After a brief hiatus, your Digest is back! After screening several hundred papers, progress seems to concentrate on a selected fields, including human gut microbiome and plant/soil microbiome. The WHO advocates for a global atlas of zoonotic viruses, a PDF link to a book volume full of application of microbiome engineering in agriculture, environmental protection and industry, and 16s rDNA primers can cross-react with mitochondrial sequences in eukaryotic cells. Last but not least, what can we all do to help young scientists, including ourselves, cope with immense pressure and distress?
General microbiology
Role of Partially Saturated Canthaxanthin and Ergosterol in the Survival of Aspergillus carbonarius Mutant at Extreme Acidic Condition – A. Kumar et al. – Microbiology
Coupled iron-microbial catalysis for CO2 hydrogenation with multispecies microbial communities – Elise Blanchet et al. – Chemical Engineering Journal
An integrated membrane bioreactor system with iron-dosing and side-stream co-fermentation for enhanced nutrient removal and recovery: System performance and microbial community analysis – Ruo-hong Li et al. – Bioresource Technology
The Microbiome and Population Health: Considerations to Enhance Study Design and Data Analysis in Observational and Interventional Epidemiology – Ryan T Demmer – American Journal of Epidemiology
Robust, linear correlations between growth rates and β-lactam–mediated lysis rates – Anna J. Lee et al. – PNAS USA
Human oral microbiome
Apical periodontitis: preliminary assessment of microbiota by 16S rRNA high throughput amplicon target sequencing – Federico Mussano and Ilario Ferrocino et al. – BMC Oral Health
Human gut microbiome
A feasibility study: association between gut microbiota enterotype and antibody response to seasonal trivalent influenza vaccine in adults – Nick Shortt and Hazel Poyntz et al. – Clinical & Translational Immunology
Gut-dependent microbial translocation induces inflammation and cardiovascular events after ST-elevation myocardial infarction – Xin Zhou, Jing Li and Junli Guo et al. – Microbiome
Book chapter: Influence of the Gut Microbiome on Immune Development During Early Life – Shankar S. Iyer and Richard S. Blumberg – Physiology of the Gastrointestinal Tract (Sixth Edition)
Book chapter: Gut Barrier: Innate Immunity – Gerco den Hartog et al. – Physiology of the Gastrointestinal Tract (Sixth Edition)
Review: Molecular Pathophysiology of Epithelial Barrier Dysfunction in Inflammatory Bowel Diseases – Jessica Y. Lee et al. – Proteomes
Impact of tart cherries polyphenols on the human gut microbiota and phenolic metabolites in vitro and in vivo – Alba C. Mayta-Apaza et al. – The Journal of Nutritional Biochemistry
Characterization of the duodenal bacterial microbiota in patients with pancreatic head cancer vs. healthy controls – Qi-Xiang Mei et al. – Pancreatology
Human multi-site microbiome
Microbiota potential for the treatment of sexual dysfunction – Hassan Tirandaz et al. – Medical Hypotheses
Animal experiments
Nile tilapia: Effects of Lactogen 13, a New Probiotic Preparation, on Gut Microbiota and Endocrine Signals Controlling Growth and Appetite of Oreochromis niloticus Juveniles – Gioacchini Giorgia et al. – Microbial Ecology
Effects of shenling baizhu powder herbal formula on intestinal microbiota in high-fat diet-induced NAFLD rats – Yupei Zhang et al. – Biomedicine & Pharmacotherapy
Gut Microbiota Promotes Tumor Growth in Mice by Modulating Immune Response – Vrishketan Sethi et al. – Gastroenterology
The effects of feeding monensin on rumen microbial communities and methanogenesis in bred heifers fed in a drylot – E.A. Melchior et al. – Livestock Science
Identification, characterization and selection of autochthonous lactic acid bacteria as probiotic for feedlot cattle – Natalia C. Maldonado et al. – Livestock Science
Glyphosate based- herbicide exposure affects gut microbiota, anxiety and depression-like behaviors in mice – Yassine Aitbali et al. – Neurotoxicology and Teratology
Animal microbiome
Characterization of the bacterial community in different parts of the gut of sea cucumber (Apostichopus Japonicus) and its variation during gut regeneration – Luo Wang et al. – Aquaculture Research
Review: The adherence and colonization of microorganisms in fish gastrointestinal tract – Xuemei Li et al. – Reviews in Aquaculture
Effect of Saccharomyces boulardii and Bacillus subtilis B10 on gut microbiota modulation in broiler – Chubin Qin and Li Gong et al. – Animal Nutrition
Metabolomics Study of Immune Responses of New Zealand Greenshell™ Mussels (Perna canaliculus) Infected with Pathogenic Vibrio sp. – Thao V. Nguyen et al. – Marine Biotechnology
Review: Use of antibiotics in broiler production: Global impacts and alternatives – Youcef Mehdi et al. – Animal Nutrition
Food Microbiome
PDF: High-Throughput rRNA Gene Sequencing Reveals High and Complex Bacterial Diversity Associated with Brazilian Coffee Bean Fermentation – Dão Pedro de Carvalho Neto et al. – Food Technology and Biotechnology
The impact of vegan production on the kimchi microbiome – Michelle Zabat et al. – Food Microbiology
Plant, root and soil microbiome
Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure – Sonya Erlandson et al. – Molecular Ecology
RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi – Ko‐Hsuan Chen et al. – New Phytologist
Microbial diversity changes with rhizosphere and hydrocarbons in contrasting soils – Muhammad Atikul Islam Khan et al. – Ecotoxicology and Environmental Safety
Effects of redox potential on soil Cadmium solubility: Insight into microbial community – Delong Meng et al. – Journal of Environmental Sciences
Long-term phosphorus application to a maize monoculture influences the soil microbial community and its feedback effects on maize seedling biomass – Ming Lang et al. – Applied Soil Ecology
Book chapter: Differential Responses of Plants to Biotic Stress and the Role of Metabolites – Maham Saddique et al. – Plant Metabolites and Regulation Under Environmental Stress
Role of Phenolic Acids from the Rhizosphere Soils of Panax notoginseng as a Double-Edge Sword in the Occurrence of Root-Rot Disease – Ya-Meng Zhao et al. – Molecules
Forum: From Petri Dishes to Model Ecosystems – Oskar Siemianowski et al. – Trends in Plant Science
An Insight into Catechins Metabolic Pathways of Camellia sinensis Based on Genome and Transcriptome Analysis – Wenzhao Wang et al. – Journal of Agricultural and Food Chemistry
Seasonal characterization of sugarcane vinasse: Assessing environmental impacts from fertirrigation and the bioenergy recovery potential through biodigestion – Lucas Tadeu Fuess et al. – Science of The Total Environment
Soil microbial biomass: A key soil driver in management of ecosystem functioning – Jay Shankar Singh and Vijay Kumar Gupta – Science of The Total Environment
Phosphorus fertilising potential of fly ash and effects on soil microbiota and crop – Deborah Schönegger et al. – Resources, Conservation and Recycling
Response of the soil microbial community to different fertilizer inputs in a wheat-maize rotation on a calcareous soil – Shuikuan Bei et al. – Agriculture, Ecosystems & Environment
Water and extremophile microbiome
Bacterial Diversity and Functional Activity of Microbial Communities in Hot Springs of the Baikal Rift Zone – E. V. Lavrentyeva et al. – Microbiology
Microbial Community Composition and Rates of the Methane Cycle Microbial Processes in the Upper Sediments of the Yamal Sector of the Southwestern Kara Sea – A. S. Savvichev et al. – Microbiology
Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats – Taruna Schuelke et al. – Molecular Ecology
Discriminating activated sludge flocs from biofilm microbial communities in a novel pilot-scale reciprocation MBR using high-throughput 16S rRNA gene sequencing – Ryan De Sotto et al. – Journal of Environmental Management
PDF: Divergent assemblage patterns of abundant and rare microbial sub-communities in response to inorganic carbon stresses in a simultaneous anammox and denitrification (SAD) system – Duntao Shu et al. – Bioresource Technology
Antibiotic resistance in wastewater treatment plants: Tackling the black box – Célia M. Manaia et al. – Environment International
Phages and viruses
** Building a global atlas of zoonotic viruses – Dennis Carroll et al. – Bulletin of WHO
Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes – Jeffrey K. Cornuault et al. – Microbiome
Dual Insect specific virus infection limits Arbovirus replication in Aedes mosquito cells – Michaela J. Schultz et al. – Virology
Technology
** Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run – Yi-Chun Yeh et al. – mSystems
Hemolymph Microbiomes of Three Aquatic Invertebrates as Revealed by a New Cell Extraction Method – Xinxu Zhang et al. – Applied and Environmental Microbiology
Clinical impact of rapid bacterial identification by MALDI-TOF MS combined with the bêta-LACTA™ test on early antibiotic adaptation by an antimicrobial stewardship team in bloodstream infections – A. Mizrahi et al. – Infectious Diseases
Genetic engineering of bee gut microbiome bacteria with a toolkit for modular assembly of broad-host-range plasmids – Sean P. Leonard et al. – ACS Synthetic Biology
** Cross-Reactivity of Prokaryotic 16S rDNA-Specific Primers to Eukaryotic DNA: Mistaken Microbial Community Profiling in Environmental Samples – Shailendra Yadav et al. – Current Microbiology
Detection of Pathogenic Microorganisms by Microfluidics Based Analytical Methods – Dongxue Zhang et al. – Analytical Chemistry
** Book chapter PDF: Microbial, Plant, Environmental and Industrial Technologies – Debmalya Barh and Vasco Azevedo – Microbial Omics: Applications in Biotechnology
Metabolome- and genome-scale model analyses for engineering of Aureobasidium pullulans to enhance polymalic acid and malic acid production from sugarcane molasses – Jun Feng and Jing Yang et al. – Biotechnology for Biofuels
eDNA-based bioassessment of coastal sediments impacted by an oil spill – Yuwei Xie et al. – Environmental Pollution
Using natural biomass microorganisms for drinking water denitrification – Darleila Damasceno Costa et al. – Journal of Environmental Management
Bioinformatics
Cluster and Multiple Correspondence Analyses in Rheumatology: Paths to Uncovering Relationships in a Sea of Data – Lu Han et al. – Rheumatic Disease Clinics of North America
Microbes in the news
Faecal transplantation: do not try this at home – Talha Khan Burki – The Lancet Gastroenterology & Hepatology
Non-microbiology picks
** Editorial: Time to talk about why so many postgrads have poor mental health – Nature
Editorial: Using Preprints for Journal Clubs – Arturo Casadevall and Neil Gow – mBio
Microbiome Digest - Bik's Picks 