Animal microbiome digest, September 16, 2014

Microbiomes of baby elephants, baby macaques, cows, mice, honey bees, oysters, Panama forest trees, yoghurt, air, beer, and clothes. We also learn that oregano has no effect on piglet microbiome. Just in case you wondered.

Mammal microbiome

A Comparative Metagenome Survey of the Fecal Microbiota of a Breast- and a Plant-Fed Asian Elephant Reveals an Unexpectedly High Diversity of Glycoside Hydrolase Family Enzymes – Nele Ilmberger – PLOS ONE

“A phylogenetic and metagenomic study of elephant feces samples (derived from a three-weeks-old and a six-years-old Asian elephant) was conducted in order to describe the microbiota inhabiting this large land-living animal.”

Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems – Amir Ardeshir – Science Translational Medicine

“We show that breast-fed and bottle-fed infant rhesus macaques develop markedly different immune systems, which remain different 6 months after weaning when the animals begin receiving identical diets.”

Characterization of the rumen lipidome and microbiome of steers fed a diet supplemented with flax and echium oil – Sharon Ann Huws – Microbial Biotechnology

“Microbiome pyrosequences showed that 50% of the bacterial genera were core to all diets (found at least once under each dietary intervention)”

Metagenome of Mehsani Buffalo Rumen Microbiota: An Assessment of Variation in Feed-Dependent Phylogenetic and Functional Classification – Parmar N.R. – Journal of Molecular Microbiology and Biotechnology

“Diet composed of varying proportion of green and dry roughages along with grains was given to 8 Mehsani buffaloes, and rumen metagenome was sketched using shotgun semiconductor sequencing.”

Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high throughput parallel pyrosequencing – Jakub Kreisinger – Molecular Ecology

“Using 454 pyrosequencing, we performed 16S rDNA GTM barcoding for 30 wild house mice (Mus musculus) and wild-derived inbred strain mice belonging to two subspecies (M.m.musculus and M.m. domesticus).”

The Use of Restriction Fragment Length Polymorphism and Fluorescence in Situ Hybridization to Investigate Microbiota of Piglets after Feeding Oregano – Katrin Stelter – Food and Nutrition Sciences

“The results showed no significant changes in microbiota in response to oregano. “

Insect microbiome

Buzz off, that’s my bee! – Gemma Langridge – Nature Reviews Microbiology

“These newly sequenced bee gut symbionts have revealed multiple genes that are candidates for determining host specificity. “

Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics – Philipp Engel – PLOS Genetics

“In both species, the divergence of 16S rRNA loci appears to have been curtailed by frequent recombination within populations, while other genomic regions have continuously diverged. “

Bacterial Communities in the Gut and Reproductive Organs of Bactrocera minax (Diptera: Tephritidae) Based on 454 Pyrosequencing – Ailin Wang – PLOS ONE

“We used a 454 pyrosequencing technology to study in depth the microbial communities associated with gut and reproductive organs of Bactrocera minax.”

Invertebrate microbiome

Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection – Ana Lokmer and Karl Mathias Wegner – ISME Journal

“We monitored oyster survival and repeatedly collected hemolymph of dead and alive animals to determine the microbiome composition by 16s rRNA gene amplicon pyrosequencing. “

Plant microbiome

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest – Steven W. Kembel – PNAS

“In this study we sequenced bacterial communities present on tree leaves in a neotropical forest in Panama, to quantify the poorly understood relationships between bacterial biodiversity on leaves (the phyllosphere) vs. host tree attributes. “

Litter decomposition and soil microbial community composition in three Korean pine (Pinus koraiensis) forests along an altitudinal gradient – Yong Zhou – Plant and Soil

“Single- and mixed-species litter decomposition rates were determined by the litterbag method and soil microbial community composition was characterized by PLFAs.”

Soil microbiome

Pyrosequencing assessment of rhizosphere fungal communities from a soybean field – Akifumi Sugiyama – Canadian Journal of Microbiology

“This study utilized 454 pyrosequencing to analyze rhizosphere fungal communities during soybean growth.”

Water microbiome

Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years – Jacob A Cram – ISME Journal

“Biodiversity appeared to be driven partially by exchange of microbes between depths and was highest when communities were changing slowly over time.”

Long-term effects of the antibacterial agent triclosan on marine periphyton communities – Martin Eriksson – PeerJ PrePrints

“Pollution-Induced Community Tolerance (PICT) was observed for algae and cyanobacteria at 100 nM TCS and higher.”

Review: Master recyclers: features and functions of bacteria associated with phytoplankton blooms – Alison Buchan – Nature Reviews Microbiology

“In this Review, we discuss the central role that these bacteria have in transforming phytoplankton-derived organic matter and thus in biogeochemical nutrient cycling.”

Built environment microbiome

Diversity and dynamics of the indoor air microbiome in an urban subway network – Marcus H. Y. Leung – Applied and Environmental Microbiology

“Targeting the 16S rDNA V4 region, extensive taxonomic diversity was found, with the most common bacterial genera in the subway environment among those seen associated on skin.”

Microbial Odor Profile of Polyester and cotton clothes after a fitness session – Chris Callewaert – Applied and Environmental Microbiology

“A dissimilar bacterial growth was found in cotton versus synthetic clothing textiles. Micrococci were isolated in almost all synthetic shirts and were detected almost solely on synthetic shirts by means of DGGE fingerprinting. “

Food microbiology

Vegetable microbiomes: is there a connection among opportunistic infections, human health and our ‘gut feeling’? – Gabriele Berg – Microbial Biotechnology

“Based on these results, we discuss the question if vegetables can serve as a source of infection for immunocompromised individuals as well as possible solutions to avoid outbreaks. “

Assessment of the bacterial and fungal diversity in home-made yoghurts of Xinjiang of China by pyrosequencing – Haiyan Xu – Journal of the Science of Food and Agriculture

“The bacterial and fungal community diversity of 22 home-made yoghurt samples from Zhaosu and Tekesi counties of Xinjiang in China were analyzed with pyrosequencing. “

Victory, life-sciences firm team up to detect bacteria that can spoil beer’s taste – Diane Mastrull – Philly.com

“The list is long of the perfect accompaniments to beer: hot dogs, pizza, peanuts, and pretzels, to name just a few. Most definitely not on that list: pediococcus and lactobacillus. Consider them beer buzzkills.”

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Non-human microbiome, August 26, 2014

Microbiomes of rabbits, exercising mice, fish, bees, beetles, forest soil after a hurricane (a simulated one!), water, and – why not – the whole world.

Mammal microbiome 

* Changes in Cecal Microbiota and Mucosal Gene Expression Revealed New Aspects of Epizootic Rabbit Enteropathy – Christine Bäuerl – PLOS ONE

“Cecal microbiota was characterized in three rabbit groups (ERE-affected, healthy and healthy pretreated with antibiotics), followed by transcriptional analysis of cytokines and mucins in the cecal mucosa and vermix by q-rtPCR.”

Effect of Intestinal Microbiota on Exercise Performance in Mice – Hsu, Yi-Ju – Journal of Strength & Conditioning Research

“We investigated the association of intestinal bacteria and exercise performance in specific pathogen-free (SPF), germ-free (GF), and Bacteroides fragilis (BF) gnotobiotic mice.”

Fish microbiome

Non invasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches – Taiga Asakura – PeerJPrePrints

“We evaluated the microbial diversity in various fish species collected from Japan’s coastal waters using next-generation sequencing, followed by evaluation of the effects of feed type on co-metabolic modulations in fish-microbial symbiotic ecosystems in laboratory-scale experiments.”

Comparative Analysis of the Intestinal Bacterial Communities in Different Species of Carp by Pyrosequencing – Tongtong Li – Microbial Ecology

“In this study, we compared the bacterial communities harboured in the intestines and in the rearing water of grass carp (Ctenopharyngodon idellus), crucian carp (Carassius cuvieri), and bighead carp (Hypophthalmichthys nobilis), by using 454-pyrosequencing with barcoded primers targeting the V4 to V5 regions of the bacterial 16S rRNA gene. “

Insect microbiome

* Microbial Communities of Three Sympatric Australian Stingless Bee Species – Sara D. Leonhardt – PLOS ONE

“Here, we characterized the microbiota of three Australian stingless bee species (Apidae: Meliponini) of two phylogenetically distant genera (Tetragonula and Austroplebeia). “

Metamicrobiomics in herbivore beetles of the genus Cryptocephalus (Chrysomelidae): toward the understanding of ecological determinants in insect symbiosis – Matteo Montagna – Insect Science

“The microbiota of C. acquitanus and C. marginellus (Calanques) were the most diverse (over 100 OTUs), while that from C. zoiai yielded less bacterial diversity (45 OTUs).”

Invertebrate microbiome

Antioxidant Activity of Bacteria Associated with the Marine Sponge Tedania anhelans – Dhivya Balakrishnan – Indian Journal of Microbiology

In the present study, several Bacillus sp. with just 97 % similarity with its closest match in Gen Bank were isolated, and found to show free radical scavenging activity”

Soil and sediment microbiome

Effects of a simulated hurricane disturbance on forest floor microbial communities – Sharon A. Cantrell – Forest Ecology and Management

“We studied the independent and interactive hurricane effects of canopy openness and debris deposition on the relative abundance and diversity of microorganisms in soil and leaf litter using ester link fatty acids methyl esters (EL-FAME) analysis, and terminal restriction fragment length polymorphism (TRFLP) profile.”

Spatiotemporal changes in arbuscular mycorrhizal fungal communities under different nitrogen inputs over a 5-year period in intensive agricultural ecosystems on the North China Plain – Wei Liu – FEMS Microbiology Ecology

“Terminal restriction fragment length polymorphism and clone sequencing were used to analyse the AMF community. “

A Long-Term Cultivation of an Anaerobic Methane-Oxidizing Microbial Community from Deep-Sea Methane-Seep Sediment Using a Continuous-Flow Bioreactor – Masataka Aoki – PLOS ONE

“Phylogenetic analyses demonstrated that phylogenetically diverse Archaea and Bacteria grew in the bioreactor.”

Water microbiome

Characterization of Wastewater Treatment Plant Microbial Communities and the Effects of Carbon Sources on Diversity in Laboratory Models – Sangwon Lee – PLOS ONE

“…using PhyloChip 16S-rRNA-gene targeting microarrays, we compared the compositions of sampled communities to those of inocula propagated in the laboratory in simulated wastewater conditionally amended with various carbon sources”

* Bacterial and archaeal communities in Lake Nyos (Cameroon, Central Africa) – Rosine E. Tiodjio – Nature Scientific Reports

“Bacterial and archaeal communities were profiled using Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) approach of the 16S rRNA gene. “

Comparative survey of bacterial and archaeal communities in high arsenic shallow aquifers using 454 pyrosequencing and traditional methods – Ping Li – Ecotoxicology

“A survey of bacterial and archaeal community structure was carried out in 10 shallow tube wells in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia by 16S rRNA gene based two-step nested PCR-DGGE, clone libraries and 454 pyrosequencing. “

* Biogeographic Congruency among Bacterial Communities from Terrestrial Sulfidic Springs – Brendan Headd – Frontiers in Microbiology

“Complementary Sanger sequencing and 454 pyrosequencing of 16S rRNA genes retrieved five proteobacterial classes, and Bacteroidetes, Chlorobi, Chloroflexi, and Firmicutes phyla from all springs, which suggested the potential for a core sulfidic spring microbiome. “

The whole world microbiome

* The Earth Microbiome project: successes and aspirations – Jack A Gilbert, Janet K Jansson, and Rob Knight – BMC Biology

“ ‘Knight and Gilbert literally talk about sampling the entire planet. It is ludicrous and not feasible – yet they are doing it’”

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