalide-respiring guild members compared to Sulfurospirillum spp. and Dehalobacter spp.”

Screen shot 2014-06-09 at 03.01PM, Jun 09Variables Influencing Extraction of Nucleic Acids from Microbial Plankton (Viruses, Bacteria, and Protists) Collected on Nanoporous Aluminum Oxide Filters – Jaclyn A. Mueller – Applied and Environmental Microbiology

“Anodic aluminum oxide (AAO) filters have high porosity and can be manufactured with a pore size that is small enough to quantitatively capture viruses. These properties make the filters potentially useful for harvesting total microbial communities from water samples for molecular analyses, but their performance for nucleic acid extraction has not been systematically or quantitatively evaluated. “

Screen shot 2014-06-09 at 03.08PM, Jun 09MS2 Bacteriophage Reduction and Microbial Communities in Biosand Filters – Hanting Wang – Environmental Science & Technology

” In the upper layers, “CandidatusNitrosopumilus maritimus” and “Ca. Nitrospira defluvii” were found as dominant populations, while significant amounts of Thiobacillus-related OTUs were detected in the lower layers. “

Ponds, lakes, and ocean microbiomes

Screen shot 2014-06-09 at 02.48PM, Jun 09Diversity and Transport of Microorganisms in Intertidal Sands of the California Coast – Alexandria B. Boehm – Applied and Environmental Microbiology

“The present study uses next-generation massively parallel sequencing to characterize the microbial community present at 49 beaches along the coast of California. In addition, we characterize the transport of microorganisms within intertidal sands using laboratory column experiments. We identified extensive diversity in the beach sands.”

Screen shot 2014-06-09 at 02.46PM, Jun 09From Metagenomics to Pure Culture: Isolation and Characterization of the Moderately Halophilic Bacterium Spiribacter salinus gen. nov., sp. nov. – María José León – Applied and Environmental Microbiology

“We report the isolation and taxonomic characterization of this new, never before cultured microorganism, designated M19-40T, isolated from a saltern located in Isla Cristina, Spain, using a medium with a mixture of 15% salts, yeast extract, and pyruvic acid as the carbon source. “

Screen shot 2014-06-09 at 03.05PM, Jun 09The Pattern of Change in the Abundances of Specific Bacterioplankton Groups Is Consistent across Different Nutrient-Enriched Habitats in Crete – Stilianos Fodelianakis – Applied and Environmental Microbiology

“Here, we investigated the bacterial community changes at three different nutrient-enriched and adjacent undisturbed habitats along the north coast of Crete, Greece: a fish farm, a closed bay within a town with low water renewal rates, and a city port where the level of nutrient enrichment and the trophic status of the habitat were different. “

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Animal, plant, environmental microbiome digest, June 3, 2014

Microbiomes of wild mice, antibiotic treated cattle, catfish, insects, soil, and water. And some good old plagiarism.

Mammalian microbiome

Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice – Jun Wang – PNAS

“By performing stable isotope analysis of environmental samples, monitoring communities during dietary shifts, and collecting functional metagenomic sequence data, we provide novel insight into the origins and dynamics of enterotype-like community clustering in wild house mice.”

Impact of treatment strategies on cephalosporin and tetracycline resistance gene quantities in the bovine fecal metagenome – Neena Kanwar – Nature Scientific Reports

“The study objective was to determine the effects of two treatment regimens on quantities of ceftiofur and tetracycline resistance genes in feedlot cattle. “

Fish microbiome

An Asian Origin of Virulent Aeromonas hydrophila Responsible for Disease Epidemics in United States-Farmed Catfish – Mohammad J. Hossain – mBio

“Our phylogenomic analyses suggest that U.S. catfish isolates emerged from A. hydrophila populations of Asian origin.”

Insect microbiome

Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics – Joel Gibson – PNAS

“We show that next-generation sequencing (NGS) of cytochrome c oxidase subunit I (COI) DNA barcodes can accurately detect 83.5% of individually sequenced species (corresponding to 91% of individuals) in a bulk sample of terrestrial arthropods from a Costa Rican species-rich site.”

GroEL from the endosymbiont Buchnera aphidicola betrays the aphid by triggering plant defense – Ritu Chaudhary – PNAS

“By means of mass spectrometry, we identified 105 proteins in the saliva of the potato aphid Macrosiphum euphorbiae. Among these proteins were some originating from the proteobacterium Buchnera aphidicola, which lives endosymbiotically within bacteriocytes in the hemocoel of the aphid. “

Soil and rock microbiome

Deep 16S rRNA Pyrosequencing Reveals a Bacterial Community Associated with Banana Fusarium Wilt Disease Suppression Induced by Bio-Organic Fertilizer Application – Zongzhuan Shen – PLOS ONE

“Compared to the other soil samples, BIO-treated soil revealed higher abundances of Gemmatimonadetes and Acidobacteria, while Bacteroidetes were found in lower abundance”

Evaluation of Molecular Techniques in Characterization of Deep Terrestrial Biosphere – Malin Bomberg – Open Journal of Ecology

“our results show that the inferred diversity and composition of microbial communities in deep fracture fluids is highly dependent on analytical technique and that the method should be carefully selected with this in mind.”

Detecting Nitrous Oxide Reductase (nosZ) Genes in Soil Metagenomes: Method Development and Implications for the Nitrogen Cycle – L. H. Orellana – mBio

“we analyzed the abundance and diversity of both nosZ types in whole-genome shotgun metagenomes from sandy and silty loam agricultural soils that typify the U.S. Midwest corn belt”

Water microbiome

Survival secrets of Deep Lake – Graeme O’Neill – LifeScientist.com

“Deep Lake, in Antarctica’s Vestfold Hills, harbours a unique flora of salt-loving Archaea that survive at temperatures way below freezing. Professor Rick Cavicchioli’s team at UNSW has been plumbing the lake’s mysteries”

Accumulation and enhanced cycling of polyphosphate by Sargasso Sea plankton in response to low phosphorus – Patrick Martin – PNAS

” We show here that phytoplankton in the ultra–low-phosphorus Sargasso Sea are enriched in polyphosphate (polyP)”

Commonness and rarity in the marine biosphere – Sean R. Connolly – PNAS

“By identifying common features of different neutral models, we conduct a uniquely robust test of neutral theory across a global dataset of marine assemblages.”

Temporal Changes in Microbial Ecology and Geochemistry in Produced Water from Hydraulically Fractured Marcellus Shale Gas Wells – Maryam A. Cluff – Environmental Science & Technology

“This study tracked microbial community dynamics using pyrotag sequencing of 16S rRNA genes in water samples from three hydraulically fractured Marcellus shale wells in Pennsylvania, USA over a 328-day period.”

General Ecology

Effects of differential habitat warming on complex communities – Tyler D. Tunney – PNAS

“To demonstrate differential warming effects on food webs, we use boreal lakes to show that the energy pathways leading to an apex predator shift, according to thermal preference, and the vertical pathway lengthened in warmer climate.”

Microbes in Space

Protein patterns of black fungi under simulated Mars-like conditions – Kristina Zakharova – Nature Scientific Reports

“In this study the alterations at the protein expression level from various fungi species under Mars-like conditions were analyzed for the first time using 2D gel electrophoresis.”

Data mining and Bioinformatics

Detecting a Weak Association by Testing its Multiple Perturbations: a Data Mining Approach – Min-Tzu Lo & Wen-Chung Lee – Nature Scientific Reports

“Here, we propose a novel method which hinges on increasing sample size in a different direction–the total number of variables”

This paper contains plagiarized text, but I will toss it in anyway:
An Integrated Strategy for Functional Analysis of Microbial Communities Based on Gene Ontology and 16S rRNA Gene – Su-Ping Deng, De-Shuang Huang – SciencePaperOnline

“We analyzed the similarity between two microbial communities on functional state. In the experimental results, it shows that the semantic similarity can quantify the difference between two compared species on function level. “

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Digest May 27, 2014

Today’s Picks feature thousand cultured GI tract species, host-microbiome interactions during pregnancy, metagenome assemblies using Hi-C, and the microbiomes of snow leopards and possums.

Human microbiome general

Human Gut Microbiome

Pregnancy and birth microbiome

Respiratory tract microbiome

Mammalian microbiome

Amphibian microbiome

Insect microbiome

Fish microbiome

Animal and bioreactor models of gut microbiome

Environmental microbiome

Microbiome and Metabolomics

Phages and viruses

  • Beyond Antibiotics – “Today there is renewed interest in phages as warnings intensify that a “post-antibiotic” era looms” – Roger Highfield – Newsweek

Infection, sepsis, and host response

Microbial Ecology papers

Arsenic metabolism

Chromosome organization

General lab techniques papers

Dr. Bik’s Picks

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