Category Archives: Animal microbiome

General microbiology and science, June 27

Posted on by

Viruses in primate genomes, viruses altering shrimp metabolome, transposable elements and repeats, dengue, other infectious diseases in developing countries and Dr. Bik’s Picks.

Metagenomics / viruses

Screen Shot 2014-06-27 at 9.21.29 PMCute animal alert! A tarsier is a tiny primate with huge eyes.
The First Endogenous Herpesvirus, Identified in the Tarsier Genome, and Novel Sequences from Primate Rhadinoviruses and Lymphocryptoviruses – Amr Aswad, Aris Katzourakis – PLOS Genetics

“We describe the first endogenous herpesvirus from the genome of the Philippine tarsier, belonging to the Roseolovirus genus, and characterize its highly defective genome that is integrated and flanked by unambiguous host DNA. From a draft assembly of the aye-aye genome, we use bioinformatic tools to reveal over 100,000 bp of a novel rhadinovirus that is the first lemur gammaherpesvirus, closely related to Kaposi’s sarcoma-associated virus.”

 Metabolomics

Screen Shot 2014-06-27 at 9.32.37 PMAn Invertebrate Warburg Effect: A Shrimp Virus Achieves Successful Replication by Altering the Host Metabolome via the PI3K-Akt-mTOR Pathway – Mei-An Su – PLOS Pathogens

“We show that the PI3K-Akt-mTOR pathway was of central importance in triggering this WSSV-induced Warburg effect. Although dsRNA silencing of the mTORC1 activator Rheb had only a relatively minor impact on WSSV replication, in vivo chemical inhibition of Akt, mTORC1 and mTORC2 suppressed the WSSV-induced Warburg effect and reduced both WSSV gene expression and viral genome replication.”

Biofilms

Screen Shot 2014-06-27 at 9.33.21 PMFilaments in curved streamlines: rapid formation of Staphylococcus aureus biofilm streamers – Minyoung Kevin Kim – New Journal of Physics

“We discovered that S. aureus rapidly forms flow-induced, filamentous biofilm streamers, and furthermore if surfaces are coated with human blood plasma, streamers appear within minutes and clog the channels more rapidly than if the channels are uncoated. “

Chromosomal organization

Screen Shot 2014-06-27 at 9.34.04 PMDigital Genotyping of Macrosatellites and Multicopy Genes Reveals Novel Biological Functions Associated with Copy Number Variation of Large Tandem Repeats – Manisha Brahmachary – PLOS Genetics

“Here, we demonstrate the utility of Nanostring technology as a targeted approach to perform accurate measurement of tandem repeats even at extremely high copy number, and apply this technology to genotype 165 HapMap samples from three different populations and five species of non-human primates. “

Screen Shot 2014-06-27 at 9.34.37 PMLarge-Scale Genomic Analysis Suggests a Neutral Punctuated Dynamics of Transposable Elements in Bacterial Genomes – Jaime Iranzo – PLOS Computational Biology

“In this work, we take advantage of the large amount of genomic data currently available and study the abundance distributions of 33 IS families in 1811 bacterial chromosomes. This allows us to test simple models of IS dynamics and estimate their key parameters by means of a maximum likelihood approach. “

Microbial Ecology

Screen Shot 2014-06-27 at 9.35.00 PMEx Uno Plures: Clonal Reinforcement Drives Evolution of a Simple Microbial Community – Margie Kinnersley – PLOS Genetics

“We previously showed that a population of E. coli that originated from a single clone and was cultured in the presence of a single limiting resource, evolves into a stable, three-membered community, wherein one clone excretes metabolites that the others utilize as carbon sources. To discern the genetic factors at work in producing this outcome and to illuminate the community’s physiology, we sequenced the genomes of the ancestral and evolved clones.”

Infectious diseases in developing countries

Screen Shot 2014-06-27 at 9.35.43 PMExploring the Relationship between Access to Water, Sanitation and Hygiene and Soil-Transmitted Helminth Infection: A Demonstration of Two Recursive Partitioning Tools – Katherine Gass – PLOS Neglected Tropical Diseases

“Improvements to water, sanitation and hygiene (WASH) likely provide sustained benefit, but few rigorous studies have evaluated the specific WASH components most influential in reducing infection. “

Screen Shot 2014-06-27 at 9.36.14 PMSocial Sciences Research on Infectious Diseases of Poverty: Too Little and Too Late? – José Azoh Barry – PLOS Neglected Tropical Diseases

“Besides the vicious circle these diseases maintain with dire conditions of poverty, an increased microbial resistance to some therapeutic drugs adds to the complexity of health disparities and human suffering among the socially disadvantaged, marginalized, and prejudiced against.”

Dengue

Screen Shot 2014-06-27 at 9.36.37 PMVariability in Dengue Titer Estimates from Plaque Reduction Neutralization Tests Poses a Challenge to Epidemiological Studies and Vaccine Development – Henrik Salje – PLOS Neglected Tropical Diseases

“We used repeated assays on the same two pools of serum using five different viruses (2,319 assays) to characterize the variability in the technique under identical experimental conditions. We also assessed the performance of multiple statistical models to interpolate continuous values of neutralization titer from discrete measurements from serial dilutions.”

Science and career

PLOSTen Simple Rules for Approaching a New Job – Philip E. Bourne – PLOS Computational Biology

“Thinking both as a job applicant and a job interviewer about how I have approached job situations over the years before, during, and after the interview and how those situations have turned out, I can offer the following ten simple rules as you prepare.”

A New Online Computational Biology Curriculum – David B. Searls – PLOS Computational Biology

“A recent proliferation of Massive Open Online Courses (MOOCs) and other web-based educational resources has greatly increased the potential for effective self-study in many fields. This article introduces a catalog of several hundred free video courses of potential interest to those wishing to expand their knowledge of bioinformatics and computational biology. “

Arsenic metabolism

Screen Shot 2014-06-27 at 10.00.06 PMAssociations between Arsenic Species in Exfoliated Urothelial Cells and Prevalence of Diabetes among Residents of Chihuahua, Mexico – Jenna M. Currier – Environ Health Perspect

“We measured concentrations of trivalent and pentavalent iAs, methyl-As (MAs), and dimethyl-As (DMAs) species in EUC from 374 residents of Chihuahua, Mexico, who were exposed to iAs in drinking water.”

Dr. Bik’s Picks

Screen Shot 2014-06-27 at 10.09.01 PMWith pictures and videos: Duration of urination does not change with body size – Patricia J. Yang – PNAS

“In this study, we report a mathematical model that clarifies misconceptions in urology and unifies the results from 41 independent urological and anatomical studies. The theoretical framework presented may be extended to study fluid ejection from animals, a universal phenomenon that has received little attention.”

Screen Shot 2014-06-27 at 10.01.44 PMFrom Gemstones to Arsenic: How the Development of Pigment Colored Art – Allison Meier

“A new exhibition at London’s National Gallery — Making Colour — looks at the development of color in art, from the Middle Ages to 1900. “

[hr]

Non-human microbiome, June 26

Posted on by

Microbiomes of frogs in captivity, insect larvae, Senegalese sole, and Portugese sashimi.

Amphibian microbiome

Panamanian frogThe effect of captivity on the cutaneous bacterial community of the critically endangered Panamanian golden frog (Atelopus zeteki) -Matthew H. Becker – Biological Conservation

“We characterized the cutaneous bacterial community from wild and F1 captive golden frogs originating from the same population with Illumina sequencing to assess how long-term captivity has affected this community. “

Insect microbiome

Screen Shot 2014-06-26 at 9.57.25 PMMicroprofiles of oxygen, redox potential, and pH, and microbial fermentation products in the highly alkaline gut of the saprophagous larva of Penthetria holosericea (Diptera: Bibionidae) – Vladimír Šustr – Journal of Insect Physiology

“We conclude that the digestive strategy of the saprophytic larva of P. holosericea, which feeds selectively on decomposed leaves and its own microbe-rich faeces, differs fundamentally from those of detritivorous and humivorous insects, which host a highly active, fermentative microbiota in their alkaline midgut or hindgut compartments.”

Fish microbiome

SoleBenefits of probiotic administration on growth and performance along metamorphosis and weaning of Senegalese sole (Solea senegalensis) – Carmen Lobo – Aquaculture

“A short pulse of Shewanella putrefaciens Pdp11 probiotic addition (10-30 dah) is sufficient to obtain a suitable microbial modulation in Solea senegalensis larviculture.”

Food microbiology

BozaEvaluation of lactic acid bacterial strains of boza for their exopolysaccharide and enzyme production as a potential adjunct culture – Dilek Heperkan – Process Biochemistry

“Boza is a non-alcoholic beverage obtained from fermented cereals. Thirteen -lactic acid bacteria (LAB), previously isolated from boza were identified and evaluated to determine the various technological properties for selecting appropriate strains as adjunct culture in boza. “

SSashimiPMEvaluation of ready to eat sashimi in northern Portugal restaurants – S. Miguéis – Food Control

“The aim of this study was to evaluate some of the microbiological and physicochemical characteristics of sashimi served at different restaurants in Northern Portugal, in order to determine whether or not the sashimi was safe for consumption.”

Soil, sediments, and rock microbiology

Screen Shot 2014-06-26 at 9.12.55 PMSearching for life in the deep shale – Elizabeth Pennisi – Science

“The two researchers are part of a pioneering effort to explore what is living in the deep layers of rock—and how the gas drilling boom might affect long-isolated ecosystems.”

Screen Shot 2014-06-26 at 9.57.00 PMLong term effects of nutrient management regimes on abundance of bacterial genes and soil biochemical processes for fertility sustainability in a semi-arid tropical Alfisol
Chinnappan Chinnadurai – Geoderma

“Organic manures increased the density of 16S rRNA and nifH gene copies.”

[hr]

 

Non-human microbiome, June 25

Posted on by

Mongolian Gerbils, soil microbiome affects plant flowering time, soybeans, and seawater viruses.

Mammalian microbiome

Screen shot 2014-06-25 at 01.26PM, Jun 25Helicobacter pylori Induced Gastric Immunopathology Is Associated with Distinct Microbiota Changes in the Large Intestines of Long-Term Infected Mongolian Gerbils – Markus M. Heimesaat – PLOS ONE

“Comprehensive cultural analyses revealed that severe gastric diseases such as atrophic pangastritis and precancerous transformations were accompanied by elevated luminal loads of E. coli and enterococci in the caecum and together with Bacteroides/Prevotella spp. in the colon of H. pylori WT, but not MUT infected gerbils as compared to naïve animals. “

Plant microbiome

Screen shot 2014-06-25 at 01.27PM, Jun 25Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field – Akifumi Sugiyama – PLOS ONE

“Pyrosequencing analysis revealed that differences between the bacterial communities of rhizosphere and bulk soils at the phylum level; i.e., Proteobacteria were increased, while Acidobacteria and Firmicutes were decreased in rhizosphere soil during growth. “

Screen shot 2014-06-25 at 06.41PM, Jun 25Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative – Maggie R. Wagner – Ecology Letters

“Here, we tested separately the effects of four naturally occurring soil microbiomes and their constituent soil chemistries on flowering phenology and reproductive fitness of Boechera stricta, a wild relative of Arabidopsis. “

Water microbiology

Screen shot 2014-06-25 at 01.27PM, Jun 25 1Anthropogenic Litter in Urban Freshwater Ecosystems: Distribution and Microbial Interactions – Timothy Hoellein – PLOS ONE

“To assess microbial interactions with AL, we incubated AL and natural substrates in 3 freshwater ecosystems, quantified biofilm metabolism as gross primary production (GPP) and community respiration (CR), and characterized biofilm bacterial community composition via high-throughput sequencing of 16S rRNA genes.”

Screen shot 2014-06-25 at 01.28PM, Jun 25Comparison of Deep-Water Viromes from the Atlantic Ocean and the Mediterranean Sea – Christian Winter – PLOS ONE

“The identifiable richness and relative abundance in both viromes were dominated by archaeal and bacterial viruses accounting for 92.3% of the relative abundance in the Atlantic Ocean and for 83.6% in the Mediterranean Sea. “

Screen shot 2014-06-25 at 01.28PM, Jun 25 1The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing – Patrick J. Keeling – PLOS Biology

“The MMETSP relies primarily on cultured organisms, and this introduces a different set of biases, most obviously, favoring organisms that are photosynthetic. “

[hr]

Non-human microbiome, June 24

Posted on by

Lots of marine microbiotas for you today, from corals, sponges, bivalves, to seawater and sediments.

Coral, sponges and other invertebrate microbiome

Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata – Collin J Closek – ISME Journal

“We profiled three conditions: (1) healthy-appearing colonies (HH), (2) healthy-appearing tissue on diseased colonies (HD), and (3) diseased lesion (DD). Restriction fragment length polymorphism analysis revealed health state-specific diversity in Symbiodinium clade associations. “

Quantification of bacterial and archaeal symbionts in high and low microbial abundance sponges using real-time PCR – Kristina Bayer – FEMS Microbiology Ecology

“Here, we established qPCR assays for the specific quantification of four bacterial phyla of representative sponge symbionts as well as the kingdoms Eubacteria and Archaea. “

Comparative modifications in bacterial gill-endosymbiotic populations of the two bivalves Codakia orbiculata and Lucina pensylvanica during bacterial loss and reacquisition – Nathalie H. Elisabeth – FEMS Microbiology Ecology

“We used in situ hybridization, flow cytometry and X-ray fluorescence to characterize the symbiont population hosted in the gills of both species. I”

Plant microbiology

Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest – Rebecca C Mueller – ISME Journal

“We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation.”

Soil microbiology

High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation – Dawei Ren – ISME Journal

“Our results show a high prevalence of synergy in biofilm formation in multispecies consortia isolated from a natural bacterial habitat and suggest that interspecific cooperation occurs.”

High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments – Tim Engelhardt – ISME Journal

“Phages were detected by electron microscopy in deep (320 m below seafloor), ancient (~14 Ma old) and the most oligotrophic subsurface sediments of the world’s oceans (South Pacific Gyre (SPG)).”

Water and sediment microbiology

Contrasting spatiotemporal patterns and environmental drivers of diversity and community structure of ammonia oxidizers, denitrifiers, and anammox bacteria in sediments of estuarine tidal flats – Anjing Yang – Annals of Microbiology

“The alpha diversities (Shannon and Simpson indices) and community structure of ammonia oxidizing bacteria (AOB) and archaea (AOA), denitrifier and anammox bacteria (AMB) were revealed using denaturing gradient gel electrophoresis and clone library analysis of amoA, nosZ and 16S rRNA gene markers. “

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill – Olivia U Mason – ISME Journal

“The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. “

Microorganisms persist at record depths in the subseafloor of the Canterbury Basin – Maria-Cristina Ciobanu – ISME Journal

“Here we show that not only Bacteria and Archaea but also Eukarya occur at record depths in the subseafloor of the Canterbury Basin. Shifts in microbial community composition along a core of nearly 2 km reflect vertical taxa zonation influenced by sediment depth. “

The niche of an invasive marine microbe in a subtropical freshwater impoundment – K David Hambright – ISME Journal

“Using a long-term field study of the ‘invasive’ marine haptophyte Prymnesium parvum, we characterize the environmental niche of P. parvum in a subtropical impoundment in the southern United States.”

Unveiling microbial activities along the halocline of Thetis, a deep-sea hypersaline anoxic basin – Maria G Pachiadaki – ISME Journal

“This first metatranscriptome analysis of DHAB samples provides significant insights into shifts in metabolic activities of microorganisms as physicochemical conditions change from deep Mediterranean sea water to brine.”

Oxygen availability and distance to surface environments determine community composition and abundance of ammonia-oxidizing prokaroytes in two superimposed pristine limestone aquifers in the Hainich region, Germany –
Sebastian Opitz – FEMS Microbiology Ecology

“We followed the abundance and compared the diversity of ammonia oxidizing archaea (AOA) and bacteria (AOB) in the groundwater of two superimposed pristine limestone aquifers located in the Hainich region (Thuringia, Germany) over 22 months”

Intertidal epilithic bacteria diversity changes along a naturally occurring carbon dioxide and pH gradient – Joe D Taylor – FEMS Microbiology Ecology

“Biofilms were sampled from three sites exposed to seawater with different pH/CO2 levels and diversity determined using high-throughput sequencing of 16S rRNA genes. “

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype –
J Cameron Thrash – ISME Journal

“Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%–86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets.”

A microarray for assessing transcription from pelagic marine microbial taxa –
Irina N Shilova – ISME Journal

“Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. “

[hr]

Non-human microbiome, June 23

Posted on by

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.

Screen Shot 2014-06-23 at 10.57.57 PM

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.”

[hr]

Non-human microbiome, June 19

Posted on by

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.”

[hr]

Non-human microbiome, June 18

Posted on by

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.”

[hr]

Non-human microbiome, June 17

Posted on by

You waited for it: the Cannabis microbiome! But also microbiotas of salmon, a quail, coral, sponges, water, and ice.

Bird microbiome

Cultivable Bacterial Microbiota of Northern Bobwhite (Colinus virginianus): A New Reservoir of Antimicrobial Resistance? – Hongwen Su – PLOS ONE

“Firmicutes was the most commonly encountered phylum (57%) followed by Actinobacteria (24%), Proteobacteria (17%) and Bacteroidetes (0.02%). Extensive diversity in the species composition of quail microbiota was observed among individual birds and anatomical locations.”

Fish microbiome

Pyrosequencing-based characterization of gastrointestinal bacteria of Atlantic salmon (Salmo salar L.) within a commercial mariculture system – K.Z. Zarkasi – Journal of Applied Microbiology

“Salmon GI tract bacterial communities commercially farmed in south-eastern Tasmania were analysed, over a 13-month period across a standard commercial production farm cycle, using 454 16S rRNA-based pyrosequencing. “

Coral and sponge microbiome

Community Shifts in the Surface Microbiomes of the Coral Porites astreoides with Unusual Lesions – Julie L. Meyer – PLOS ONE

“The presence of lesions in P. astreoides coincided with a decrease in the relative abundance of Endozoicomonas, rather than the appearance of specific pathogenic taxa.”

Bacterial suspects identified in Caribbean coral deaths – NewScientist

“Three bacteria seem to be responsible for a disease that has killed most of the Caribbean’s reef-building corals.”

Effects of salinity on antibiotic production in sponge-derived Salinispora actinobacteria – Y.K. Ng – Journal of Applied Microbiology

“Fingerprint data were generated from extracts of S. arenicola broth cultures grown in media of varying salt (NaCl) concentrations.”

Plants microbiome

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome – Max E. Winston – PLOS ONE

“Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity.”

The Role of Abiotic Environmental Conditions and Herbivory in Shaping Bacterial Community Composition in Floral Nectar – Michal Samuni-Blank – PLOS ONE

“ We studied culturable bacterial communities in Asphodelus aestivus floral nectar and in its typical herbivorous bug Capsodes infuscatus, along an aridity gradient.”

Microbial community structure during fluoranthene degradation in the presence of plants – S. Storey – Journal of Applied Microbiology

“Bacterial and fungal community composition in the rhizosphere was significantly different from that in nonrhizospheric and unplanted samples.”

Soil microbiome

Omics-based interpretation of synergism in a soil-derived cellulose-degrading microbial community – Yizhuang Zhou – Scientific Reports

“Analyses of reconstructed bacterial draft genomes from all seven uncultured phylotypes in F1RT indicate that its constituent microbes cooperate in both cellulose-degrading and other important metabolic processes.”

Structure, Composition and Metagenomic Profile of Soil Microbiomes Associated to Agricultural Land Use and Tillage Systems in Argentine Pampas – Belén Carbonetto – PLOS ONE

“The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas.”

 

Dust microbiome

Richness and Diversity in Dust Stormborne Biomes at the Southeast Mediterranean – Itzhak Katra – Scientific Reports

“In addition to the physico-chemical compositions, organismal diversities of dust from two storm events in southern Israel, December 2012 (Ev12) and January 2013 (Ev13), were determined by pyro-sequencing using primers universal to 16S and 18S rRNA genes and compared.”

Bioreactors

The maximum specific hydrogen-producing activity of anaerobic mixed cultures: definition and determination – Yang Mu – Scientific Reports

“ Our results demonstrate that this novel SHAm assay was a rapid, accurate and simple methodology for determining the hydrogen-producing activity of anaerobic mixed cultures.”

Methanogenic community changes, and emissions of methane and other gases, during storage of acidified and untreated pig slurry – S.O. Petersen – Journal of Applied Microbiology

“Pig slurry from two farms, acidified by different techniques or untreated, was stored for 83 days in a pilot-scale facility. Methanogens were characterized before and after storage by T-RFLP and qPCR targeting mcrA.”

Water and ice

The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics – Alexander I. Culley – mBio

“In this study, we investigated the diversity of the RNA virus assemblages in tropical coastal seawater samples using targeted PCR and metagenomics.”

Variations of algal communities cause darkening of a Greenland glacier – Stefanie Lutz – FEMS Microbiology Ecology

“We have assessed the microbial ecology on the surface of Mittivakkat glacier in SE-Greenland during the exceptional high melting season in July 2012 when the so far most extreme melting rate for the Greenland Ice Sheet has been recorded.”

Pyrosequencing reveals correlations between extremely acidophilic bacterial communities with hydrogen sulphide concentrations, pH and inert polymer coatings at concrete sewer crown surfaces – E. Pagaling – Journal of Applied Microbiology

“Pyrosequencing and cloning showed that Mycobacterium and Acidithiobacillus dominated the acidophilic microbial communities. Methylacidiphilum was also dominant in samples where methane was detected.”

Bacterial community dynamics during the early stages of biofilm formation in a chlorinated experimental drinking water distribution system: implications for drinking water discolouration – I. Douterelo – Journal of Applied Microbiology

“Selected samples were analysed by cloning and sequencing of the 16S rRNA gene. Fingerprinting analysis revealed significant changes in the bacterial community structure over time (P < 0·05). “

[hr]

Non-human microbiomes, June 16

Posted on by

Microbiomes of tse-tse flies, fish, lettuce, spruce. And also some salty sisters!

Insect microbiome

Identification of overexpressed genes in Sodalis glossinidius inhabiting trypanosome-infected self-cured tsetse flies – Illiassou Hamidou Soumana – Frontiers in Microbiology

“The aim of the work was to investigate whether fly refractoriness could be associated with specific Sodalis gene expression. The transcriptome of S. glossinidius harbored by flies that were fed either with a non-infected blood meal (control) or with a trypanosome-infected meal but that did not develop infection were analyzed, using microarray technology, and compared. “

Fish microbiome

Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries – Martin S. Llewellyn – Frontiers in Microbiology

“We discuss teleost microbiomes in health and disease, microbiome ontogeny, prospects for successful microbiome manipulation (especially in an aquaculture setting) and attempt to identify important future research themes. “

Plant microbiomes

Effect of the strain Bacillus amyloliquefaciens FZB42 on the microbial community in the rhizosphere of lettuce under field conditions analyzed by whole metagenome sequencing – Magdalena Kröber – Frontiers in Microbiology

“Rhizosphere microbial communities of lettuce treated with B. amyloliquefaciens FZB42 and non-treated plants were profiled by high-throughput metagenome sequencing of whole community DNA. “

Loss of diversity in wood-inhabiting fungal communities affects decomposition activity in Norway spruce wood – Lara Valentín – Frontiers in Microbiology

“ The number of observed OTUs in DGGE was used as a measure of fungal diversity. Respiration rate increased between early- and late-decay stages. “

Specificity of plant-microbe interactions in the tree mycorrhizosphere biome and consequences for soil C cycling – Carolyn Churchland – Frontiers in Microbiology

“In this review we examine evidence for tree species- mycorrhizal specificity, and the mechanisms involved (e.g., signal compounds)”

Sludge and bioreactors

Pyrosequencing Analysis Yields Comprehensive Assessment of Microbial Communities in Pilot-Scale Two-Stage Membrane Biofilm Reactors – Aura Ontiveros-Valencia – Environmental Science & Technology

“UniFrac, principal coordinate analysis (PCoA), and diversity analyses documented that the microbial community of biofilms sampled when the MBfRs had a high acceptor loading were phylogenetically distant from and less diverse than the microbial community of biofilm samples with lower acceptor loadings. “

Sludge As a Potential Important Source of Antibiotic Resistance Genes in Both the Bacterial and Bacteriophage Fractions – William Calero-Cáceres – Environmental Science & Technology

“This study evaluates the prevalence of ARGs in the bacterial and phage fractions of anaerobic digested sludge; five ARGs (blaTEM, blaCTX-M, qnrA, qnrS, and sul1) are quantified by qPCR.”

Water and salt microbiology

Salty sisters: the women of halophiles – Bonnie K. Baxter – Frontiers in Microbiology

“This essay emphasizes the “her story” (not “history”) of halophile discovery.”

The feasibility of automated online flow cytometry for in-situ monitoring of microbial dynamics in aquatic ecosystems – Michael D. Besmer – Frontiers in Microbiology

“As proof-of-concept we demonstrate examples of microbial dynamics in (i) flowing tap water from a municipal drinking water supply network and (ii) river water from a small creek subject to two rainfall events.”

Cytometric fingerprints: evaluation of new tools for analyzing microbial community dynamics – Christin Koch – Frontiers in Microbiology

“The source of inoculum (four different types of wastewater samples) showed the strongest influence on the microbial community structure and biofilm performance while the choice of substrate (acetate or lactate) had no significant effect in the present study.”

Subseafloor bacteria survive by over-activating DNA-repair and antibiotic target genes – Phys.org

“A group of researchers at Woods Hole Oceanographic Institute and University of Delaware* developed techniques to analyse the messenger RNA (mRNA) molecules produced by subseafloor microbes.”

Unexplored hypersaline habitats are sources of novel actinomycetes – Polpass Arul Jose – Frontiers in Microbiology

“….diverse actinomycetes from poorly studied unusual environments promises a raise in the prospect of discovering novel compounds with potential activities that can be developed as a resource for drug discovery “

From Twitter, thanks to @DeepMicrobe: Eight plenary speakers, all of them male.
Ninth International Symposium on Subsurface Microbiology – ISSM 2014

Vibrio ecology, pathogenesis, and evolution – Daniela Ceccarelli and Rita R. Colwell – Frontiers in Microbiology

“This Research Topic brings together 24 articles that highlight the most recent research findings concerning the biology of the genus Vibrio and covers pathogenicity and host interaction, genome plasticity and evolution, and the dynamics of factors influencing the ecology of vibrios.”

[hr]

Non-human microbiome, June 13

Posted on by

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.”

[hr]