Tag Archives: Fungi

March 27, 2024

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Built environment microbiome

Genomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station – Pratyay Sengupta et al – BMC Microbiome

An overview of the bacterial microbiome of public transportation systems-risks, detection, and countermeasures – Yen-Tran Ly et al – Frontiers in Public Health

Bioinformatics and computational methods

Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics – Enhui Wu et al – BMC Microbiome

Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes – Jasper van Bemmelen et al – BMC Bioinformatics

Multi-omic integration of microbiome data for identifying disease-associated modules – Efrat Muller – Nature Communications

Animal experiments

Gender affirming hormone therapy preserves skeletal maturation in young mice via the gut microbiome – Subhashis Pal et al – Journal of Clinical Investigation

Microbiota-derived indoles alleviate intestinal inflammation and modulate microbiome by microbial cross-feeding – Gang Wang et al – BMC Microbiome

[PREPRINT] Akkermansia muciniphila identified as key strain to alleviate gut barrier injury through Wnt signaling pathway – Xin Ma et al – bioRxiv

Microbiota from human infants consuming secretors or non-secretors mothers’ milk impacts the gut and immune system in mice – Manoj Gurung et al – mSystems

Plant and soil microbiome

Lose-lose consequences of bacterial community-driven invasions in soil – Xipeng Liu & Joana Falcão Salles – BMC Microbiome

Manipulating the physical distance between cells during soil colonization reveals the importance of biotic interactions in microbial community assembly – Sana Romdhane et al – BMC Environmental Microbiome

Soil fungal communities varied across aspects of restored grassland in former mining areas of the Qinghai-Tibet Plateau – Xioaqing Li et al – PLOS One

Animal microbiome

Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota – Marie Bouilloud et al – BMC Animal Microbiome

Bats, Bacteria, and Bat Smell V.2.0: Repeatable Sex-Specific Differences in Scent Organ Microbiota – Öncü Maraci et al – Microbial Ecology

Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs – Jacoba I. Bromfield et al – mSphere

Phylosymbiosis and metabolomics resolve phenotypically plastic and cryptic sponge species in the genus Agelas across the Caribbean basin – M.S. Pankey et al – Molecular Ecology

Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition – C. E. Dubé et al – Nature Communications

March 20, 2024

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Human gut and general microbiome

Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition – Hao-Wei Chang et al – Nature Microbiology

Outcomes after Fecal Microbiota Transplantation in combination with Bezlotoxumab for Inflammatory Bowel Disease and Recurrent C. difficile Infection – Jessica R Allegretti – American Journal of Gastroenterology

Diosmin alleviates ulcerative colitis in mice by increasing Akkermansia muciniphila abundance, improving intestinal barrier function, and modulating the NF-κB and Nrf2 pathways – Maha Badr Salem et al – Cell Heliyon

Gut microbiota profiling in obese children from Southeastern China – Jingjing Wang et al – BMC Pediatrics

A flexible high-throughput cultivation protocol to assess the response of individuals’ gut microbiota to diet-, drug-, and host-related factors – Janina N Zünd et al – ISME Communications

Animal experiments

Intact lung tissue and bronchoalveolar lavage fluid are both suitable for the evaluation of murine lung microbiome in acute lung injury – Lijun Zheng et al – BMC Microbiome

Microbiota-derived indoles alleviate intestinal inflammation and modulate microbiome by microbial cross-feeding – Gang Wang et al – BMC Microbiome

Plant, soil, and environmental microbiome

Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development – Chao Xiong et al – mSystems

Bacterial communities associated with an island radiation of lichen-forming fungi – Miguel Blázquez et al – PLOS ONE

Built environment microbiome

Early assessment of fungal and oomycete pathogens in greenhouse irrigation water using Oxford nanopore amplicon sequencing – Enoch Narh Kudjordjie et al – PLOS One

The composition of the bacterial communities collected from the PM10 samples inside the Seoul subway and railway station – Shambhavi Sharma et al – Nature Scientific Reports

Bioinformatics

Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values – Seungjun Ahn & Somnath Datta – BMC Bioinformatics

Beneficial microbes & microbial metabolites
Natural intestinal metabolite xylitol reduces BRD4 levels to mitigate renal fibrosis – Zhouke Tan et al – Clinical and Translational Science

Probiotics supplementation during pregnancy or infancy on multiple food allergies and gut microbiota: a systematic review and meta-analysis – Lan Jiang et al – Nutrition Reviews

Non-Microbiome Microbiology

Koch’s curse: How models of extreme pathology bias studies of host–pathogen interactions – Kalyan K. Dewan & Eric T. Harvill – PLOS Pathogens

July 3, 2023

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Human and General Microbiome

Bacterial Community Modifies Host Genetics Effect on Early Childhood Caries – F Blostein – Journal of Dental Research

Clostridioides difficile infection in infants: a case report and literature review – Zhirong Li – Gut Pathogens

The microbiota of pregnant women with SARS-CoV-2 and their infants – Heidi K Leftwich – Microbiome

Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles – James T Morton – Nature Neuroscience

Human gut bacteria tailor extracellular vesicle cargo for the breakdown of diet- and host-derived glycans – Mariana G Sartorio – PNAS

Site-specialization of human oral Gemella species – Julian Torres-Morales – Journal of oral Microbiology

Review: Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy – Andrew Maltez Thomas – Nature Reviews. Clinical Oncology

Review: Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics – Teija Ojala – Trends in Genetics

Review: Bacteria from the gut influence the host micronutrient status – Dorgeles Kouakou Dje Kouadio – Critical Reviews in Food Science and Nutrition

Beneficial Microbes and Compounds

Milk kefir alters fecal microbiota impacting gut and brain health in mice – Mariana de Fátima Albuquerque Pereira – Applied Microbiology and Biotechnology

Review: Calorie restriction mimetic drugs could favorably influence gut microbiota leading to lifespan extension – Tomoya Shintani – GeroScience

Are probiotics, prebiotics, and synbiotics beneficial in primary thyroid diseases? A systematic review with meta-analysis – Karolina Zawadzka – Annals of Agricultural and Environmental Medicine

Akkermansia muciniphila and Lactobacillus plantarum ameliorate systemic lupus erythematosus by possibly regulating immune response and remodeling gut microbiota – Mengchen Guo – mSphere

Effect of prebiotics, probiotics, synbiotics on depression: results from a meta-analysis – Qin Zhang – BMC Psychiatry

Animal Microbiome and Animal Model Microbiome

Patterns and determinants of the global herbivorous mycobiome – Casey H Meili – Nature Communications

Resistant starches from dietary pulses modulate the gut metabolome in association with microbiome in a humanized murine model of ageing – Saurabh Kadyan – Scientific Reports

The microbial composition of larval airways from Drosophila melanogaster differ between specimens from laboratory and natural habitats – Hanna Angstmann – Environmental Microbiome

Plant Microbiome

Different Techniques reveal the Difference of Community Structure and Function of Fungi from Root and Rhizosphere of Salvia miltiorrhiza Bunge – C Li – Plant Biology (Stuttgart, Germany)

Rhizobial nitrogen fixation efficiency shapes endosphere bacterial communities and Medicago truncatula host growth – Beatriz Lagunas – Microbiome

Core community drives phyllosphere bacterial diversity and function in multiple ecosystems – Ran Xue – The Science of the Total Environment

Environmental Microbiome

A Metagenomic Time-Series Approach to Assess the Ecological Stability of Microbial Mats in a Seasonally Fluctuating Environment – David Madrigal-Trejo – Microbial Ecology

Microbiome Research: Resources, Tools and Techniques

MetaPro: a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities – Billy Taj – Microbiome

Supervised learning and model analysis with compositional data – Shimeng Huang – PLoS Computational Biology

Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities – Qi Wang – Bioinformatics

Creation of a milk oligosaccharide database, MilkOligoDB, reveals common structural motifs and extensive diversity across mammals – Sierra D Durham – Scientific Reports

Review: Genetic Engineering of Resident Bacteria in the Gut Microbiome – Jack Arnold – Journal of Bacteriology

Review: Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA – Lin Yang – Nature Protocols

October 3, 2022

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Human and General Microbiome

Mucus-degrading Bacteroides link carbapenems to aggravated graft-versus-host disease – Eiko Hayase – Cell

Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions – Lian Narunsky-Haziza – Cell

A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors – Anders B Dohlman – Cell

Gut microbiota of hepatitis B virus-infected patients in the immune-tolerant and immune-active phases and their implications in metabolite changes – Ya-Nan Li – World Journal of Gastroenterology

Streptococcus mutans promotes tumor progression in oral squamous cell carcinoma – Ming-Shao Tsai – Journal of Cancer

Short-chain fatty acid concentrations in the incidence and risk-stratification of colorectal cancer: a systematic review and meta-analysis – Ehsan Alvandi – BMC Medicine

Mycobacterium potentiates protection from colorectal cancer by gut microbial alterations – Yu-Mi Kim – Immunology

Nutrition, Immunosenescence, and Infectious Disease: An Overview of the Scientific Evidence on Micronutrients and on Modulation of the Gut Microbiota – Philip C Calder – Advances in Nutrition 

Unfermented β-fructan fibers fuel inflammation in select inflammatory bowel disease patients – Heather K Armstrong – Gastroenterology

Machine-learning algorithms for asthma, COPD, and lung cancer risk assessment using circulating microbial extracellular vesicle data and their application to assess dietary effects – Andrea McDowell – Experimental & Molecular Medicine

Microbiome ethics, guiding principles for microbiome research, use and knowledge management – Lene Lange – Environmental Microbiome

Review: The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly – Fen Zhang – The Lancet. Microbe

Beneficial Microbes and Compounds

Review: Tailoring gut microbiota with a combination of Vitamin K and probiotics as a possible adjuvant in the treatment of rheumatic arthritis: a systematic review – Luciana Pereira – Clinical Nutrition ESPEN

Dietary Isoflavones Alter Gut Microbiota and Lipopolysaccharide Biosynthesis to Reduce Inflammation – Sudeep Ghimire – Gut Microbes

Bacteroides thetaiotaomicron rough-type lipopolysaccharide: The chemical structure and the immunological activity – Molly Dorothy Pither – Carbohydrate Polymers

Animal Microbiome

Study of cattle microbiota in different regions of Kazakhstan using 16S metabarcoding analysis – Aida Daugaliyeva – Scientific Reports

Microscopic marine invertebrates are reservoirs for cryptic and diverse protists and fungi – Corey C Holt – Microbiome

Plant Microbiome

Review: Microbiomes in agroecosystem: Diversity, function and assembly mechanisms – Chao Xiong – Environmental Microbiology Reports

Bioinformatics and Microbiome Analysis

Integrating Phylogenetic and Functional Data in Microbiome Studies – Gavin M Douglas – Bioinformatics 

Higher off-target amplicon detection rate in MiSeq v3 compared to v2 reagent kits in the context of 16S-rRNA-sequencing – Mari-Lee Odendaal – Scientific Reports

March 25, 2022

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Human gut microbiome

In Vitro and In Silico Based Approaches to Identify Potential Novel Bacteriocins from the Athlete Gut Microbiome of an Elite Athlete Cohort – Wosinska et al. Microorganisms

Cancer pharmacomicrobiomics: targeting microbiota to optimise cancer therapy outcomes – Ting et al. Gut

Human respiratory microbiome

Inhibition of lung microbiota-derived proapoptotic peptides ameliorates acute exacerbation of pulmonary fibrosis – D’Alessandro-Gabazza et al. Nature Communications

Probiotics

Gut microbiota and fermentation-derived branched chain hydroxy acids mediate health benefits of yogurt consumption in obese mice – Daniel et al. Nature Communications

Animal experiments

Gut microbiota determines the social behavior of mice and induces metabolic and inflammatory changes in their adipose tissue – Agranyoni et al. npj biofilms and microbiomes

The microbiota restrains neurodegenerative microglia in a model of amyotrophic lateral sclerosis – Cox et al. Microbiome

Water & Extremophile microbiome

Spatial organization of the kelp microbiome at micron scales – Ramirez-Puebla et al. Microbiome

Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light-harvesting mechanisms in glacier cryoconite – Murakami et al. Microbiome.

Virome

Phages and their satellites encode hotspots of antiviral systems – Rousset et al. Cell Host & Microbe

Fungi

Fungal sensing enhances neutrophil metabolic fitness by regulating antifungal Glut1 activity – Li et al. Cell Host & Microbe

The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors – Sharma et al. npj Biofilms and microbiomes

Bioinformatics

Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases – Armstrong et al. mSystems

March 1, 2022

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General microbiome

Phylogenomics, Epigenomics, Virulome, and Mobilome of Gram-negative Bacteria Co-resistant to Carbapenems and Polymyxins: A One-Health Systematic Review and Meta-analyses – Ramaloko et al. – Environmental Microbiology

Global diversity and distribution of mushroom-inhabiting bacteria – Gohar et al. – Environmental Microbiology Reports

Genomic Epidemiology Insights on NDM-Producing Pathogens Revealed the Pivotal Role of Plasmids on blaNDM Transmission – Dong et al. – Microbiology Spectrum

Multi-site human microbiome

Contributions of Human-Associated Archaeal Metabolites to Tumor Microenvironment and Carcinogenesis – Cai et al. – Microbiology Spectrum

Human respiratory microbiome

Early life inter-kingdom interactions shape the immunological environment of the airways – C Pattaroni et al. – Microbiome

Human gut microbiome

Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers – Coker et al. – Microbiome

Animal experiments

Development of a rational framework for the therapeutic efficacy of fecal microbiota transplantation for calf diarrhea treatment – Islam et al. – Microbiome

Animal microbiome

Comparative microbiome analysis of Diaphorina citri and its associated parasitoids Tamarixia radiata and Diaphorencyrtus aligarhensis reveals Wolbachia as a dominant endosymbiont – Ashraf et al. – Environmental Microbiology

Plant, root, and soil microbiome

Core arbuscular mycorrhizal fungi are predicted by their high abundance-occupancy relationship while host-specific taxa are rare and geographically structured – Kajihara et al. – New Phytologist

Embracing mountain microbiome and ecosystem functions under global change –  Wang et al. – New Phytologist

Nitrogen fertilization disrupts the temporal dynamics of arbuscular mycorrhizal fungal hyphae but not spore density and community composition in a wheat field – Babalola et al. – New Phytologist

Multiomics Reveals the Effect of Root Rot on Polygonati Rhizome and Identifies Pathogens and Biocontrol Strain – Pang et al. – Microbiology Spectrum

Seed microbiota revealed by a large-scale meta-analysis including 50 plant species – Simonin et al. – New Phytologist

Viewpoint: Plant–microbe eco-evolutionary dynamics in a changing world – Angulo et al. – New Phytologist

Stem traits, compartments, and tree species affect fungal communities on decaying wood – Yang et al. – Environmental Microbiology

Microplastics reduce soil microbial network complexity and ecological deterministic selection – Shi et al. – Environmental Microbiology

The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA – Rolando et al. – Microbiome

Water and extremophile

“Boom-and-busted-dynamics” of phytoplankton-virus interactions explain the paradox of the plankton – Flynn et al. – New Phytologist

Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts – Taylor et al. – Environmental Microbiology

Global 16S rRNA diversity of provannid snail endosymbionts from Indo-Pacific deep-sea hydrothermal vents – Breusing et al. – Environmental Microbiology Reports

Sources of protein diet differentially stimulate the gut and water microbiota under freshwater crayfish, marron (Cherax cainii, Austin 2002) culture – Foysal et al. – Environmental Microbiology Reports

September 15, 2021

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Today’s digest is fairly light. It includes an article focused on the protective role of bacterial endosymbionts on soil fungus, a preprint on the indoor environment as a source for human-associated anaerobes, and work demonstrating how protein biosensors can be used to track the effects osmotic stress on cells.

Happy reading!

General microbiome

Preprint: Comprehensive comparative genomics analysis for the emerging human pathogen Streptococcus dysgalactiae subsp. equisimilis (SDSE): A case study and Pan-subspecies genomic analysis – Saeb & Tayeb – bioRxiv

Preprint: The model arbuscular mycorrhizal fungus Rhizophagus irregularis harbours endosymbiotic bacteria with a highly reduce genome – Savary et al. – bioRxiv

Preprint: A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare? – van Vilet et al. – bioRxiv

Animal microbiome (for animals in the wild)

Differences in gut microbiome composition between sympatric wild and allopatric laboratory populations of omnivorous cockroaches – Tinker et al. – Frontiers in Microbiology

Plant, root, and soil microbiome

Bacterial endosymbionts protect beneficial soil fungus from nematode attack – Büttner et al. – Proceedings of the National Academy of Sciences of the United States of America

Built environment

Preprint: The indoor environment – A potential source for intact human-associated anaerobes – Pausan et al. – bioRxiv

Techniques

Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells – Cuevas-Velazquez et al. – Nature Communications

Mycobiome (Early 2021 Semi-Annual Fungal Microbiome Picks)

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It’s been a while, but its time to highlight some recent mycobiome articles!

Human mycobiome

Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities – Wu et al. – Microbiome

Gut mycobiota in immunity and inflammatory disease – Li et al. – Immunity

Response to fungal dysbiosis by gut-resident CX3CR1(+) mononuclear phagocytes aggravates allergic airway disease.- Li et al. – Cell Host Microbe. 

Human anti-fungal Th17 immunity and pathology rely on cross-reactivity against Candida albicans. – Bacher et al. – Cell. 

Prevalence and diversity of filamentous fungi in the airways of cystic fibrosis patients – a Dutch, multicentre study. – Engle et al. – J Cyst Fibros.

Early gut mycobiota and mother-offspring transfer. – Schei – Microbiome

Fungi form interkingdom microbial communities in the primordial human gut that develop with gestational age. – Willis et al – FASEB J.

Investigating colonization of the healthy adult gastrointestinal tract by fungi. – Auchtung et al. – mSphere.

CX3CR1+ mononuclear phagocytes control immunity to intestinal fungi. – Leonardi et al. – Science.

Commensal Candida albicans positively calibrates systemic Th17 immunological responses. – Shao et al – Cell Host Microbe. 

Macrophages maintain epithelium integrity by limiting fungal product absorption. – Chikina et al. – Cell.

Fungal symbionts produce prostaglandin E2 to promote their intestinal colonization. – Tan et al. – Front Cell Infect Microbiol.

The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL. – Aykut et al – Nature. 

Fungal microbiota dysbiosis in IBD. – Sokol et al – Gut.

Malassezia is associated with Crohn’s disease and exacerbates colitis in mouse models. – Limon et al – Cell Host Microbe.

Macrophage interactions with fungi and bacteria in inflammatory bowel disease. – Leonardi et al. – Curr Opin Gastroenterol.

Fungi participate in the dysbiosis of gut microbiota in patients with primary sclerosing cholangitis. – Lemoinne et al – Gut

Intestinal fungi contribute to development of alcoholic liver disease. – Yang et al – J Clin Invest.

Animal mycobiome

The gut mycobiome of healthy mice is shaped by the environment and correlates with metabolic outcomes in response to diet – Mims and Al Abdallah et al. – Communications Biology

Profound mycobiome differences between segregated mouse colonies do not influence Th17 responses to a newly introduced gut fungal commensal. – Doron et al. – Fungal Genet Biol.

Season, age, and sex affect the fecal mycobiota of free-ranging Tibetan macaques (Macaca thibetana). – Sun et al – Am J Primatol.

Altered immunity of laboratory mice in the natural environment is associated with fungal colonization. – Yeung et al – Cell Host Microbe. 

Mycobiome techniques

The fungal frontier: a comparative analysis of methods used in the study of the human gut mycobiome. – Huseyin et al. – Front Microbiol. 

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics – Karen et al. – Microbiome

Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing – Lind et al – Microbiome

Tiara: Deep learning-based classification system for eukaryotic sequences –  Karlicki et al – bioRxiv.org

~ Kent Willis, MD

November 2, 2019

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Good Weekend morning for all!

Today’s digest is highly rich with plant and soil microbiome papers (notice a great Science paper regarding soil suppressiveness phenomena), as well as bacterial metabolism papers and more. Have a great and peaceful weekend!

Human and animal microbiome

Studying the gut virome in the metagenomic era: challenges and perspectives, Sanzhima Garmaeva, BMC Biology

Cortisol-induced signatures of stress in the fish microbiome, Tamsyn M Uren Webster, bioRxiv

Influence of pig gut microbiota on Mycoplasma hyopneumoniae susceptibility, Meera Surendran Nair, Veterinary Research

Natural variation in the contribution of microbial density to inducible immune dynamics, Derrick Jent, Molecular Ecology

Metabolism

The ecology and evolution of microbial metabolic strategies, Djordje Bajic & Alvaro Sanchez, Curr. Opin. In. Biotechnology

Is the enzymatic hydrolysis of soil organic phosphorus compounds limited by enzyme or substrate availability?, K.A. Jarosch ,SBB

Plant and Soil microbiome

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome, Victor J. Carrio, Science

Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands, Selma Vieira, ISME

Analysis of soil bacterial communities associated with genetically modified drought-tolerant corn, Jose G. Ibaraa ,Applid Soil Ecology

Phyllosphere of Submerged Plants in Bathing Lakes as a Reservoir of Fungi Potential Human Pathogens, Anna Biedunkiewicz, Microbial Ecology

Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada, Jorge Cordero, Can. J. of Microbiology

Comparative metagenomics of two distinct biological soil crusts in the Tengger Desert, China, Jin-Yu Li , SBB

In planta bacterial multi-omics analysis illuminates regulatory principles underlying plant-pathogen interactions, Tatsuyas Nobori, bioRxiv

Air microbiome

Microbial communities in the tropical air ecosystem follow a precise diel cycle, Elena S. Gusareva, PNAS

Bioinformatics

Evaluating Bioinformatic Pipeline Performance for Forensic Microbiome Analysis, Kierra F. Kaszubinski, J. o. Forensic Sci.

April 16, 2019

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Good morning everyone! Today’s digest will deal a lot of disturbance in various ecosystems- starvation of the oral microbiota, forest fires, elevated CO2 levels and rising temperatures and more. Additionally, interesting pieces about science communication and education are recommended (bottom of the post).

Animal microbiome

Effects of diet on gut microbiota of soil collembolans– Qian Xiang- Science of the Total Environment

Diel population and functional synchrony of microbial communities on coral reefs– Winda Wegley-Kelly- Nature Communications

Human microbiome

Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota– Jonathon L. Baker- PNAS

Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation– Hyeonsoo Jeong- Scientific Reports

Dysbiosis patterns during re-induction/salvage versus induction chemotherapy for acute leukemia– Armin Rashidi- Scientific Reports

The personalized temporal dynamics of microbiome in the airways of cystic fibrosis patients– Giovanni Baci- bioRxiv

Plant, root and soil microbiome

Maize synthesized benzoxazinoids affect the host associated microbiome- Enoch Narh Kodjordjie- Microbiome

Utilization of carbon sources in the rice rhizosphere and non-rhizosphere soils with different long-term fertilization management– Tang H- J of Basic Microbiology

Effect of forest fire prevention treatments on bacterial communities associated with productive Boletus edulis sites- Olaya Mediavilla- Microbial Biotechnology

Effects of elevated temperature and elevated CO2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop– Linh T.T Nguyen- Science of the Total Environment

Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem– Hui Yao- Microbiome

Changes in fungal communities across a forest disturbance gradient– Lingling Shi- AEM

Water microbiome

Wetland sediments host diverse microbial taxa capable of cycling alchohols- Paula Dalcin Martins- AEM

Review- The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally– Gregory J. Dick- N. Reviews Microbiology

Bioinformatics

DeeplyEssential: A Deep Neural Network for Predicting Essential Genes in Microbes- Md Abid Hassan- bioRxiv

Microbiome news and science communication

Biotech company launches animal models with custom microbiome profiles

Microbial biotechnology for water treatment- A collection of high-quality websites (from Microbial Biotechnology)

Thematic series on scholarly communications in the digital age

The urgent need for microbiology literacy in society