13 July, 2019

Good morning everyone!

Today’s digest is kind of diverse (as always), with great papers about women microbiome, sardines gut microbiome, a great review about soil aggregates and, corals microbiomes and much more. Be sure to read the first paper right down here- The Conceptual Ecology of the Human Microbiome. Have a great weekend!

Human microbiome

**From June 2019, but a must-read nonetheless: The Conceptual Ecology of the Human Microbiome, Morar and Bohannan, Q. R. Biology

Interaction between the nasal microbiota and S. pneumoniae in the context of live-attenuated influenza vaccine, Wouter A. A. de Steenhuijsen Piters, Nature Communications

Selected Immunological Mediators and Cervical Microbial Signatures in Women with Chlamydia trachomatis Infection, Simone Filardo, mSystems

Discovery of potential genes contributing to the biosynthesis of short-chain fatty acids and lactate in gut microbiota from systematic investigation in E. coli, Chunhua Zhao, MPMI

Secondary bile acid ursodeoxycholic acid (UDCA) alters weight, the gut microbiota, and the bile acid pool in conventional mice, Jenessa A. Winston, bioRxiv

Microbiota supplementation with Bifidobacterium and Lactobacillus modifies the preterm infant gut microbiota and metabolome, Cristina Alcon-Giner, bioRxiv

Animal microbiome

A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians, Lu Wu, mSystems

Contribution of gut microbiota to metabolism of dietary glycine betaine in mice and in vitro colonic fermentation, Ville M. Koistinen, Microbiome

Coral bacterial community structure responds to environmental change in a host-specific manner, Maren Ziegler, Nature Communications

Soil microbiome

**Mini-review: Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales, Regina L. Wilpiszeski , AEM

Continuous monoculture shapes root and rhizosphere fungal communities of corn and soybean in soybean cyst nematode-infested soil, Noah Strom, Phytobiomes

Engineered root bacteria release plant-available phosphate from phytate, Christine N. Shulse, AEM

Diversity and Characterization of Oomycetes Associated with Corn Seedlings in Michigan, J. A. Rojas, Phytobiomes

Environmental microbiome

Diverse, abundant and novel viruses infecting “unculturable” but abundant marine bacteria, Zefeng Zhang, bioRxiv

Biocide resistance and transmission of Clostridium difficile spores spiked onto clinical surfaces from an American healthcare facility, Calie Dyer, AEM

Microbiome in the news

Lab Startup uBiome Laying Off About Half of Global Workforce

Microbiome Repairing Food for Malnourished Children Beats Current Therapy

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Non-human microbiome digest, October 27, 2014

Microbiomes of camels, cheetahs, jackals, birds and reptiles, limpets, corals, plant roots, soils, and sea water.

Animal microbiome

* In-depth diversity analysis of the bacterial community resident in the camel rumen – Javad Gharechahi – Systematic and Applied Microbiology

“In this study, 16S rRNA gene amplicon pyrosequencing was applied in order to explore the structure of the bacterial community inhabiting the camel rumen.”

Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level – Sebastian Menke – Frontiers in Microbiology

“Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas).”

Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia – Marius Vital – ISME Journal

“We investigated the butyrate-producing community in hindgut-fermenting Mammalia (n=38), Aves (n=8) and Reptilia (n=8) using a gene-targeted pyrosequencing approach of the terminal genes of the main butyrate-synthesis pathways”

Decadal changes in common reef coral populations and their associations with algal symbionts (Symbiodinium spp.) – Timothy R. McClanahan – Marine Ecology

“Decadal populations changes in four coral taxa and their patterns of association with algal symbionts (Symbiodinium spp. – 10 years of sampling) were examined on Kenyan back reefs over a period of climatic disturbances (1991−2009). “

Metaphylogenomic and Potential Functionality of the Limpet Patella pellucida’s Gastrointestinal Tract Microbiome – Magda Dudek – International Journal of Molecular Sciences

“This study investigated the microbial diversity associated with the digestive tract of the seaweed grazing marine limpet Patella pellucida.”

Plant microbiome

* Distinct root-associated bacterial communities on three wild plant species growing in a common field – Kristin Aleklett – PeerJ Preprints

“We sampled endophytic and epiphytic bacteria in root tissues from a population of a wild, clonal plant… as well as two neighboring plant species … to determine if plant species hosted unique root microbiota”

The fungal leaf endophyte Paraconiothyrium variabile specifically metabolizes the host-plant metabolome for its own benefit – Yuan Tian – Phytochemistry

“..we have investigated the action of the endophytic fungus Paraconiothyrium variabile, isolated from the leaves of Cephalotaxus harringtonia, on the secondary metabolome of the host-plant. “

Soil microbiome

Late winter under ice pelagic microbial communities in the high Arctic Ocean and the impact of short-term exposure to elevated CO2 levels – Adam Monier – Frontiers in Microbiology

“Phylogenetic diversity was greater in the attached fraction compared to the free-living fraction in situ, in the controls and in the treatments.”

The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys – Catarina M. Magalhães – Frontiers in Microbiology

“Here we showed that AOB and AOA amoA gene diversity was generally low; only four AOA and three AOB operational taxonomic units (OTUs) were identified from a total of 420 AOA and AOB amoA clones.”

Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils – Akihiro Koyama – Frontiers in Microbiology

“Fertilization significantly altered overall bacterial community composition and reduced evenness, to a greater degree in organic than mineral soils, and in the 1989 compared to the 2006 site.”

Effect of volatile organic compounds absorbed to fresh biochar on survival of Bacillus mucilaginosus and structure of soil microbial communities – Daquan Sun – Journal of Soils and Sediments

“The structure of a soil microbial community incubated in biochar was examined via denaturing gradient gel electrophoresis (DGGE). “

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community – Uli Klümper – ISME Journal

“We identified transfer to many different recipients belonging to 11 different bacterial phyla. “

Water microbiome

Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities – Chris L Dupont – ISME Journal

“Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses.”

Aerobic methanotrophic communities at the Red Sea brine-seawater interface – Rehab Z. Abdallah – Frontiers in Microbiology

“The current study analyzed the aerobic free–living methane-oxidizing bacterial communities that potentially contribute to methane oxidation at the brine-seawater interfaces of the three aforementioned brine pools, using metagenomic pyrosequencing, 16S rRNA pyrotags and pmoA library constructs. “

Bacterial community structure is indicative of chemical inputs in the Upper Mississippi River – Christopher Staley – Frontiers in Microbiology

“Bacterial communities were characterized by Illumina sequencing of the V6 region of 16S rDNA and compared to >40 chemical and nutrient concentrations. “

Semiconductor Sequencing Reveals the Diversity of Bacterial Communities in an Amazonian Reservoir – Diego Assis das Graças – Aquatic Science and Technology

“In this study, we used a next-generation sequencing platform, the Ion Torrent Personal Genome Machine, and employed a barcode library to investigate the bacterial diversity along a 70-m deep water column in the proximity of the dam. “

Seasonal changes of microbial communities in two shallow peat bog lakes – Sylwia Lew – Folia Microbiologica

“We investigated the seasonal dynamics of the microbial community in two small peat bog lakes, Kuźnik Olsowy and Kuźnik Bagienny, located in western Poland.”

Bioreactor microbiome

Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response – Igor Y Oshkin – ISME Journal

“We report observations on the dynamics of bacterial communities in response to methane stimulus in laboratory microcosm incubations prepared with lake sediment samples.”

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