Category Archives: Extremophiles

January 31, 2024

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General microbiome

Finding Candida auris in public metagenomic repositories – Mario-Vasquez et al. – PLOS One

Pregnancy and early life

A pilot study of fecal pH and redox as functional markers in the premature infant gut microbiome – Letourneau et al. – PLOS One

[PREPRINT]Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother’s milk – Allert et al. – bioRxiv

Human nasal microbiome

A genome-wide association study reveals the relationship between human genetic variation and the nasal microbiome – Liu et al. – Communications Biology

Human gut microbiome

Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans – Link et al. – Nature Medicine

Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago – Nishimura et al. – PLOS One

[PREPRINT]Unravelling the ancient fungal DNA from the Iceman’s gut – Oskolkov et al. – bioRxiv

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

Streptococcus anginosus promotes gastric inflammation, atrophy, and tumorigenesis in mice – Fu et al. – Cell

Gut complement induced by the microbiota combats pathogens and spares commensals – Wu et al. – Cell

Complement in breast milk modifies offspring gut microbiota to promote infant health – Xu et al. – Cell

Antidiabetic effects and mechanism of γ-polyglutamic acid on type II diabetes mice – Li et al. – International Journal of Biological Macromolecules

Bacterial microbiome associated with cigarette beetle Lasioderma serricorne (F.) and its microbial plasticity in relation to diet sources – Srinivasan et al. – PLOS One

Animal microbiome (for animals in the wild)

Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids – Chai et al. – Microbiome

[PREPRINT]Thermal fluctuations independently modulate physiological plasticity and the dynamics of the gut microbiome in a tropical rocky shore oyster – Arromrak et al. – bioRxiv

[PREPRINT]Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean – Williams et al. – bioRxiv

Plant, root, and soil microbiome

[PREPRINT]Temporal and spatial dynamics within the fungal microbiome of grape fermentation – Onetto et al. – bioRxiv

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

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism – Valentin-Alvarado et al. – Microbiome

Phages and viruses

[PREPRINT]Viroid-like colonists of human microbiomes – Zheludev et al. – bioRxiv

Bioinformatics

[PREPRINT]DeepGOMeta: Predicting functions for microbes – Hoehndorf et al. – bioRxiv

[PREPRINT]Predicting microbial genome-scale metabolic networks directly from 16S rRNA gene sequences – Øyås et al. – bioRxiv

Techniques

[REVIEW]Unraveling metagenomics through long-read sequencing: a comprehensive review – Kim et al. – Journal of Translational Medicine

Microbes in the news

Non-prescription therapeutics for IBS: where are we? – Costantino – Gut Microbiota for Health by ESNM

May 16, 2023

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Happy Tuesday! Today’s microbiome digest is microbial ecology heavy, with articles focused on the gut microbiome, Antarctic endoliths’, water microbiomes, and more.

Human gut microbiome

Pathobionts in the tumour microbiota predict survival following resection for colorectal cancer – Alexander et al. – Microbiome

Gut microbiome transitions across generations in different ethnicities in an urban setting—the HELIUS study – van der Vossen et al. – Microbiome

Water and extremophile microbiome

Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability – Ettinger et al. – Microbiome

Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes – Vigneron et al. – Microbiome

preprint: Allochthonous groundwater microorganisms affect coastal seawater microbial abundance, activity and diversity – Yanuka-Golub et al. – bioRxiv

Built environment

preprint: Microbial Diversity on Ancestral Halls with Different Visitor Flow Rates Using Amplicon Sequencing – Liu et al. – bioRxiv

Techniques

Comparing genomes recovered from time-series metagenomes using long- and short-read sequencing technologies – Orellana et al. – Microbiome

May 5, 2023

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Today’s microbiome digest is a grab bag that includes ten simple rules for working with other people’s code, an article examining Wolbachia infections in native cockroach populations, and an article examining the role in lactic acid in shaping the human microbiome. Also highlighted is an article focused on human viruses residing within our cells and tissues, which demonstrated a unique virome in nine different human organs through targeted-enrichment viral metagenomics and virus specific qPCRs.

Happy reading!

General microbiome

The structure of prevacuolar compartments in Neurospora crassa as observed with super-resolution microscopy – Bowman – PLOS One

Phylogenetic trees of closely related bacterial species and subspecies based on frequencies of short nucleotide sequences – Nakano et al. – PLOS One

***Unmasking the tissue-resident eukaryotic DNA virome in humans – Pyöriä et al. – Nucleic Acids Research

Predicting partner fitness based on spatial structuring in a light-driven microbial community – Sakkos et al. – PLOS Computational Biology

Multi-site human microbiome

Evaluation of alcohol-free mouthwash for studies of the oral microbiome – Yano et al. – PLOS One

A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome – Zhang et al. – Microbiome

Human gut microbiome

Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the “Lunar Palace 365” experiment – Hao et al. – Microbiome

Animal microbiome

Wolbachia infection in native populations of Blattella germanica and Periplaneta americana – Choubdar et al. – PLOS One

Plant, root, and soil microbiome

Bacterial and fungal community composition and community-level physiological profiles in forest soils – Kunito et al. – PLOS One

Water and extremophile microbiome

Predicting microbial community compositions in wastewater treatment plants using artificial neural networks – Liu et al. – Microbiome

Open ocean and coastal strains of the N2-fixing cyanobacterium UCYN-A have distinct transcriptomes – Muñoz-Marín et al. – PLOS One

Meta-organism gene expression reveals that the impact of nitrate enrichment on coral larvae is mediated by their associated Symbiodiniaceae and prokaryotic assemblages – Tong et al. – Microbiome

Bioinformatics

Ten simple rules for working with other people’s code – Pilgrim et al. – PLOS Computational Biology

Predicting microbe organisms using data of living micro forms of life and hybrid microbes classifier – Raza et al. – PLOS One

iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria – Roux et al. – PLOS Biology

December 12, 2022

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Today’s digest has the kind of articles I like best–they are all focused on the unique relationship between microbial communities and their niche environments. These environments span everything from rice seeds to the Mariana Trench to the gut microbiome and even Appalachian coalbeds. Happy reading!


Human gut microbiome

Gut microbiome of helminth-infected indigenous Malaysians is context dependent – Tee et al. – Microbiome

Animal experiments

Taurine metabolism is modulated in Vibrio-infected Penaeus vannamei to shape shrimp antibacterial response and survival – Wang et al. – Microbiome


Plant, root, and soil microbiome

Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome – Mataigne et al. – Microbiome

Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes – Zhang et al. – Microbiome


Water and extremophile microbiome

Comparison of prokaryotes between Mount Everest and the Mariana Trench – Liu et al. – Microbiome


Built environment

Predominance of Methanomicrobiales and diverse hydrocarbon-degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome-resolved metabolisms – Ross et al. – Environmental Microbiology

Evaluation of the Microbial Community and Geochemistry in Produced Waters Collected from CO2 EOR in the Niagaran Pinnacle Reef – Stemple et al. – ACS Earth Space Chem

September 22, 2022

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Happy almost Friday! Today’s digest includes a time series tracking changes after fecal transplant, biofilm-formation analysis from isolations from swine slaughterhouses as well as techniques to improve computational notebooks, rapid genotyping, and more.

Enjoy!

Human gut microbiome

Time series strain tracking analysis post fecal transplantation identifies individual specific patterns of fecal dominant donor, recipient, and unrelated microbial strains – Koo & Morrow – PLOS One

Animal experiments

Microbiome complexity shapes metabolism – Litichevskiy & Thaiss – PLOS Biology

Minimal overall divergence of the gut microbiome in an adaptive radiation of Cyprinodon pupfishes despite potential adaptive enrichment for scale-eating – Heras & Martin – PLOS One

Molecular characterization and biofilm-formation analysis of Listeria monocytogenes, Salmonella spp., and Escherichia coli isolated from Brazilian swine slaughterhouses – Santos et al. – PLOS One

Animal microbiome

Ecology and distribution of Leptospira spp., reservoir hosts and environmental interaction in Sri Lanka, with identification of a new strain – Sluydts et al. – PLOS Neglected Tropical Diseases

Techniques

A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research – Figueiredo et al. – PLOS Computational Biology

Bacterial concentration and Campylobacter spp. quantification differ when fresh or ultra-frozen samples are analysed over time using molecular biology and culture-based methods – Khattak et al. – Plos One

Robust inference of population size histories from genomic sequencing data – Upadhya & Steinrücken – PLOS Computational Biology

Rapid genotyping of targeted viral samples using Illumina short-read sequencing data – Váradi et al. – PLOS One

Improved assessments of bulk milk microbiota composition via sample preparation and DNA extraction methods – Xue & Marco – PLOS ONE

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

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 4, 2022

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Highlights!

Review: Translating Microbiome Research From and To the Clinic – Zhenrun J Zhang – Annual Review of Microbiology → An exploration of different experimental studies associating the gut microbiota with certain human diseases, highlighting translational advances 

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome – Wenshan Zheng – Science → A powerful technique to obtain single amplified genomes (SAG) from human microbiome samples 

Human and General Microbiome

Review: Gut microbiota and atopic dermatitis in children: a scoping review – Yue Liu – BMC Pediatrics

Review: Gut microbiome and autoimmune disorders – Walaa Abdelaty Shaheen – Clinical and Experimental Immunology

Altered Vaginal Microbiota Composition Correlates With Human Papillomavirus and Mucosal Immune Responses in Women With Symptomatic Cervical Ectopy – Mariana López-Filloy – Frontiers in Cellular and Infection Microbiology

Profile of the Nasopharyngeal Microbiota Affecting the Clinical Course in COVID-19 Patients – Ornella la Fortune Tchoupou Saha – Frontiers in Microbiology

Machine learning aided construction of the quorum sensing communication network for human gut microbiota – Shengbo Wu – Nature Communications

Metagenomic assembled plasmids of the human microbiome vary across disease cohorts – S R Stockdale – Scientific Reports

Gut microbial metabolites in Parkinson’s disease: Association with lifestyle, disease characteristics, and treatment status – Robin M Voigt – Neurobiology of Disease

Mechanistic insights into accelerated α-synuclein aggregation mediated by human microbiome-associated functional amyloids – Sujeet S Bhoite – The Journal of Biological Chemistry

Gut bacterial isoamylamine promotes age-related cognitive dysfunction by promoting microglial cell death – Yun Teng – Cell Host & Microbe

Beneficial Microbes and Compounds

Review: A Review: Cereals on Modulating the Microbiota/Metabolome for Metabolic Health – Jayani Kulathunga – Current Nutrition Reports

Anti-Diabetic Potential of Chlorella pyrenoidosa-Based Mixture and its Regulation of Gut Microbiota – Wenyu Xiong – Plant Foods for Human Nutrition

Exploring the Ecological Effects of Naturally Antibiotic-Insensitive Bifidobacteria in the Recovery of the Resilience of the Gut Microbiota during and after Antibiotic Treatment – Chiara Argentini – Applied and Environmental Microbiology

Animal Microbiome

Synchrony and idiosyncrasy in the gut microbiome of wild baboons – Johannes R Björk – Nature Ecology & Evolution

Environmental Microbiome

A synergistic bacterial pool decomposes tebuthiuron in soil – Edivaldo Wilson de Lima – Scientific Reports

The microbiome of cryospheric ecosystems – Massimo Bourquin – Nature Communications

Extremophiles

Bacterial diversity and community structure in the rhizosphere of the halophyte Halocnemum strobilaceum in an Algerian arid saline soil – Sabrina Behairi – Extremophiles

Bioinformatics and Microbiome Analysis

Multiscale analysis of count data through topic alignment – Julia Fukuyama – Biostatistics

SAMBA: A Multicolor Digital Melting PCR Platform for Rapid Microbiome Profiling – Yongqiang Luo – Small Methods

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