November 8, 2022

Greetings from Pittsburgh, PA!

It’s election day here, which means I have low grade nausea and am looking for a distraction. If you’re in the same boat, check out today’s awesome articles on a holobiont deep sea shrimp, plant-microbiome assemblies of poplar trees, and viral community-wide auxiliary metabolic genes. I also included a few interesting preprints, my favorite of which is noted below and uses a microbiome public dataset to compare different normalization and transformation methods.

Animal microbiome

A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata – Aubé et al. – Microbiome

Plant, root, and soil microbiome

Plant sex affects plant-microbiome assemblies of dioecious Populus cathayana trees under different soil nitrogen conditions – Guo et al. – Microbiome

Phages and viruses

Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts – Luo et al. – Microbiome

Techniques

*Preprint: Alpha and beta-diversities performance comparison between different normalization methods and centered log-ratio transformation in a microbiome public dataset – Bars-Cortina – bioRxiv

Preprint: Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts – McCallum et al. – bioRxiv

Preprint: Targeted metagenomics using probe capture detects a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics – Siljanen et al. – bioRxiv

November 02, 2022

General microbiome

[RETRACTION]Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake – Ahmad et al. – PLOS One

Pregnancy and early life

A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning – Vatanen et al. – Clee

Multi-site human microbiome

[REVIEW]Recent advances in systemic lupus erythematosus and microbiota: from bench to bedside – Zhan et al. –

Human vaginal microbiome

Identification of shared bacterial strains in the vaginal microbiota of related and unrelated reproductive-age mothers and daughters using genome-resolved metagenomics – France et al. – PLOS One

Human gut microbiome

Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia – Bernard-Raichon et al. – Nature Communications

Gut microbiota and myocardial fibrosis – Xu, Yang & Bao – European Journal of Pharmacology

Assessing the relationship between physical activity and the gut microbiome in a large, population-based sample of Wisconsin adults – Holzhausen et al. – PLOS One

Challenges and costs of donor screening for fecal microbiota transplantations – Bernard et al. – PLOS One

Animal microbiome

Gut colonization by Proteobacteria alters host metabolism and modulates cocaine neurobehavioral responses – Cuesta et al. – Cell Host & Microbe

Enriching captivity conditions with natural elements does not prevent the loss of wild-like gut microbiota but shapes its compositional variation in two small mammals – Koziol et al. – Microbiology Open

Understanding the Dynamic of POMS Infection and the Role of Microbiota Composition in the Survival of Pacific Oysters, Crassostrea gigas – Delisle et al. – Microbiology Spectrum

Changes in Gut Microbiota Structure: A Potential Pathway for Silver Nanoparticles to Affect the Host Metabolism – Wang et al. – ACS Nano

Skin microbiota of oxazolone-induced contact hypersensitivity mouse model – Mäenpää et al. – PLOS One

Effects of a farm-specific fecal microbial transplant (FMT) product on clinical outcomes and fecal microbiome composition in preweaned dairy calves – Slanzon et al. – PLOS One

Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes – Gil & Hird – Microbiology Spectrum

Uropygial gland microbiota differ between free-living and captive songbirds – Grieves et al. – Scientific Reports

Plant, root, and soil microbiome

Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere – Muscatt et al. – Microbiome

Bioinformatics

CRAMdb: a comprehensive database for composition and roles of microbiome in animals – Lei et al. – NAR

Techniques

DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes – Brauer & Bengtsson – Microbiology Open

synDNA—a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing – Zaramela et al. – mSystems

September 28, 2022

General microbiome

[Personal View]Causal discovery for the microbiome – Corander, Hanage & Pensar – The Lancet Microbe

Integrative functional analysis uncovers metabolic differences between Candida species – Begum et al. – Communications Biology

Human skin microbiome

Evolution of the facial skin microbiome during puberty in normal and acne skin – Schneider et al. – JEADV

Human gut microbiome

[REVIEW]Harnessing Microbiota to Improve Immunotherapy for Gastrointestinal Cancers – Goc & Sonnenberg – Cancer Immunol Res

[REVIEW]Gut microbiome in multiple sclerosis-related cognitive impairment – Ghadiri et al. – Multiple Sclerosis and Related Disorders

[REVIEW]The Microbiome in Gastrointestinal Cancers – White & Wargo – Gastroenterology Clinics of North America

Human gut microbiota and its metabolites impact immune responses in COVID-19 and its complications – Nagata et al. – Gastroenterology

Gut microbial fermentation promotes the intestinal anti-inflammatory activity of Chinese yam polysaccharides – Bai et al. – Food Chemistry

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

The preventive effects of probiotic Akkermansia muciniphila on D-galactose/AlCl3 mediated Alzheimer’s disease-like rats – He et al. – Experimental Gerontology

Characterizing the chicken gut colonization ability of a diverse group of bacteria – Poudel et al. – Poultry Science

Obesity induced gut dysbiosis contributes to disease severity in an animal model of multiple sclerosis – Shahi et al. – Front. Immunol.

Animal microbiome (for animals in the wild)

Impact of aluminum exposure on oxidative stress, intestinal changes and immune responses in red swamp crayfish (Procambarus clarkii) – Zhang et al. – Science of The Total Environment

Network analysis reveals significant joint effects of microplastics and tetracycline on the gut than the gill microbiome of marine medaka – Liao et al. – Journal of Hazardous Materials

Xenobiotic estradiol-17ß alters gut microbiota of hatchling American Alligators (Alligator mississippiensis) – Murphy et al. – Environmental Microbiology

Sustained Drought, but Not Short-Term Warming, Alters the Gut Microbiomes of Wild Anolis Lizards – Williams et al. – Applied and Environmental Microbiology

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

Microbial Composition of Freshwater Marsh Sediment Responds more Strongly to Microcosm Seawater Addition than Simulated Nitrate or Phosphate Eutrophication – Weingarten & Jackson – Microbial Ecology

Built environment (subways, indoor surfaces)

Microbial community regulation and performance enhancement in gas biofilters by interrupting bacterial communication – Wang et al. – Microbiome

Bioinformatics

Identification of microbial features in multivariate regression under false discovery rate control – Srinivasan, Xue and Zhan – Computational Statistics & Data Analysis

Techniques

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

September 8, 2022

Today’s microbiome digest includes ten rules for teaching yourself R, food safety profiles of ready-to-eat raw minced meat, teaching that addresses eco-anxiety, as well as both pathogenic and entomopathogenic fungi!

Human gut microbiome

Meals, Microbiota and Mental Health in Children and Adolescents (MMM-Study): A protocol for an observational longitudinal case-control study – Asbjornsdottir et al. – PLOS One

Strongyloides stercoralis infection induces gut dysbiosis in chronic kidney disease patients – Hai et al. – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Mycoparasitism capability and growth inhibition activity of Clonostachys rosea isolates against fungal pathogens of grapevine trunk diseases suggest potential for biocontrol – Geiger et al. – PLOS One

Impact of endophytic colonization by entomopathogenic fungi on the behavior and life history of the tobacco peach aphid Myzus persicae var. nicotianae – Wilberts et al. – PLOS One

Food microbiology

Bacteriological quality and antimicrobial susceptibility profiles of isolates of ready-to-eat raw minced meat from hotels and restaurants in Arba Minch, Ethiopia – Tonjo et al. – PLOS One

Bioinformatics

Ten simple rules for teaching yourself R – Lawlor et al. – PLOS Computational Biology

Techniques

Laboratory evaluation of RealStar Yellow Fever Virus RT-PCR kit 1.0 for potential use in the global yellow fever laboratory network – Basile et al. – PLOS Neglected Tropical Diseases

Science, publishing, and career )

Insufficient yet improving involvement of the global south in top sustainability science publications – Dangles et al. – PLOS One

Adapt conservation biology teaching to address eco-anxiety in students – São Pedro et al. – PLOS Biology

August 24, 2022

General microbiome

[REVIEW]Detecting bacterial adaptation within individual microbiomes – Liebermann – Phil. Trans. R. Soc. B

[REVIEW]Soil microbiomes and one health – Banerjee & van der Heijden – Nature Reviews Microbiology

Pregnancy and early life

Microbial Analysis of Umbilical Cord Blood Reveals Novel Pathogens Associated with Stillbirth and Early Preterm Birth – Vander Haar et al. – mBio

Human respiratory microbiome

The respiratory microbiota alpha-diversity in chronic lung diseases: first systematic review and meta-analysis – Avalos-Fernandez et al. – Respiratory Research

Human saliva microbiome

Saliva microbiome, dietary, and genetic markers are associated with suicidal ideation in university students – Ahrens et al. – Scientific Reports

Human gut microbiome

The gut microbiota is associated with immune cell dynamics in humans – Schluter et al. – Nature

The systemic anti-microbiota IgG repertoire can identify gut bacteria that translocate across gut barrier surfaces – Vujkovic-Cvijin et al. – Science Translational Medicine

Higher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling – Kim et al. – ISME Communications

Correlation of inflammatory biomarkers with the diversity of Bacteroidaceae, Bifidobacteriaceae, Prevotellaceae and Lactobacillaceae families in the intestinal microbiota of patients with end stage renal disease – Asgharian et al. – Advances in Medical Sciences

Impact of the Host Microbiome on Vaccine Responsiveness: Lessons Learned and Future Perspective – Stefanetti & Kasper – Biochemistry

Location-specific signatures of Crohn’s disease at a multi-omics scale – Gonzalez et al. – Microbiome

Association of food insecurity on gut microbiome and metabolome profiles in a diverse college-based sample – Mohr et al. – Scientific Reports

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

The Diversity and Functional Capacity of Microbes Associated with Coastal Macrophytes – Miranda et al. – mSystems

Microbes in space

Machine learning algorithm to characterize antimicrobial resistance associated with the International Space Station surface microbiome – Madrigal et al. – Microbiome

Bioinformatics

[PREPRINT]Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4 – Blanco-Miguez et al. – bioRxiv

Linear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data – Lin, Eggesbø & Peddada – Nature Communications

Techniques

Primers matter: Influence of the primer selection on human fungal detection using high throughput sequencing – Wiemann et al. – Gut Microbes

Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples – Baker et al. – mSystems

August 19, 2022

Today’s digest is short and sweet! We have articles on the gut microbiota in rats, the influence of host genetics on the leaf fungal microbiome, and biofilm fouling in drinking water. There are also two manuscripts which provide tips for pathway enrichment analysis and biomarker discovery.

Happy reading! Also, if you’re in Scotland, consider checking out the enormous E. coli in Edinburgh this weekend!

Animal experiments

Effects of sea salt intake on metabolites, steroid hormones, and gut microbiota in rats – Chanmuang et al. – PLOS One

Plant, root, and soil microbiome

The changing influence of host genetics on the leaf fungal microbiome throughout plant development – Karasov & Lundberg – PLOS Biology

Water and extremophile microbiome

Impacts of temperature and hydraulic regime on discolouration and biofilm fouling in drinking water distribution systems – Fish et al. – PLOS Water

Bioinformatics

Nine quick tips for pathway enrichment analysis – Chicco & Agapito – PLOS Computational Biology

Ten quick tips for biomarker discovery and validation analyses using machine learning – Diaz-Uriarte et al. – PLOS Computational Biology

August 5, 2022

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

August 1st, 2022

God morgon!

Good morning from Sweden.

Today’s digest has studies from diverse topics but the one that caught my attention is a preprint that addresses the controversial question of presence of a ‘normal blood microbiota’ in humans. The authors of this preprint analysed about 10,000 humans samples and provide evidence that there is no core blood microbiota.

A new preprint describes a unique Taleocin (a bacteriocin) from Pseudomonas syringae which defies the convention that bacteriocins have a narrow spectrum. The bacteriocin has a broad range killing activity against agriculturally important pathogens like Erwinia amylovora and Xanthomonas perforans as well as against the clinical human pathogen Salmonella choleraesuis.

Another preprint reports metabolic interactions responsible for unusually high Iron and lipid content in Geobacter sulfurreducens, a bacterium known iron reducing bacterium in the soil. Another environmental study found that human pathogens are the major carriers of antibiotic resistance genes in the Yangtze river – one of the longest in the world. This is in contrast to prevalent belief that conventional supercarriers are Enterococcus spp. and other fecal indicator bacteria.

Elsewhere in the digest is a preprint from my previous lab where my old colleagues have reported a small RNA and metal dependent mechanism that regulates the survival of Acinetobacter baumannii under oxidative stress.

As a bonus, there is a super intriguing preprint where the authors have actually provided evidence that coming up with creative and funny titles for your papers can help them gain more visibility and citations! So, all of you writing an article or planning to write one soon, this is a great tip!

I hope you will enjoy reading today’s digest and have a great week ahead!

Human gut

Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake – Zachary C. Holmes, et al., Microbiome

Near-sterile sites

Preprint: No evidence for a common blood microbiome based on a population study of 9,770 healthy humans – Cedric C.S. Tan, et al.

Water microbiome

Supercarriers of antibiotic resistome in a world’s large river – Jiawen Wang, et al., Microbiome

Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater – Jingli Liu, et al., Microbiome

Community structure of coral microbiomes is dependent on host morphology – Kathleen M. Morrow, et al., Microbiome

Preprint: The impact of primary colonizers on the community composition of river biofilm – Roshan Angoshtari, et al.

Soil microbiome

Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity – Xingyu Ma, et al., Microbiome

Animal microbiome

Host-microbiota interaction-mediated resistance to inflammatory bowel disease in pigs – Xuan Zhao, et al., Microbiome

Preprint: The differing roles of flavins and quinones in extracellular electron transfer in Lactiplantibacillus plantarum – Joe Gregory Tolar, et al.

Bacteria Hysteria

Preprint: Interspecies Killing Activity of Pseudomonas syringae Tailocins – Savannah L Weaver, et al.

Preprint: Enhanced production of natural shiga toxin by overexpressing A subunit of Stx2e in Stx2e-producing Escherichia coli isolated in South Korea – Jin Hur, et al.

Preprint: Geobacter sulfurreducens′ unique metabolism results in cells with a high iron and lipid content – Ethan T Howley, et al.

Preprint: Cloning, heterologous expression and characterization of o-phthalyl-CoA decarboxylase from phthalate degrading denitrifying bacterium – Madan Junghare

Preprint: Acinetobacter baumannii defends against oxidative stress through a Mn2+-dependent small RNA-mediated suppression of type VI secretion system – Somok Bhowmik, et al.

Techniques

Preprint: Programmable acetylation modification of bacterial proteins by a Cas12a-guided acetyltransferase – Liu yanqiang, et al.

Fun

Preprint: If this title is funny, will you cite me? Citation impacts of humour and other features of article titles in ecology and evolution – Stephen B Heard, et al.

July 16, 2022

Human and General Microbiome

Advances and challenges in cataloging the human gut virome – Junhua Li – Cell Host & Microbe

Genomic diversity of genus Limosilactobacillus – Magdalena Ksiezarek – Microbial Genomics

Comparison of the respiratory tract microbiome in hospitalized COVID-19 patients with different disease severity – Jiali Chen – Journal of Medical Virology

An international report on bacterial communities in esophageal squamous cell carcinoma – Jason Nomburg – International Journal of Cancer

Beneficial Microbes and Compounds

Phenolic-rich beverages reduce bacterial TMA formation in an ex vivo-in vitro colonic fermentation model – Lisard Iglesias-Carres – Food & Function

Lactobacillus paragasseri OLL2809 Improves Depression-Like Behavior and Increases Beneficial Gut Microbes in Mice – Narumi Hashikawa-Hobara – Frontiers in Neuroscience

In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus – Linda B Oyama – NPJ Biofilms and Microbiomes

Review: How Dietary Fibre, Acting via the Gut Microbiome, Lowers Blood Pressure – Chudan Xu – Current Hypertension Reports

Review: Low FODMAP diet in irritable bowel syndrome: a review of recent clinical trials and meta-analyses – Kevin Whelan – Current Opinion in Clinical Nutrition and Metabolic Care

Review: Prebiotic effects of plant-derived (poly)phenols on host metabolism: Is there a role for short-chain fatty acids? – Perla Lopes de Freitas – Critical Reviews in Food Science and Nutrition

Animal Microbiome

Unveiling biogeographic patterns in the worldwide distributed Ceratitis capitata (medfly) using populations genomics and microbiome composition – María Belén Arias – Molecular Ecology

Differential oral microbiome in nonhuman primates from periodontitis susceptible and resistant matrilines – Jeffrey L Ebersole – Molecular Oral Microbiology

Chicken jejunal microbiota improves growth performance by mitigating intestinal inflammation – Xiaolong Zhang – Microbiome

Bioinformatics and Microbiome Analysis

Comparison Analysis of Different DNA Extraction Methods on Suitability for Long-Read Metagenomic Nanopore Sequencing – Lei Zhang – Frontiers in Cellular and Infection Microbiology

KOMB: K-core based de novo characterization of copy number variation in microbiomes – Advait Balaji – Computational and Structural Biotechnology Journal

CASPER: An Integrated Software Platform for Rapid Development of CRISPR Tools – Brian Mendoza – The CRISPR Journal

Integrating Choline and Specific Intestinal Microbiota to Classify Type 2 Diabetes in Adults: A Machine Learning Based Metagenomics Study – Qiang Zeng – Frontiers in Endocrinology

July 14, 2022

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