Category Archives: Food Microbiology

May 6, 2022

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Happy Friday! Today’s microbiome digest is a grab bag of articles on topics such as antibiotic cycling and bacterial contamination in surgery, phage isolated from diseased seafood, and microbial communities in snuff. I was particularly interested to see the article focused on degradation genes found in steel industrial soil communities. Finally, I enjoyed checking out two preprints on oral microbiota in Agta, a group of hunter-gatherers from the Philippines.

General microbiome

Preprint: The making of the oral microbiome in Agta hunter-gatherers – Dobon et al. – bioRxiv

Preprint: Microbial population dynamics decouple nutrient affinity from environmental concentration – Fink et al. – bioRxiv

Beneath the surface: Amino acid variation underlying two decades of dengue virus antigenic dynamics in Bangkok, Thailand – Huang et al. – PLOS Pathogens

Preprint: Hunter-gatherer oral microbiomes are shaped by contact network structure – Muscitto et al. – bioRxiv

Which vaccine attributes foster vaccine uptake? A cross-country conjoint experiment – Stöckli et al. – PLOS ONE

Associations between microbial communities and key chemical constituents in U.S. domestic moist snuff – Tyxobert et al. – PLOS ONE

Multi-site human microbiome

Mycobacterium tuberculosis infection, immune activation, and risk of HIV acquisition – Bender Ignacio et al. – PLOS ONE

The effects of antibiotic cycling and mixing on acquisition of antibiotic resistant bacteria in the ICU: A post-hoc individual patient analysis of a prospective cluster-randomized crossover study – van Duijin et al. – PLOS ONE

Human gut microbiome

Efficacy of laparotomy sponges to reduce bacterial contamination using an in vitro gastrointestinal surgery model – Bezhentseva et al. – PLOS ONE

Animal experiments

Virulence and antimicrobial resistance gene profiles of Staphylococcus aureus associated with clinical mastitis in cattle – Neelam et al. – PLOS ONE

Preexisting Trichinella spiralis infection attenuates the severity of Pseudomonas aeruginosa-induced pneumonia – Rong Long et al. – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Metagenomic analysis for taxonomic and functional potential of Polyaromatic hydrocarbons (PAHs) and Polychlorinated biphenyl (PCB) degrading bacterial communities in steel industrial soil – Sandhu et al. – PLOS ONE

Water and extremophile microbiome

Transcriptomic analysis of chloride tolerance in Leptospirillum ferriphilum DSM 14647 adapted to NaCl – Rivera-Araya et al. – PLOS ONE

Food microbiology

Sole and combined effect of foliar zinc and arbuscular mycorrhizae inoculation on basmati rice growth, productivity and grains nutrient – Mehmood et al. – PLOS ONE

Characterization and complete genome sequence analysis of a newly isolated phage against Vibrio parahaemolyticus from sick shrimp in Qingdao, China – Tian et al. – PLOS ONE

Techniques

Financial incentives to increase stool collection rates for microbiome studies in adult bone marrow transplant patients – Thompson et al. – PLOS ONE

April 27, 2022

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Pregnancy and early life

Maternal breast milk microbiota and immune markers in relation to subsequent development of celiac disease in offspring – Štšepetova et al. – Scientific Reports

Human gut microbiome

The gut fungal and bacterial microbiota in pediatric patients with inflammatory bowel disease introduced to treatment with anti-tumor necrosis factor-α – Ventin-Holmberg et a. – Scientific Reports

Integrated fecal microbiome–metabolome signatures reflect stress and serotonin metabolism in irritable bowel syndrome – Mujagic et al. – Gut Microbes

Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer – Wolf et al. – Microbiome

Clinical significance and intestinal microbiota composition in immunocompromised children with norovirus gastroenteritis – Lin et al. – PLOS One

Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China – Li et al. – Microbiology Spectrum

A multi-omics machine learning framework in predicting the survival of colorectal cancer patients – Yang et al. – Computers in Biology and Medicine

[REVIEW]The gut microbiome as a modulator of healthy ageing – Ghosh, Shanahan & O’Toole – Nature Reviews Gastroenterology & Hepatology

Multiple sclerosis patients have an altered gut mycobiome and increased fungal to bacterial richness – Yadav et al. – PLOS One

[REVIEW]Cancer immunotherapy resistance: The impact of microbiome-derived short-chain fatty acids and other emerging metabolites – Hersi et al. – Life Sciences

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Oral administration of Akkermansia muciniphila elevates systemic antiaging and anticancer metabolites – Grajeda-Iglesias et al. – Aging

Lower abundance of Bacteroides and metabolic dysfunction are highly associated with the post-weaning diarrhea in piglets – Ren et al. – Science China Life Sciences

Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice – Jangid et al. – Scientific Reports

Animal microbiome

Carbendazim shapes microbiome and enhances resistome in the earthworm gut – Song et al. – Microbiome

Fungal signatures of oral disease reflect environmental degradation in a facultative avian scavenger – Pitarch et al. – Science of The Total Environment

Whole-Genome Shotgun Metagenomic Sequencing Reveals Distinct Gut Microbiome Signatures of Obese Cats – Ma et al. – Microbiology Spectrum

Species divergence in gut-restricted bacteria of social bees – Li et al. – PNAS

Bioinformatics

[PREVIEW]EggVio: a user friendly and versatile pipeline for assembly and functional annotation of shallow depth sequenced samples – Pinto, Vogel & Larose – bioRxiv

[PREVIEW]FoodMicrobionet v4: a large, integrated, open and transparent database for food bacterial communities – Parente, Zotta & Ricciardi – bioRxiv

Techniques

[PREPRINT]Run-on sequencing reveals nascent transcriptomics of the human microbiome – Vill et al. – bioRxiv

April 8, 2022

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Good morning! Today’s microbiome digest is brought to you by mild insomnia induced by a mid-afternoon coffee. It includes two food related studies, one on pathogenic E. coli found in ready-to-eat foods and the other focused on a antifungal lipopeptide produced by B. velezensis isolated from honey, and an an article focused on a new approach for processing frozen lung and lavage samples for use in microbiome studies. Also included are several articles focused on the gut microbiome, and several preprints focused on soil microbiome studies. Finally, I want to highlight a piece that details the positive outcomes associated with the National Summer Undergraduate Research Project (NSURP). Registration for this year’s program is still open until April 15th, and the organizers are looking for both mentors, mentees, and donors!


Pregnancy and early life

Group B Streptococcus colonization at delivery is associated with maternal peripartum infection – Brigtsen et al. – PLOS ONE

Human gut microbiome

Mycobacterium avium subsp. paratuberculosis and microbiome profile of patients in a referral gastrointestinal diseases centre in the Sudan – Elmagzoub et al. – PLOS ONE

Animal experiments

Vertical transmission of attaching and invasive E. coli from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life – Brand et al. – PLOS ONE

Sex differences in the fecal microbiome and hippocampal glial morphology following diet and antibiotic treatment – Saxena et al. – PLOS ONE

Animal microbiome

Preprint: Anthropogenic disturbance impacts gut microbiome homeostasis in a Malagasy primate – Wasimuddin et al. – bioRxiv

Plant, root, and soil microbiome

Preprint: Microclimate is a strong predictor of the native and invasive plant-associated soil microbiota on San Cristóbal Island, Galápagos archipelago – Schoenborn et al. bioRxiv

Preprint: The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types – Vitamaki et al. – bioRxiv

Preprint: Tracing carbon metabolism with stable isotope metabolomics reveals the legacy of diverse carbon sources in soil – Wilhelm et al. – bioRxiv

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Preprint: Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments – Kohtz et al. – bioRxiv

Food microbiology

Processed ready-to-eat (RTE) foods sold in Yenagoa Nigeria were colonized by diarrheagenic Escherichia coli which constitute a probable hazard to human health – Beshiru et al. – PLOS ONE

Purification and characterization of antifungal lipopeptide produced by Bacillus velezensis isolated from raw honey – Ziong et al. – PLOS ONE

Techniques

An optimized approach for processing of frozen lung and lavage samples for microbiome studies – Wiscovitch-Russo et al. – PLOS ONE

Science, publishing, and career

***National Summer Undergraduate Research Project (NSURP): A Virtual Research Experience to Deliver REAL (Retention, Equity, Access, and Life-Changing) Outcomes for Underrepresented Minorities in STEM – Johnson & Knox – JMBE

March 30, 2022

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General microbiome

[REVIEW]Glycan processing in gut microbiomes – La Rosa et al. – Current Opinion in Microbiology

Multi-site human microbiome

[REVIEW]The Oral-Microbiome-Brain Axis and Neuropsychiatric Disorders: An Anthropological Perspective – Bowland & Weyrich – Frontiers in Psychiatry

Human oral microbiome

Microbial and molecular differences according to the location of head and neck cancers – Kim et al. – Cancer Cell International

Microbial differences between active and remission peri-implantitis – Hashimoto et al. – Scientific Reports

Human gut microbiome

Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden – Olsson et al. – Cell Host & Microbe

Microbiota-microglia connections in age-related cognition decline – Zhou et al. – Aging Cell

Patients with psoriasis have a dysbiotic taxonomic and functional gut microbiota – Todberg – British Journal of Dermatology

[PREPRINT]Distinct Colon Mucosa Microbiomes associated with Tubular Adenomas and Serrated Polyps – Avelar-Barragan et al. – bioRxiv

Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting – Liu et al. – Cell Metabolism

Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth – Testerman et al. – Hepatology Commonications

Dietary Patterns and Gut Microbiota: the Crucial Actors in Inflammatory Bowel Disease – He et al. – Advances in Nutrition

A Guide to Dietary Pattern–Microbiome Data Integration – Choi et al. – The Journal of Nutrition

Functional Significance of Different Milk Constituents in Modulating the Gut Microbiome and Infant Health – Yadav et al. – J. Agric. Food Chem.

The gut microbiome as mediator between diet and its impact on immune function – Shi et al. – Scientific Reports

Differences in the intestinal microbiome associated with diarrhea during lenvatinib treatment for hepatocellular carcinoma – Inuai et al. – Digestive Diseases

16S rDNA sequencing analyzes differences in intestinal flora of human immunodeficiency virus (HIV) patients and association with immune activation – Mingjun et al. – Bioengineered

[REVIEW]Profile of Gut Microbiota of Adults with Diabetes Mellitus Type 1: A Systematic Review – Moreira et al. – Current Diabetes Reviews

Association between systemic lupus erythematosus and disruption of gut microbiota: a meta-analysis – Xiang et al. – Immunology and Inflammation

[REVIEW]The Bridge Between Ischemic Stroke and Gut Microbes: Short-Chain Fatty Acids – Fang et al. – Cellular and Molecular Neurobiology

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Prophylactic effects of hyperforin on anhedonia-like phenotype in chronic restrain stress model: A role of gut microbiota – Zhang et al. – Letters in Applied Microbiology

Metabolome and microbiome multi-omics integration from a murine lung inflammation model of bronchopulmonary dysplasia – Saie et al. – Pediatric Research

Microbiome applications for laying hen performance and egg production – Ricke, Dittoe & Olson – Poultry Science

Animal microbiome (for animals in the wild)

[PREPRINT]The connection between the gut mycobiome community of natural black soldier fly populations and their environment – Vitenberg, Goldway & Opatovsky – bioRxiv

Inhibitory Bacterial Diversity and Mucosome Function Differentiate Susceptibility of Appalachian Salamanders to Chytrid Fungal Infection – Jimenez et al. – Applied and Environmental Microbiology

Composition and short-term stability of gut microbiota in lean and spontaneously overweight healthy Labrador retriever dogs – Söder et al. – Acta Veterinaria Scandinavica

Alterations in common marmoset gut microbiome associated with duodenal strictures – Sheh et al. – Scientific Reports

Plant, root, and soil microbiome

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

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

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

Bacterial communities in surface and basal ice of a glacier terminus in the headwaters of Yangtze River on the Qinghai–Tibet Plateau – Ren et al. – Envionmental Microbiome

Built environment (subways, indoor surfaces)

Multikingdom interactions govern the microbiome in subterranean cultural heritage sites – Liu et al. – PNAS

Indoor green can modify the indoor dust microbial communities – Dockx et al. – Indoor Air

Forensics

Microbial community succession of submerged bones in an aquatic habitat – Kaszubinski et al . – Journal of Forensic Sciences

Bioinformatics

Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation – Podlesny et al. – Microbiome

[PREPRINT]Detection of Parasites in Microbiomes using Metagenomics – Kirstagler, Aarestrup & Pamp – bioRxiv

Techniques

Tryptophan Supplementation Increases the Production of Microbial-Derived AhR Agonists in an In Vitro Simulator of Intestinal Microbial Ecosystem – Koper et al. – J. Agric. Food Chem.

March 23, 2022

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General microbiome

Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance – Yu et al. – Nature Microbiology

Human skin microbiome

Skin microbiota diversity among genetically unrelated individuals of Indian origin – Pothbhare et al. – PeerJ

Human gut microbiome

[REVIEW]Gut microbiota and allergic diseases in children – Akagawa & Kaneko – Allergology International

[REVIEW]Gut microbiome: New biomarkers in early screening of colorectal cancer – Zhou et al. – Journal of Clinical Laboratory Analysis

Can gut microbiota throughout the first 10 years of life predict executive functioning in childhood? – Eckermann et al. – Developmental Psychobiology

[PREPRINT]Meta-analysis of the autism gut microbiome identifies factors influencing study discrepancies and machine learning classification – Chavira, Wang & Mills – bioRxiv

Changes of Intestinal Microflora in Colorectal Cancer Patients after Surgical Resection and Chemotherapy – Huang et al. – Computational and Mathematical Methods in Medicine

Animal microbiome

Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation – Dallas & Warne – Microbial Ecology

Changes in gut microbiota composition with age and correlations with gut inflammation in rats – Meng et al. – PLOS One

[REVIEW]Translational multi-omics microbiome research for strategies to improve cattle production and health – Wang & Guan – Emerging Topics in Lefe Sciences

Multi-omics reveals host metabolism associated with the gut microbiota composition in mice with dietary ε-polylysine – Zhang et al. – Food & Function

Soil causes gut microbiota to flourish and total serum IgE levels to decrease in mice – Zhou et al. – Environmental Microbiology

Microbiome-metabolomics deciphers the effects of Cistanche deserticola polysaccharides on agedconstipated rats – Liu et al. – Food & Function

Plant, root, and soil microbiome

[PREPRINT]Plant Virus Database: a resource for exploring the diversity of plant viruses and their interactions with hosts – Wu et al. – bioRxiv

Waste microbiome

[PREPRINT]Identification of Microbial Flora and Isolation of Functional Strains Related to the Degradation of Domestic Waste – Huang, Liu & Zong – bioRxiv

Food microbiology

Comprehensive characterization of the bacterial community structure and metabolite composition of food waste fermentation products via microbiome and metabolome analyses – Li et al. – PLOS One

Bioinformatics

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations – Gregory et al. – Microbiome

HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities – Kalmar et al. – PLOS Genetics

Techniques

[PREPRINT]Vaginal microbiome-host interactions modeled in a human vagina-on-a-chip – Mahajan et al. – bioRxiv

Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)

Florence tomb by Michelangelo restored with aid of bacteria – The Guardian

March 09, 2022

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General microbiome

Public human microbiome data are dominated by highly developed countries – Abdill, Adamowicz & Blekhman – PLOS Biology

Beyond the Microbiome: Germ-ganism? An Integrative Idea for Microbial Existence, Organization, Growth, Pathogenicity, and Therapeutics – Kambouris et al. – OMICS

Quantifying and Cataloguing Unknown Sequences within Human Microbiomes – Modha et al. – mSystems

Human respiratory microbiome

Alterations of lung microbiota in patients with non-small cell lung cancer – Zeng et al. – Bioengineered

Human vaginal microbiome

Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore’s adaptive sequencing – Marquet et al. – Scientific Reports

Human gut microbiome

[REVIEW]Personal diet–microbiota interactions and weight loss – Roager & Christensen

Integrated analysis of gut microbiome and host immune responses in COVID-19 – Xu et al. – Frontiers in Medicine

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Gut microbiome modifications over time when removing in-feed antibiotics from the prophylaxis of post-weaning diarrhea in piglets – Cremonesi et al. – PLOS One

Complete Genome Sequences of Three Staphylococcus haemolyticus Strains Isolated from the Lung of a TGFβ1 Transgenic Mouse with Lung Fibrosis – Abdel-Hamid et al. – Microbiology Resource Announcements

Colitis-associated microbiota drives changes in behaviour in male mice in the absence of inflammation – Vicentini et al. – Brain, Behaviour, and Immunity

Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart – Kieser, Zdobnov & Trajkovski – PLOS Comp Biol

Plant, root, and soil microbiome

The microbiome and resistome of apple fruits alter in the post-harvest period – Wassermann et al. – Environmental Microbiome

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Effects of Ocean Warming on the Underexplored Members of the Coral Microbiome – Maire et al. – Integrative and Comparative Biology

Techniques

[PREPRINT]A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities – Shaffer et al. – bioRxiv

[PREPRINT]A comparison of hard and soft direct methods for DNA extraction from soil – Hill et al. – bioRxiv

March 3, 2022

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Today’s digest is heavy on studies focused on the gut and soil microbiomes. It also includes articles focused on microbial indoor air quality as well as bacterial vaginosis and aerobic vaginitis among pregnant women. If you’d still like more, I’ve also included several preprints.

Happy reading!


Human vaginal microbiome

Prevalence of bacterial vaginosis and aerobic vaginitis and their associated risk factors among pregnant women from northern Ethiopia: A cross-sectional study – Yalew et al. – PLOS One

Human gut microbiome

Systematically assessing microbiome–disease associations identifies drivers of inconsistency in metagenomic research – Tierney et al. – PLOS Biology

Preprint: Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation – Venzon et al. – bioRxiv

Hydrogen-producing small intestinal bacterial overgrowth is associated with hepatic encephalopathy and liver function – Yokoyama et al. – PLOS One

Plant, root, and soil microbiome

Preprint: Deciphering the potential niche of two novel black yeast fungi from a biological soil crust based on their genomes, phenotypes, and melanin regulation – Carr et al. – bioRxiv

Bacterial age distribution in soil—Generational gaps in adjacent hot and cold spots – Borer & Or – PLOS Computational Biology

Deciphering the influence of Bacillus subtilis strain Ydj3 colonization on the vitamin C contents and rhizosphere microbiomes of sweet peppers – Liang et al. – PLOS One

Antimicrobial effect and mechanism of bovine lactoferrin against the potato common scab pathogen Streptomyces scabiei – Nakamura et al. – PLOS One

Preprint: Arbuscular mycorrhizal fungal composition across US citrus orchards, management strategies, and disease severity spectrum – Xi et al. – bioRxiv

Built environment

Comprehensive health risk assessment of microbial indoor air quality in microenvironments – Kumar et al. – PLOS One

Phages and viruses

Preprint: Modelling the synergistic effect of bacteriophage and antibiotics on bacteria: killers and drivers of resistance evolution – Leclerc et al. -bioRxiv

Bioinformatics

Preprint: Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution – Kiefl et al. – bioRxiv

January 28, 2022

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Human and General Microbiome

Diet leaves a genetic signature in a keystone member of the gut microbiota – Tanja Dapa – Cell Host & Microbe

Multi-omics investigation of Clostridioides difficile-colonized patients reveals pathogen and commensal correlates of C. difficile pathogenesis – Skye Rs Fishbein – eLife

Large-scale characterization of the macrolide resistome reveals high diversity and several new pathogen-associated genes – David Lund – Microbial Genomics

The small bowel microbiome changes significantly with age and aspects of the ageing process – Gabriela Leite – Microbial Cell

Intestinal microbiota profiles in a genetic model of colon tumorigenesis correlates with colon cancer biomarkers – Francesco Vitali – Scientific Reports

Skin microbiome profile of healthy Cameroonians and Japanese – Kazuhiro Ogai – Scientific Reports

Interactions between human milk oligosaccharides, microbiota and immune factors in milk of women with and without mastitis – Irma Castro – Scientific Reports

Microbiota of the prostate tumor environment investigated by whole-transcriptome profiling – Paul Vinu Salachan – Genome Medicine

Preview: Microbiome engineering: Taming the untractable – James W Marsh – Cell

Review: Microbiomes in physiology: Insights into 21(st) century global medical challenges – Emad Shehata – Experimental Physiology

Respiratory Tract Microbiome – Highlights

Gut microbiota dynamics in a prospective cohort of patients with post-acute COVID-19 syndrome – Qin Liu – Gut

Characteristics of Lung Microbiota in Children’s Refractory Mycoplasma pneumoniae Pneumonia Coinfected with Human Adenovirus B – Wenxiang Zhou – The Canadian Journal of Infectious Diseases & Medical Microbiology

The lung microbiota in children with cystic fibrosis captured by induced sputum sampling – Rebecca Weiser – Journal of Cystic Fibrosis 

Beneficial Microbes and Compounds

Bifidobacterium animalis subsp. lactis BB-12 Has Effect Against Obesity by Regulating Gut Microbiota in Two Phases in Human Microbiota-Associated Rats – Kemin Mao – Frontiers in Nutrition

Effects of a 10-Strain Oral Probiotic on Parameters of Vaginal Health and Microbial Community: A Pilot Clinical Study – Christopher J Martoni – International Journal of Women’s Health

A randomised, double-blind, placebo-controlled trial of Bifidobacterium bifidum CCFM16 for manipulation of the gut microbiota and relief from chronic constipation – Luyao Wang – Food & Function

Vaginal states: detection of conversion processes in women using contraception and characterization of vaginal Lactobacillus species – Sonia Elena María Fosch – Infectious Disorders Drug Targets

The probiotic properties and potential of vaginal Lactobacilli spp. isolated from healthy women against some vaginal pathogens – Arezoo Asadi – Letters in Applied Microbiology

Review: Protective Effects of Natural Polysaccharides on Intestinal Barrier Injury: A Review – Jiaying Huo – Journal of Agricultural and Food Chemistry

Animal Microbiome

Nitrogen recycling via gut symbionts increases in ground squirrels over the hibernation season – Matthew D Regan – Science

Robust host source tracking building on the divergent and non-stochastic assembly of gut microbiomes in wild and farmed large yellow croaker – Jun Zhu – Microbiome

Evaluation of three Bacillus spp. isolated from the gut of giant freshwater prawn as potential probiotics against pathogens causing Vibriosis and Aeromonosis – Muhamad Firdaus Syahmi Sam-On – Microbial Pathogenesis

Gut Microbial Trimethylamine is Elevated in Alcohol-Associated Hepatitis and Contributes to Ethanol-Induced Liver Injury in Mice – Robert N Helsley – eLife

Intestinal gluconeogenesis shapes gut microbiota, fecal and urine metabolome in mice with gastric bypass surgery – Justine Vily-Petit – Scientific Reports

Food Microbiome

To culture or not to culture: careful assessment of metabarcoding data is necessary when evaluating the microbiota of a modified-atmosphere-packaged vegetarian meat alternative throughout its shelf-life period – E Duthoo – BMC Microbiology

Plant Microbiome

Root Morphogenesis of Arabidopsis thaliana Tuned by Plant Growth-Promoting Streptomyces Isolated From Root-Associated Soil of Artemisia annua – Wenbo Fu – Frontiers in Plant Science

Environmental Microbiome

Soil microbial community development across a 32-year coastal wetland restoration time series and the relative importance of environmental factors – Katherine M Abbott – The Science of the Total Environment

Emerging frontiers in microbe mediated pesticide remediation: Unveiling role of omics and In silico approaches in engineered environment – Muneer Ahmad Malla – Environmental Pollution 

Review: Emerging investigator series: microplastic sources, fate, toxicity, detection, and interactions with micropollutants in aquatic ecosystems – a review of reviews – Mohamed Ateia – Environmental Science. Processes & Impacts

Techniques

Alternating Dual-Collision Energy Scanning Mass Spectrometry Approach: Discovery of Novel Microbial Bile-Acid Conjugates – Quan-Fei Zhu – Analytical Chemistry

Genetic tools for the redirection of the central carbon flow towards the production of lactate in the human gut bacterium Phocaeicola (Bacteroides) vulgatus – Rebecca Lück – Applied Microbiology and Biotechnology

Lipidomics Analysis of Outer Membrane Vesicles and Elucidation of the Inositol Phosphoceramide Biosynthetic Pathway in Bacteroides thetaiotaomicron – Mariana G Sartorio – Microbiology Spectrum

January 7, 2022

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Today’s digest covers a range of topics including a duplex qPCR assay to detect lung infections, an investigation into sand fly symbionts, and a characterization of a fermented soybean food (Pe poke). If you want to end the week on a good note, I’d suggest reading the two articles I’ve highlighted below. One demonstrates that flooding and ecological restoration of former cranberry farmland also restores wetland microbial communities and soil function. The second provides a new barcoding strategy for the phenotypic screening of mosquitos that can be applied towards malaria research.

Happy reading!

General microbiome

Controlled spatial organization of bacterial growth reveals key role of cell filamentation preceding Xylella fastidiosa biofilm formation – Anbumani et al. – npj Biofilms and Microbiomes

Bacteria can be selected to help beneficial plasmids spread – Dimitriu et al. – PLOS Biology

Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network – Urchueguía et al. – PLOS Biology

Human respiratory microbiome

Detection of Pneumocystis jirovecii and Toxoplasma gondii in patients with lung infections by a duplex qPCR assay – Wu et al. – PLOS Neglected Tropical Diseases

Animal experiments

***Barcoded Asaia bacteria enable mosquito in vivo screens and identify novel systemic insecticides and inhibitors of malaria transmission – Sturm et al. – PLOS Biology

Molecular phylogeny of heritable symbionts and microbiota diversity analysis in phlebotominae sand flies and Culex nigripalpus from Colombia – Vivero-Gomez – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar – Tamang et al. – PLOS One

***Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland – Rubin et al. – PLOS One

Water and extremophile microbiome

Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment – Remple et al. – npj Biofilms and Microbiomes

November 15, 2021

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Today’s digest contains an article about the effect of shale flowback fluid on the polluted soil microbiome. It also includes multiple preprints on topics such as long-read sequencing on the Oxford Nanopore, arctic marine protists, rapid antibiotic susceptibility testing for mixed infections, and more.

Happy reading!

General microbiome

Preprint: Rapid antibiotic susceptibility testing and species identification for mixed infections – Kandavalli et al. – bioRxiv

Preprint: Bacterial quorum sensing allows graded and bimodal cellular responses to variations in population density – Rattray et al. – bioRxiv

Preprint – Phage-encoded sigma factors alter bacterial dormancy – Schwartz et al. – bioRxiv

Human respiratory microbiome

Preprint: Aspergillus fumigatus drives tissue damage via iterative assaults upon mucosal integrity and immune homeostasis – Okaa et al. – bioRxiv

Human skin microbiome

Preprint: Cobamide sharing drives skin microbiome dynamics – Swaney et al. – bioRxiv

Plant, root, and soil microbiome

Toxic effects of shale gas fracturing flowback fluid on microbial communities in polluted soil – Zudong Mei et al. – Environmental Monitoring and Assessment

Water and extremophile microbiome

Preprint: Colonial choanoflagellate isolated from Mono Lake harbors a microbiome – Hake et al. – bioRxiv

Preprint: Linking extreme seasonality and gene expression in arctic marine protists – Wutkowska et al. – bioRxiv

Preprint: Biosorption potential and molecular characterization of metal resistant autochthonous microbes from tannery solid waste – Younas et al. – bioRxiv

Techniques

Preprint: Oxford Nanopore R10.4 long-read sequencing enables near-perfect bacterial genomes from pure cultures and metagenomes without short-read or reference polishing – Sereika et al. – bioRxiv

Preprint: Going through phages: A Computational approach to Revealing the role of prophage in Staphylococcus aureus – Sweet et al. – bioRxiv