Category Archives: Uncategorized

August 13, 2022

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Human and General Microbiome

Integrated metagenomic and metabolomic analysis reveals distinct gut-microbiome-derived phenotypes in early-onset colorectal cancer – Cheng Kong – Gut

A decrease in functional microbiomes represented as Faecalibacterium affects immune homeostasis in long-term stable liver transplant patients – Soon Kyu Lee – Gut Microbes

Longitudinal study of the vaginal microbiome in pregnancies involving preterm labor – Yoshiko Sakabe – Fujita Medical Journal

Oral microbiome and serological analyses on association of Alzheimer’s disease and periodontitis – Kuan-Lun Fu – Oral Diseases

Review: Ultra-processed foods and human health: from epidemiological evidence to mechanistic insights – Bernard Srour – The Lancet. Gastroenterology & Hepatology

Beneficial Microbes, Compounds and Interventions

Dietary Fiber Modulates the Release of Gut Bacterial Products Preventing Cognitive Decline in an Alzheimer’s Mouse Model – Daniel Cuervo-Zanatta – Cellular and Molecular Neurobiology

Functional and safety characterization of beneficial vaginal lactic acid bacteria for the design of vaginal hygiene products – Jessica Alejandra Silva – Journal of Applied Microbiology

Butyrate-producing Eubacterium rectale suppresses lymphomagenesis by alleviating the TNF-induced TLR4/MyD88/NF-κB axis – Haiyang Lu – Cell host & Microbe

Review: The double-edged sword of probiotic supplementation on gut microbiota structure in Helicobacter pylori management – Ali Nabavi-Rad – Gut Microbes

Non-Model Animal Microbiome

Functional Redundancy in Bat Microbial Assemblage in the Presence of the White Nose Pathogen – Matthew Grisnik – Microbial Ecology

Non-steroidal anti-inflammatory drugs caused an outbreak of inflammation and oxidative stress with changes in the gut microbiota in rainbow trout (Oncorhynchus mykiss) – N Hodkovicova – The Science of the Total Environment

Bees under interactive stressors: The novel insecticides flupyradifurone and sulfoxaflor along with the fungicide azoxystrobin disrupt the gut microbiota of honey bees and increase opportunistic bacterial pathogens – Yahya Al Naggar – The Science of the Total Environment

Plant Microbiome

Host genotype controls ecological change in the leaf fungal microbiome – Acer VanWallendael – PLoS Biology

Suaeda salsa Root-Associated Microorganisms Could Effectively Improve Maize Growth and Resistance under Salt Stress – Yongdong Wang – Microbiology Spectrum

Review: Regulation of immune complex formation and signalling by FERONIA, a busy goddess in plant-microbe interactions – Zhikun Duan – Molecular Plant Pathology

Food Microbiome

A systematic, complexity-reduction approach to dissect the kombucha tea microbiome – Xiaoning Huang – eLife

Bioinformatic Tools and Microbiome Analysis Techniques

ProbeTools: designing hybridization probes for targeted genomic sequencing of diverse and hypervariable viral taxa – Kevin S Kuchinski – BMC Genomics

A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications – Maaly Nassar – GigaScience

MetaProClust-MS1: an MS1 Profiling Approach for Large-Scale Microbiome Screening – Caitlin M A Simopoulos – mSystems

August 5, 2022

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Today’s digest is brief and includes research examining the association between the gut microbiota and Gulf War illness, determining the distribution of psychrophilic microorganisms in a beef slaughterhouse, measuring the quality of DNA sequences via degradation, and more.

Happy Friday!

General microbiome

Measuring quality of DNA sequence data via degradation – Karr et al. – PLOS One

Atypical integrative element with strand-biased circularization activity assists interspecies antimicrobial resistance gene transfer from Vibrio alfacsensis – Nonaka et al. – PLOS One

Human vaginal microbiome

Association of key species of vaginal bacteria of recurrent bacterial vaginosis patients before and after oral metronidazole therapy with short- and long-term clinical outcomes – Mollin et al. – PLOS One

Human gut microbiome

Examining the association between the gastrointestinal microbiota and Gulf War illness: A prospective cohort study – Kates et al. – PLOS One

Food microbiology

Distribution of psychrophilic microorganisms in a beef slaughterhouse in Japan after cleaning – Nakamura et al. – PLOS One

Science, publishing, and career

Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses – Bacon et al. – PLOS Computational Biology

July 14, 2022

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Today’s digest has multiple articles on statistical and bioinformatic techniques! Also included is a job ad from my research team, so check it out if you’re interested in gaining geomicrobiology research experience at a national laboratory.

Events and jobs

Our geomicrobiology research group at the National Energy Technology Lab – Pittsburgh is looking for a technician/researcher. Exact responsibilities are somewhat flexible depending on interest and education-level; we are accepting applications from current students at all levels as well as postdocs.

General microbiome

Mycobacteriophages: From Petri dish to patient – Hatfull – PLOS Pathogens

Animal microbiome

Reconstructing the ecosystem context of a species: Honey-borne DNA reveals the roles of the honeybee – Wirta et al. – PLOS One

Plant, root, and soil microbiome

Patterns of microbial communities were shaped by bioavailable P along the elevation gradient of Shergyla Mountain, as determined by analysis of phospholipid fatty acids – Ba et al. – PLOS One

Preprint: Soil chemistry and soil history significantly structure oomycete communities in Brassicaceae crop rotations – Blakney et al. – bioRxiv

Community succession and straw degradation characteristics using a microbial decomposer at low temperature – Zhang et al. – PLOS One

Built Environment

Indoor air microbial load, antibiotic susceptibility profiles of bacteria, and associated factors in different wards of Arba Minch General Hospital, southern Ethiopia – Kayta et al. – PLOS One

Techniques

moreThanANOVA: A user-friendly Shiny/R application for exploring and comparing data with interactive visualization – Jiang et al. – PLOS One

Preparation of biological monolayers for producing high-resolution scanning electron micrographs – Mentor et al. – PLOS One

The accuracy of absolute differential abundance analysis from relative count data – Roche & Mukherjee – PLOS Computational Biology

AC-PCoA: Adjustment for confounding factors using principal coordinate analysis – Wang et al. – PLOS Computational Biology

Microbes in the news

The Art of Science: Students Participate in University’s First-Ever Bio-Art Class – Bernardi – Syracuse University News

June 8, 2022

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Happy Friday! Today’s digest includes articles about Gardnerella vaginalis clades in pregnancy, how a Japanese herbal medicine may alleviate a leaky gut, and a feasibility study of the impact of oral activated charcoal on healthy volunteers.

General microbiome

Clinical Burkholderia pseudomallei isolates from north Queensland carry diverse bimABm genes that are associated with central nervous system disease and are phylogenomically distinct from other Australian strains – Burnard et al. – PLOS Neglected Tropical Diseases

Preprint: The energy requirements of ion homeostasis determine the lifespan of starving bacteria – Schink et al. – bioRxiv

Preprint: A novel bacterial speciation process observed in a symbiotic marine population – Wang et al. – bioRxiv

Human vaginal microbiome

Gardnerella vaginalis clades in pregnancy: New insights into the interactions with the vaginal microbiome – Severgnini et al. – PLOS One

Human gut microbiome

Saireito, a Japanese herbal medicine, alleviates leaky gut associated with antibiotic-induced dysbiosis in mice – Ozaka et al. – PLOS One

A dose-finding safety and feasibility study of oral activated charcoal and its effects on the gut microbiota in healthy volunteers not receiving antibiotics – Rashidi et al. – PLOS One

Water and extremophile microbiome

The microbial community and functional potential in the Midland Basin reveal a community dominated by both thiosulfate and sulfate-reducing microorganisms – Tinker et al. – Microbiology Spectrum

Techniques

Performance of the TaqMan COVID-19 Pooling Kit for detection of SARS-CoV-2 in asymptomatic and symptomatic populations – Ganz et al.- PLOS One

June 3, 2022

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Happy Friday!

Today’s digest has articles on COVID-19 vaccine hesitancy, a new R package to extract network backbones, and a class of novel antibiotics that targets a Mycobacterium tuberculosis PE-PGRS protein. There also preprints on biofilm winkling in Bacillus subtilis, the dental calculus microbiome, and the relationship between eukaryotic genomes and ocean plankton in a global metagenomic dataset.

Events

Next week is ASM Microbe! I’ll be there, wearing a KN-95 and clutching a box of rapid tests. Feel free to comment or reach out if you’re also attending.

COVID-19

Oro-facial mucocutaneous manifestations of Coronavirus Disease-2019 (COVID-19): A systematic review – Fakhruddin et al. – PLOS ONE

Preprint: The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity – Kim et al. – bioRxiv

Determinants of the COVID-19 vaccine hesitancy spectrum – Piltch-Loeb et al. – PLOS ONE

General microbiome

Preprint: Fatty acid synthesis knockdown promotes biofilm wrinkling and inhibits sporulation in Bacillus subtilis – Arjes et al. – bioRxiv

Association of Strongyloides stercoralis infection and type 2 diabetes mellitus in northeastern Thailand: Impact on diabetic complication-related renal biochemical parameters – Yingklang et al. – PLOS ONE

Analysis of secondary metabolite gene clusters and chitin biosynthesis pathways of Monascus purpureus with high production of pigment and citrinin based on whole-genome sequencing – Zhang et al. – PLOS ONE

Human respiratory microbiome

A novel class of antimicrobial drugs selectively targets a Mycobacterium tuberculosis PE-PGRS protein – Seo et al. – PLOS Biology

Human oral microbiome

Preprint: Assessing the influence of the Mediterranean diet on dental calculus microbiome composition: a pilot study – Innocenti et al. – bioRxiv

Human gut microbiome

Lactobacillus plantarum improves LPS-induced Caco2 cell line intestinal barrier damage via cyclic AMP-PKA signaling – Wei et al. – PLOS ONE

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

Preprint: Eukaryotic genomes from a global metagenomic dataset illuminate trophic modes and biogeography of ocean plankton – Alexander et al. – bioRxiv

Bioinformatics

backbone: An R package to extract network backbones – Neal – PLOS ONE


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

May 04, 2022

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Human gut microbiome

Associations between self-reported psychological symptom severity and gut microbiota: further support for the microgenderome – Ganci et al. – BMC Psychiatry

Impacts of dietary exposure to pesticides on faecal microbiome metabolism in adult twins – Mesnage – Environmental Health

Diversity and Metabolic Potential of the Gut Microbiome in Adolescents with Functional Bowel Disorder – Klimenko et al. – Bulletin of Experimental Biology and Medicine

[REVIEW]Diet-microbiome interactions in cancer treatment: Opportunities and challenges for precision nutrition in cancer – Greathouse et al. – Neoplasia

Fermented brown rice beverage distinctively modulates the gut microbiota in Okinawans with metabolic syndrome: A randomized controlled trial – Akamine et al. – Nutrition Research

Gut Microbiome Characteristics in Mothers and Infants According to the Presence of Atopic Dermatitis – Sung et al. – BioMed Research International

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

Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain – Parker – Microbiome

Bacteria and Bellicosity: Photoperiodic Shifts in Gut Microbiota Drive Seasonal Aggressive Behavior in Male Siberian Hamsters – Shor, Brown & Freeman – Journal of Biological Rhythms

Microbial DNA enrichment promotes liver steatosis and fibrosis in the course of non-alcoholic steatohepatitis – Luo et al. – Acta Physiologica

[PREPRINT]High fat diet changes bacterial signatures in the murine pancreas – Scheithauer et al. – bioRxiv

Animal microbiome (for animals in the wild)

Geographical resistome profiling in the honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids – Sun et al. – Microbiome

Plant, root, and soil microbiome

Phytobeneficial traits of rhizobacteria under the control of multiple molecular dialogues – Laveilhé – Microbial Biotechnology

Bioinformatics

[PREPRINT]Modeling complex measurement error in microbiome experiments – Clausen & Willis – arXiv

Techniques

[PREPRINT]You will know by its tail: a method for quantification of heterogeneity of bacterial populations using single cell MIC profiling – Pacocha 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 6, 2022

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Good morning, everyone! Finally, the microbiome digest is ready after a long break.

In today’s digest, there are several interesting research articles to read specifically from two main sections Gut microbiome and Animal microbiome/Animal experiments. A few of them are highlighted as follows: 1) Use of machine learning approaches to mine functional peptides from metagenomic datasets; 2) An ultimate effort to mine host-microbiome protein-protein interactions which are mostly unexplored to understand mechanistic links with a variety of diseases; 3) Important role of mucosa-associated fungi with host-protective immunity and epithelial barrier function; 4) A fantastic review article summarizes gut microbial regulation of host 5-HT and 5-HT-mediated gut functions and its implications in the microbiota-gut-brain axis; 5) Another study showed; how gut microbiota regulates specific features of microglia from aged mice; 6) A method named MAGISTA to assess intra-bin statistics of metagenome-assembled genomes.

Enjoy reading. Happy Sunday.

General microbiome

Host-microbiome protein-protein interactions capture disease-relevant pathways – Zhou et al. – Genome Biology

Review: Periodontitis, chronic liver diseases, and the emerging oral-gut-liver axis –Albuquerque-Souza et al. – Periodontology 2000

Review: tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes – Zhang et al. – Molecular Cell

Gut microbiome

Socioeconomic disparities and household crowding in association with the fecal microbiome of school-age children – Lapidot et al. – npj biofilms and microbiomes

Oligofructose-Enriched Inulin Intake, Gut Microbiome Characteristics, and the V̇O2 Peak Response to High-Intensity Interval Training in Healthy Inactive Adults – Williams et al. – The Journal of Nutrition

Helicobacter pylori infection affects the human gastric microbiome, as revealed by metagenomic sequencing – Wang et al. – FEBS Openbio

Microbiota dynamics in a randomized trial of gut decontamination during allogeneic hematopoietic cell transplantation – Severyn et al. – JCI insight

Review: Direct and indirect mechanisms by which the gut microbiota influence host serotonin systems – Legan et al. – Neurogastroenterology & Motility

Tree-Based Analysis of Dietary Diversity Captures Associations Between Fiber Intake and Gut Microbiota Composition in a Healthy US Adult Cohort – Kable et al. – The Journal of Nutrition

Spatial distribution of live gut microbiota and bile acid metabolism in various parts of human large intestine – Chinda et al. – Scientific Reports

Review: Understanding the mechanism underlying the anti-diabetic effect of dietary component: a focus on gut microbiota – Zhao et al. – Critical Reviews in Food Science and Nutrition

Intestinal AMPK modulation of microbiota mediates crosstalk with brown fat to control thermogenesis – Zhang et al. Nature Communications

Impact of wheat aleurone on biomarkers of cardiovascular disease, gut microbiota and metabolites in adults with high body mass index: a double-blind, placebo-controlled, randomized clinical trial – Fava et al. – European Journal of Nutrition

Oral microbiome

Alterations in the oral microbiome of individuals with a healthy oral environment following COVID-19 vaccination – Uehara et al. – BMC Oral Health

Respiratory microbiome

Age-related changes in the nasopharyngeal microbiome are associated with SARS-CoV-2 infection and symptoms among children, adolescents, and young adults – Hurst et al. – Clinical Infectious Diseases

Animal microbiome / Animal experiments

Animal gut microbiome mediates the effects of antibiotic pollution on an artificial freshwater system – Zhu et al. – Journal of Hazardous Materials

Metagenomic analysis explores the interaction of aged microplastics and roxithromycin on gut microbiota and antibiotic resistance genes of Carassius auratus – Zhang et al. – Journal of Hazardous Materials

Identification and functional expression of a new xylose isomerase from the goat rumen microbiome in Saccharomyces cerevisiae – Colombo et al. – Letters in Applied Microbiology

Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance – Zhou et al. – Microbiome

Mucosal fungi promote gut barrier function and social behavior via Type 17 immunity – Leonardi et al. – Cell

Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine – Mossad et al. – Nature Neuroscience

Kaempferol acts on bile acid signaling and gut microbiota to attenuate the tumor burden in ApcMin/+ mice – Li et al.- European Journal of Pharmacology

Changes of gut microbiota in diabetic nephropathy and its effect on the progression of kidney injury – Cai et al. – Endocrine

The Novel Interplay between Commensal Gut Bacteria and Metabolites in Diet-Induced Hyperlipidemic Rats Treated with Simvastatin – Zhang et al. – Journal of Proteome Research

Changes to gut amino acid transporters and microbiome associated with increased E/I ratio in Chd8+/− mouse model of ASD-like behavior – Yu et al. – Nature Communications

Novel Selenium Peptides Obtained from Selenium-Enriched Cordyceps militarisAlleviate Neuroinflammation and Gut Microbiota Dysbacteriosis in LPS-Injured Mice – Wu et al. – Journal of Agricultural and Food Chemistry

Microbiome-metabolomics analysis of the effects of decreasing dietary crude protein content on goat rumen mictobiota and metabolites – Zhu et al. – Animal Bioscience

Methods/Tools/Pipelines

Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics – Goussarov et al. – Environmental Microbiome

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