Monthly Archives: August 2022

August 10, 2022

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General microbiome

Microbiome-associated human genetic variants impact phenome-wide disease risk – Markowitz et al. – PNAS

Microbial risk score for capturing microbial characteristics, integrating multi-omics data, and predicting disease risk – Wang et al. – Microbiome

[REVIEW]A framework for testing the impact of co-infections on host gut microbiomes – Schmid et al. – Animal Microbiome

Human vaginal microbiome

Vaginal microbiota and personal risk factors associated with HPV status conversion—A new approach to reduce the risk of cervical cancer? – Yang et al. – PLOS One

Human gut microbiome

[REVIEW]The role of the gut microbiota in multiple sclerosis – Correale, Hohlfeld & Baranzini

Specific gut microbiota alterations in essential tremor and its difference from Parkinson’s disease – Zhang et al. – NPJ Parkinson’s Disease

Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics – Podlesny et al. – Cell Reports Medicine

Alterations in gut microbiota of esophageal squamous cell carcinoma patients – Cheung et al. – Journal of Gastroenterology and Hepatology

Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation – Federici et al. – Cell

Animal microbiome

Camel milk microbiota: A culture-independent assessment – Rahmeh et al. – Food Research International

Effect of processing on the anti-inflammatory efficacy of cocoa in a high fat diet-induced mouse model of obesity – Weikart et al. – The Journal of Nutritional Biochemistry

The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs – Gaire et al. – Microbiome

Plant, root, and soil microbiome

Soil microbial community structures are shaped by agricultural systems revealing little temporal variation – Fox, Widmer & Lüscher – Environmental Research

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

The streamwater microbiome encodes hydrologic data across scales – URycki et al. – Science of The Total Environment

Bioinformatics / Data

[PREPRINT]Lake iTag measurements over nineteen years, introducing the limony dataset – Rohwer & McMahon – bioRxiv

August 6, 2022

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Human and General Microbiome

The oral microbiome and lung cancer risk: An analysis of 3 prospective cohort studies – Emily Vogtmann – Journal of the National Cancer Institute

Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries – M J Carvalho – Nature Microbiology

Crosstalk between mucosal microbiota, host gene expression, and sociomedical factors in the progression of colorectal cancer – Namjoo Kim – Scientific Reports

Using Culture-Enriched Phenotypic Metagenomics for Targeted High-Throughput Monitoring of the Clinically Important Fraction of the β-Lactam Resistome – Zhiguo Zhang – Environmental Science & Technology

Review: Porphyromonas gingivalis and dental stem cells crosstalk amplify inflammation and bone loss in the periodontitis niche – Devaraj Ezhilarasan – Journal of Cellular Physiology

Beneficial Microbes and Compounds

On the effect of flavonoids and dietary fibre in lingonberries on atherosclerotic plaques, lipid profiles and gut microbiota composition in Apoe(-/-) mice – Jiyun Liu – International Journal of food Sciences and Nutrition

The Gut-Brain-Microbiome Connection: Can Probiotics Decrease Anxiety and Depression? – Jennifer Maybee – Issues in Mental Health Nursing

The effect of Lactobacillus rhamnosus B10 on alcoholic liver injury and intestinal microbiota in alcohol-induced mice model – Xia Li – Journal of Food Biochemistry

Model Animal Microbiome

The effect of young blood plasma administration on gut microbiota in middle-aged rats – Taha Ceylani – Archives of Microbiology

Non-Model Animal Microbiome

Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus – Aleksandra I Krawczyk – Microbiome

Host taxonomy determines the composition, structure, and diversity of the earthworm cast microbiome under homogenous feeding conditions – Manuel Aira – FEMS Microbiology Ecology

Ruminal Microbiota Determines the High-Fiber Utilization of Ruminants: Evidence from the Ruminal Microbiota Transplant – Xiaodong Chen – Microbiology Spectrum

Bioinformatics and Microbiome Analysis Techniques

Computational approach to modeling microbiome landscapes associated with chronic human disease progression – Lu Li – PLoS Computational Biology

Guideline for the analysis of the microbial communities of the human upper airways – Leonardo Mancabelli – Journal of Oral Microbiology

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

August 03, 2022

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Pregnancy and early life

The abundance of Ruminococcus bromii is associated with faecal butyrate levels and atopic dermatitis in infancy – Sasaki et al. – Allergy

Human oral microbiome

Smokeless tobacco consumption induces dysbiosis of oral mycobiome: a pilot study – Sajid et al. – Applied Microbiology and Biotechnology

Human gut microbiome

The Proteome of Extracellular Vesicles Produced by the Human Gut Bacteria Bacteroides thetaiotaomicron In Vivo Is Influenced by Environmental and Host-Derived Factors – Stentz et al. – Applied and Environmental Microbiology

Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains – FitzGerald et al. – Gut Microbes

[REVIEW]Targeting microbiota-host interactions with resveratrol on cancer: Effects and potential mechanisms of action – Wang et al. – Critical Reviews in Food Science and Nutrition

Emerging frontiers of antibiotics use and their impacts on the human gut microbiome – Kumari et al. – Microbiological Research

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

Microbiota of the Pregnant Mouse: Characterization of the Bacterial Communities in the Oral Cavity, Lung, Intestine, and Vagina through Culture and DNA Sequencing – Greenberg et al. – Microbiology Spectrum

Phages and viruses

Viral biogeography of the mammalian gut and parenchymal organs – Shkoporov – Nature Microbiology

Bioinformatics

Namco: a microbiome explorer – Dietrich et al. – Microbial Genomics

MiCloud: A unified web platform for comprehensive microbiome data analysis – Gu et al. – PLOS One

August 1st, 2022

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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.