Tag Archives: coral microbiome

April 17, 2024

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Good morning and welcome to another MicrobiomeDigest! Did you know that one group of scientists is using video games to crowdsource puzzle solutions to improve microbiome research? What a neat way to approach citizen science! On deck today we have a study about pesticide exposure and the gut microbiome, a review of the emerging field of skin microbiome-focused cosmetics, insights into the viral diversity of bats and rodents in East Africa, an editorial exploring research into microbial symbiosis through the lens of modern tools, and more.

Human microbiome

Modulation of the gut microbiome and Firmicutes phylum reduction by a nutraceutical blend in the obesity mouse model and overweight humans: A double-blind clinical trial – Victor Nehmi-Filho et al – Food Science & Nutrition

Ambient long-term exposure to organophosphorus pesticides and the human gut microbiome: an observational study – Keren Zhang et al – BMC Environmental Health

[REVIEW] Skin Deep: The Potential of Microbiome Cosmetics – Ju Hee Han & Hei Sung Kim – Journal of Microbiology

Metabolic Interaction Between Host and the Gut Microbiota During High-Fat Diet-Induced Colorectal Cancer – Chaeeun Lee et al – Journal of Microbiology

Longitudinal microbiome changes in children exposed to proton pump inhibitors – Jason Yanjia Zhang et al – Clinical and Translational Gastroenterology

High temperature and humidity in the environment disrupt bile acid metabolism, the gut microbiome, and GLP-1 secretion in mice – Song Chen et al – Nature Communications Biology

Plant, root, and soil microbiome

Exploring the interplay between the core microbiota, physicochemical factors, agrobiochemical cycles in the soil of the historic tokaj mád wine region – Judit Remenyik et al – PLOS One

[PREPRINT] Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands – Emily Bechtold et al – bioRxiv

An in-depth evaluation of metagenomic classifiers for soil microbiomes – Niranjana Rose Edwin – BMC Environmental Microbiome

Animal microbiome

Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation – Daxi Wang et al – BMC Microbiome

Association between the gut microbiome and carotenoid plumage phenotype in an avian hybrid zone – Marcella D. Baiz et al – Proceedings of the Royal Soc. of Biological Sciences

Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs – Juan M Ortiz Sanjuan et al – BMC Animal Microbiome

Integrated analysis of gut metabolome, microbiome, and exfoliome data in an equine model of intestinal injury – C.M. Whitfield-Gargile et al – BMC Microbiome

Responses of the coral reef cryptobiome to environmental gradients in the Red Sea – Rodrigo Villalobos et al – PLOS One

Microbial ecology

[EDITORIAL] Symbiosis: In search of a deeper understanding – Thomas A Richards & Nancy A Moran – PLOS Biology

Bioinformatics & techniques

Randomized feature selection based semi-supervised latent Dirichlet allocation for microbiome analysis – Namitha Pais et al – Nature Scientific Reports

Improving microbial phylogeny with citizen science within a mass-market video game – Roman Sarrazin-Gendron et al – Nature Biotechnology

April 10, 2024

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Good morning microbiome enthusiasts! Today’s MD is on the shorter side but we still have some really interesting articles picked out for you to peruse – including a microbiome-sparing targeted P. aeruginosa compound, effective probiotics for restoring a healthy coral microbiome, and a study characterizing the microbiome of metastatic cancers in over 4,000 biopsies. Plus, don’t forget that April’s Microbiome Virtual International Forum is happening next week!

Human Microbiome

Longitudinal multi-omics analysis uncovers the altered landscape of gut microbiota and plasma metabolome in response to high altitude – Yang Han et al – BMC Microbiome

Illuminating microflora: shedding light on the potential of blue light to modulate the cutaneous microbiome – Hannah J Serrage et al – Frontiers in Cellular and Infection Microbiology

Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC – Rauf Salamzade et al – Microbial Genomics

A pan-cancer analysis of the microbiome in metastatic cancer – Thomas Battaglia et al – Cell

A Lacticaseibacillus rhamnosus secretome induces immunoregulatory transcriptional, functional and immunometabolic signatures in human THP-1 monocytes – Michael P. Jeffrey et al – Nature Scientific Reports

The oral cavity and intestinal microbiome in children with functional constipation – Monika Kwiatkowska et al – Nature Scientific Reports

Characterization of the gut bacterial and viral microbiota in latent autoimmune diabetes in adults – Casper S. Poulsen et al – Nature Scientific Reports

Colonization during a key developmental window reveals microbiota-dependent shifts in growth and immunity during undernutrition – Yadeliz A. Serrano Matos et al – BMC Microbiome

Animal models

Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice – Tatsuya Dokoshi et al – Nature Communications

A folate inhibitor exploits metabolic differences in Pseudomonas aeruginosa for narrow-spectrum targeting – Connor Chain et al – Nature Microbiology

Animal microbiome

A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience – Lauren F. Messer et al – Nature Communications

Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment – Nathalia Delgadillo-Ordoñez et al – Nature Communications Biology

Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation – Daxi Wang et al – BMC Microbiome

Plant, root & soil microbiome

Root volatiles manipulate bacterial biofilms – Waseem Raza & Gaofei Jiang – Nature Ecology & Evolution

Analysis of endophytic bacterial diversity in seeds of different genotypes of cotton and the suppression of Verticillium wilt pathogen infection by a synthetic microbial community – Chong-Die Wu et al – BMC Plant Biology

Bioinformatics & tools

Holomics – a user-friendly R shiny application for multi-omics data integration and analysis – Katharina Munk et al – BMC Bioinformatics

March 6, 2024

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Vaginal Microbiome

Modeling Healthy and Dysbiotic Vaginal Microenvironments in a Human Vagina-on-a-Chip – Aakanksha Gulati et al – JoVE Bioengineering

Cancer microbiome

Multi-omics analysis elucidates the relationship between intratumor microbiome and host immune heterogeneity in breast cancer – Jia Li et al – Microbiology Spectrum

Human gut microbiome

Protein combined with certain dietary fibers increases butyrate production in gut microbiota fermentation – Rachel Jackson et al – Food & Function

A human milk oligosaccharide prevents intestinal inflammation in adulthood via modulating gut microbial metabolism – Kasey M. Schalich et al – mBio

Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation – Leonardo Mancabelli et al – mSystems

Cadaver microbiome

Decomposer communities are universal in death – Michael S. Strickland – Nature Microbiology

Animal microbiome

The coral microbiome in sickness, in health and in a changing world – Christian R. Voolstra et al – Nature Reviews Microbiology

The effects of hydrolyzed protein on macronutrient digestibility, fecal metabolites and microbiota, oxidative stress and inflammatory biomarkers, and skin and coat quality in adult dogs – Clare Hsu et al – Journal of Animal Science

Host starvation and in hospite degradation of algal symbionts shape the heat stress response of the Cassiopea-Symbiodiniaceae symbiosis – Gaëlle Toullec et al – BMC Microbiome

An engineered bacterial symbiont allows noninvasive biosensing of the honey bee gut environment – Audam Chhun et al – PLOS Biology

From phyllosphere to insect cuticles: silkworms gather antifungal bacteria from mulberry leaves to battle fungal parasite attacks – Pengfei Zhao et al – BMC Microbiome

Phages and viruses

Discovery and characterization of novel DNA viruses in Apis mellifera: expanding the honey bee virome through metagenomic analysis – Dominika Kadlečková et al – mSystems

Taxonomic difference in marine bloom-forming phytoplanktonic species affects the dynamics of both bloom-responding prokaryotes and prokaryotic viruses – Hiroaki Takebe et al – mSystems

Plant, root, and soil microbiome

Microbiome sequencing revealed the abundance of uncultured bacteria in the Phatthalung sago palm-growing soil – Pumin Nutaratat et al – PLOS ONE

The rhizosphere microbiome reduces the uptake of arsenic and tungsten by Blechnum orientale by increasing nutrient cycling in historical tungsten mining area soils – Xiaolong Lan et al – Science of the Total Environment

Non-Microbiology/Science Communication

[PREPRINT] Sci-comm “behind the scenes”: Gendered narratives of scientific outreach activities in the life sciences – Perry G. Beasley-Hall et al – bioRxiv

September 24, 2022

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Human and General Microbiome

Systemic antibody responses against human microbiota flagellins are overrepresented in chronic fatigue syndrome patients – Thomas Vogl – Science Advances

Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants – Oluwaseun Rume-Abiola Oyewole – Microbiome

Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis – Victoria M Martin – Microbiome

Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism – Peter Spanogiannopoulos – Nature Microbiology

Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome – Rebecca C Simpson – Nature Medicine

Advances in the gut microbiome and mood disorders – Sabrina Mörkl – Current Opinion in Psychiatry

Review: Modulation of the intestinal microbiota impacts the efficacy of immunotherapy in cancer patients – A recent literature survey – Stella Ziegler – European Journal of Microbiology & Immunology

Animal Microbiome

Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome – Tina Keller-Costa – Microbiome

Intestinal microbiome-mediated resistance against vibriosis for Cynoglossus semilaevis – Qian Zhou – Microbiome

Plant Microbiome

Response of soil microecology to different cropping practice under Bupleurum chinense cultivation – Li Liu – BMC Microbiology

Community Assembly of Fungi and Bacteria along Soil-Plant Continuum Differs in a Zoige Wetland – Jie Li – Microbiology Spectrum

Review: Investigating plant-microbe interactions within the root – Yuniar Devi Utami – Archives of Microbiology

Food Microbiome

Geographically Associated Fungus-Bacterium Interactions Contribute to the Formation of Geography-Dependent Flavor during High-Complexity Spontaneous Fermentation – Yuwei Tan – Microbiology Spectrum

More Microbes

A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesis – Simon Mills – NPJ Biofilms and Microbiomes

Bioinformatics and Microbiome Analysis

MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes – Lin Zhang – PLoS Computational Biology