Category Archives: Archaea

September 4, 2024

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Good morning (or afternoon, or evening, wherever you are in the world reading this,) Microbiome Digesters! Today’s post features a piece from Nature highlighting the ethical dilemmas and evolving approaches in Indigenous microbiome research. Indigenous peoples have historically faced exploitation through extraction of their lands, biological samples, and genetic data without proper consent. Researchers are re-evaluating their methods, shifting towards more respectful and collaborative practices that involve Indigenous communities in designing studies and ensuring they benefit from the findings. Check out the piece by Sam Jones for Nature to learn more.

An ethical way forward for Indigenous microbiome research – Sam Jones – Nature Outlook: The human microbiome

Human gut microbiome

Interplay between particle size and microbial ecology in the gut microbiome – Jeffrey Letourneau et al – ISME Journal

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome – Niccolò Carlino – Cell

A streamlined culturomics case study for the human gut microbiota research – Hyunjoon Park et al – Scientific Reports

Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia – Getnet Tesfaw et al – Nature Communications

Association of maternal gut microbial metabolites with gestational diabetes mellitus: evidence from an original case-control study, meta-analysis, and Mendelian randomization – Mengxin Yao et al – European Journal of Clinical Nutrition

The Microleaks study: 16S community profile and metagenomic shotgun sequencing signatures associated with anastomotic leak – Emily C. Hoedt et al – NPJ Gut & Liver

Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome – Stefanie Duller et al – Nature Communications

Characterization of gut microbiota in the Uyghur osteopenia population – Kunchen Teng et al – Scientific Reports

Spaceflight alters host-gut microbiota interactions – E. Gonzalez et al – NPJ Biofilms & Microbiomes

Other human microbiome

Bacterial association with metals enables in vivo monitoring of urogenital microbiota using magnetic resonance imaging – Sarah C. Donnelly et al – Communications Biology

Urine metabolomic profiles of autism and autistic traits – A twin study – Abishek Arora et al – PLOS One

Animal microbiome

Massive expansion of the pig gut virome based on global metagenomic mining – Jiandui Mi et al – NPJ Biofilms & Microbiomes

Marine sponge microbe provides insights into evolution and virulence of the tubercle bacillus – Sacha J. Pidot et al – PLOS Pathogens

Exploring the interactions between Nosema ceranae infection and the honey bee gut microbiome – Edmund Lau et al – Scientific Reports

Metagenomic characterisation of canine skin reveals a core healthy skin microbiome – Michaella J. Whittle et al – Scientific Reports

CHIKV infection drives shifts in the gastrointestinal microbiome and metabolites in rhesus monkeys – Hongyu Chen et al – BMC Microbiome

Effects of dietary restriction and one-carbon metabolite supplementation during the first 63 days of gestation on the maternal gut, vaginal, and blood microbiota in cattle – Sarah M. Luecke et al – BMC Animal Microbiome

Aloe arborescens supplementation in drying-off dairy cows: influence on rumen, rectum and milk microbiomes – Paola Cremonesi et al – BMC Animal Microbiome

Comparative genomics identifies key adaptive traits of sponge-associated microbial symbionts – Paul A. O’Brien et al – Environmental Microbiology

Plant, root & soil microbiome

Deciphering the role of rhizosphere microbiota in modulating disease resistance in cabbage varieties – Xingxing Ping et al – BMC Microbiome

Oak seedling microbiome assembly under climate warming and drought – Daniel Hoefle et al – BMC Environmental Microbiome

The ancestral environment of teosinte populations shapes their root microbiome – Christopher J. Barnes et al – BMC Environmental Microbiome

Water & marine microbiome

Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans – Funing Tian et al – BMC Microbiome

Global distribution, diversity, and ecological niche of Picozoa, a widespread and enigmatic marine protist lineage – BMC Microbiome

Microbial core communities in activated sludge plants are strongly affected by immigration and geography – Sofie Zacho Vertergaard et al – BMC Environmental Microbiome

The eukaryome of modern microbialites reveals distinct colonization across aquatic ecosystems – Anthony M. Bonacolta et al – NPJ Biofilms & Microbiomes

Methods & techniques

[PREPRINT] Domestic freezer storage: a solution for preserving stool microbiota integrity for at-home collection – Paula Momo Cabrera et al – bioRxiv

COVID-19 prevention behaviors and dietary habits among undergraduate students: A health belief model approach – Doreen Liou – PLOS One

A catalog of small proteins from the global microbiome – Yiqian Duan et al – Nature Communications

August 8, 2024

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Human respiratory, skin, and gut microbiome

Nurturing futures through the maternal microbiome – Roberta Pala & Katherine Kenny – Sociology of Health & Illness

The skin microbiota of preterm infants and impact of diaper change frequency – Noelle E. Younge et al – PLOS One

Vitamin A carotenoids, but not retinoids, mediate the impact of a healthy diet on gut microbial diversity – Ana M. Valdes et al – BMC Medicine

Gut microbial composition is altered in sarcopenia: A systematic review and meta-analysis of clinical studies – Xiaohong Mai et al – PLOS One

Associations of upper respiratory mucosa microbiota with Rheumatoid arthritis, autoantibodies, and disease activity – Young Bin Joo et al – PLOS One

Effect of β-lactam antibiotics on the gut microbiota of term neonates – Hongdan Gu et al – BMC Annals of Clinical Microbiology & Antimicrobials

Clinical efficacy of a multilamellar cream on skin physiology and microbiome in an epidermal stress model: A controlled double-blinded study – Joachim W Fluhr et al – Int. Journal of Cosmetic Science

Animal experiments

Mouse adaptation of human inflammatory bowel diseases microbiota enhances colonization efficiency and alters microbiome aggressiveness depending on the recipient colonic inflammatory environment – Simon M. Gray et al – BMC Microbiome

Animal microbiome

Gut microbiota composition of the isopod Ligia in South Korea exposed to expanded polystyrene pollution – Young-Mi Lee et al – PLOS One

Effects of a supplemented diet containing 7 probiotic strains (Honeybeeotic) on honeybee physiology and immune response: analysis of hemolymph cytology, phenoloxidase activity, and gut microbiome – Patrizia Robino et al – BMC Biological Research

Survey of antimicrobial and probiotic use practices in wildlife rehabilitation in the United States – Elizabeth A. Miller et al – PLOS One

The impact of management on the fecal microbiome of endangered greater sage-grouse (Centrocercus urophasianus) in a zoo-based conservation program – Emma Vaasjo et al – Conservation Physiology

Water & extremophile microbiome

Microdiversity in marine pelagic ammonia-oxidizing archaeal populations in a Mediterranean long-read metagenome – Pablo Suárez-Moo et al – Environmental Microbiology

Production of structurally diverse sphingolipids by anaerobic marine bacteria in the euxinic Black Sea water column – Su Ding et al – ISME Journal

Plant, root & soil microbiome

Characterization of fungal microbiome structure in leaf litter compost through metagenomic profiling for harnessing the bio-organic fertilizer potential – Sophayo Mahongnao et al – 3Biotech

Plant species influences the composition of root system microbiome and its antibiotic resistance profile in a constructed wetland receiving primary treated wastewater – Valentina Riva et al – Frontiers in Microbiology

DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories – Esteban E. Nieto et al – BMC Microbiome

Seed endophytes and rhizosphere microbiome of Imperata cylindrica, a pioneer plant of abandoned mine lands – Wenqin Mao et al – Frontiers in Microbiology

Temperature-dependent trophic associations modulate soil bacterial communities along latitudinal gradients – Xing Huang et al – ISME Journal.

Microbial ecology

[PREPRINT] Models of microbiome evolution incorporating host resource provisioning – Yao Xiao et al – bioRxiv

Beneficial microbes & compounds

Combining Bifidobacterium longum subsp. infantis and human milk oligosaccharides synergistically increases short chain fatty acid production ex vivo – Florac De Bruyn et al – Nature Communications Biology

July 31, 2024

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Human gut microbiome

The gut mycobiome signatures in long-lived populations – Lixia Pu et al – Cell iScience

Viral metagenomics combined with non-targeted serum metabolomics reveals the role of enteroviruses in a mouse model of coronary heart disease – Xiang Li et al – BMC Virology

Core microbiome-associated proteins associated with ulcerative colitis interact with cytokines for synergistic or antagonistic effects on gut bacteria – Ting Zhang et al – ISME Journal

Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota – David Bars-Cortina et al – BMC Genomics

Effect of different delivery modes on intestinal microbiota and immune function of neonates – Chunhui Lai et al – Scientific Reports

Animal experiments

Effects of Akkermansia muciniphila on Gut Morphology, Antioxidant Indices, and Gut Microbiome of Mice Under Heat Stress – Caiyu Luo et al – Foodborne Pathogens and Disease

Gut microbiota mediates the anti-inflammatory effects of supplemental infrared irradiation in mice – Shijing Wang et al – Photochemistry and Photobiology

Short-chain fatty acids ameliorate imiquimod-induced skin thickening and IL-17 levels and alter gut microbiota in mice: a metagenomic association analysis – Yi-Ju Chen et al – Scientific Reports

Animal microbiome

Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termite Coptotermes formosanus – Masayuki Kaneko et al – ISME Communications

Rodents consuming the same toxic diet harbor a unique functional core microbiome – Tess E. Stapleton et al – BMC Animal Microbiome

The plant-sucking insect selects assembly of the gut microbiota from environment to enhance host reproduction – Hong-Wei Shan et al – NPJ Biofilms and Microbiomes

Alterations in captive Alexandrine parakeet (Palaeornis eupatria) gut microbiome and metabolome in response to dietary change – Xin Feng et al – Comparative Biochemistry and Physiology

Link between bacterial communities and contrasted loads in ectoparasitic monogeneans from the external mucus of two wild sparid species (Teleostei) – Judith Revault et al – BMC Animal Microbiome

Beneficial microbes and compounds

Unearthing Lactococcus lactis and Scheffersomyeces symbionts from edible wood-boring beetle larvae as a bio-resource for industrial applications – Shadrick Kibet et al – BMC Microbiology

Plant, root, and soil microbiome

[OPINION] Microbiome Bioprospecting for Sustainable Agrobiome and Circular Bioeconomy – Dhananjaya Pratap Singh – Anthropocene Science

Host genetic variation and specialized metabolites from wheat leaves enriches for phyllosphere Pseudomonas spp. with enriched antibiotic resistomes – Qian Xiang et al – ISME Journal

Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health – Morgane Duret et al – Microbiological Research

Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan – Kohei Hamamoto et al – BMC Environmental Microbiome

July 25, 2024

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Pregnancy and early life

Human cytomegalovirus in breast milk is associated with milk composition and the infant gut microbiome and growth – Johnson et al. – Nature Communications

[PREPRINT]First-Year Dynamics of the Anaerobic Microbiome and Archaeome in Infants Oral and Gastrointestinal Systems – Neumann et al. – bioRxiv

Human skin microbiome

A Mendelian randomization analysis reveals the multifaceted role of the skin microbiota in liver cancer – Wang & Zhu – Frontiers in Microbiology

Metagenomic sequencing of the skin microbiota of the scalp predicting the risk of surgical site infections following surgery of traumatic brain injury in sub-Saharan Africa – Lekuya et al. – PLOS One

Human gut microbiome

[REVIEW]The interplay between diet and the gut microbiome: implications for health and disease – Ross et al. – Nature Reviews Microbiology

Microbiota composition effect on immunotherapy outcomes in colorectal cancer patients: A systematic review – Ajab et al. – PLOS One

Animal microbiome

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia – Glendinning et al. – Microbiome

Effect of soybean and seaweed-based diets on growth performance, feed utilization, and gut microbiota of tilapia: A systematic review and meta-analysis – Viagem et al. – PLOS One

Plant, root, and soil microbiome

Plant species influences the composition of root system microbiome and its antibiotic resistance profile in a constructed wetland receiving primary treated wastewater – Riva et al. – Frontiers in Microbiology

Phages and viruses

Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer – Ivancevic et al. – Science Advances

The plasma viral communities associate with clinical profiles in a large-scale haematological patients cohort – Ma et al. – Microbiome

Viruses of free-roaming and hunting dogs in Uganda show elevated prevalence, richness and abundance across a gradient of contact with wildlife – Tayebwa et al. – Journal of General Virology

July 7, 2024

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Human and General Microbiome

Changes in the gut microbiome of patients with esophageal cancer: a systematic review and meta-analysis based on 16S gene sequencing technology – Jieyin Deng – Microbial Pathogenesis

Integrated metagenomic and metabolomic analysis reveals distinctive stage-specific gut-microbiome-derived metabolites in intracranial aneurysms – Haitao Sun – Gut

After surgically induced remission, ileal and colonic mucosa-associated microbiota predicts Crohn’s disease recurrence – Cristian-Hernandez Rocha – Clinical Gastroenterology and Hepatology

Human gut microbiota analysis of cystic fibrosis infants using metaproteomics – C García-Durán – Microbiology Resource Announcements

Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages – Shivkumar Vishnempet Shridhar – Cell Reports

Perturbations in gut microbiota composition in schizophrenia – YiMeng Wang – PloS One

Maternal gestational diabetes mellitus associates with altered gut microbiome composition and head circumference abnormalities in male offspring – Shilan Wang – Cell host & Microbe

Microbial signatures and continuum in endometrial cancer and benign patients – Anita Semertzidou – Microbiome

Comparison of shipping versus immediate freezer storage of vaginal samples for vaginal microbiota assessment – Susan Tuddenham – Sexually Transmitted Infections

Letter: Real-world bisphenol A exposure not linked to microbiota dynamics in childhood obesity – Robyn L Prueitt – mSystems

Essay: Blockbuster T cells in the gut: A high-resolution view of immune modulation by the gut microbiome is presented – Kazuki Nagashima – Science

Review: Gut microbiota-lncRNA/circRNA crosstalk: implications for different diseases – Lei Zhang – Critical Reviews in Microbiology

Review: The role of gut microbiota, exosomes, and their interaction in the pathogenesis of ALD – Zilu Cheng – Journal of Advanced Research

Review: Integrating host and microbiome biology using holo-omics – Carl M Kobel – Molecular Omics

Beneficial Microbes, Compounds, and Interventions

Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments – Torben Sølbeck Rasmussen – Microbiome

Fecal microbiota transplantation alters gut phage communities in a clinical trial for obesity – Michele Zuppi – Microbiome

A meta-analysis of randomized controlled trials evaluating the effectiveness of fecal microbiota transplantation for patients with irritable bowel syndrome – Yu Wang – BMC Gastroenterology

Faecalibaterium prausnitzii strain EXL01 boosts efficacy of immune checkpoint inhibitors – Marius Bredon – Oncoimmunology

Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer’s disease – Annalise Schweickart – NPJ Metabolic Health and Disease

Oral histidine affects gut microbiota and MAIT cells improving glycemic control in type 2 diabetes patients – Moritz V Warmbrunn – Gut Microbes

The Evolution of Science and Regulation of Dietary Supplements: Past, Present, and Future – Paul M Coates – The Journal of Nutrition

Review: Dietary patterns interfere with gut microbiota to combat obesity – Xiaofan Lou – Frontiers in Nutrition

Plant Microbiome

Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health – Sang-Moo Lee – The ISME Journal

Review: Unearthing the power of microbes as plant microbiome for sustainable agriculture – Arpan Mukherjee – Microbiological Research

Review: Surviving the Stress: Understanding the Molecular Basis of Plant Adaptations and Uncovering the Role of Mycorrhizal Association in Plant Abiotic Stresses – Vivek Sharma – Microbial Pathogenesis

Environmental Microbiome

The drainome: longitudinal metagenomic characterisation of wastewater from hospital ward sinks to characterize the microbiome and resistome and assess the effects of decontamination interventions – Luke B Snell – The Journal of Hospital Infection

Review: Beyond Meta-Omics: Functional Genomics in Future Marine Microbiome Research – Yin Chen – Annual Review of Marine Science

Review: Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges – Haixia Pan – Current Microbiology

Forensic Microbiome

16S rRNA, metagenomics and 2bRAD-M sequencing to decode human thanatomicrobiome – Xin Huang – Scientific Data

Microbiome Analysis

A graph neural network approach for predicting drug susceptibility in the human microbiome – Maryam – Computers in Biology and Medicine

Protocol for the construction and functional profiling of metagenome-assembled genomes for microbiome analyses – Goutam Banerjee – STAR Protocols

DeepPIG: deep neural network architecture with pairwise connected layers and stochastic gates using knockoff frameworks for feature selection – Euiyoung Oh – Scientific Reports

CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets – Orges Koci – Microbiome

June 19, 2024

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Oral and respiratory microbiota

Safety, Feasibility, and Advantages of Oral Microbiota Transplantation: The First Clinical Case – Oleg V. Goloschapov – Journal of Pediatric Hematology/Oncology

Oral microbial dysbiosis in patients with oral cavity cancers – Ozge Unlu – Clinical Oral Investigations

Nasal cathelicidin is expressed in early life and is increased during mild, but not severe respiratory syncytial virus infection – Sofia Sintoris – Nature Scientific Reports

Human gut microbiome

Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges – Lucas Masier – Nature Metabolism

Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice – Yohannes Seyoum – Nature Communications

Beneficial microbes and compounds

Short-chain fatty acid valerate reduces voluntary alcohol intake in male mice – Suresh C. Bokoliya – BMC Microbiome

Sleep promoting and omics exploration on probiotics fermented Gastrodia elata Blume – Chao-Qi Zhang – NPJ Science of Food

Animal microbiome

Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human – Li Tian – BMC Microbiome

Water and extremophile microbiome

Bacterial community and cyanotoxin gene distribution of the Winam Gulf, Lake Victoria, Kenya – Katelyn M. Brown – Environmental Microbiology

Genome-wide screen of genetic determinants that govern Escherichia coli growth and persistence in lake water – Nataliya Teteneva – ISME Journal

Plant, root, and soil microbiomes

Root-associated Streptomyces produce galbonolides to modulate plant immunity and promote rhizosphere colonization – Clément Nicolle – ISME Journal

Organic fertilization co-selects genetically linked antibiotic and metal(loid) resistance genes in global soil microbiome – Zi-Teng Liu – Nature Communications

Conceptualizing soil fauna effects on labile and stabilized soil organic matter – Gerrit Angst – Nature Communications

Fungi

The first ITS1 profiling of honey samples from the Southeast Asian region Lombok, Bali and Banggi Island – Saeed Ullah – Nature Scientific Reports

Archaea

Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery – Biyan Huang – ISME Journal

Microbial Ecology

Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution – Hagay Enav – Nature Biotechnology

Methods

High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding – Karl D. Gaisser – Nature Protocols

Commentary and opinions

SeqCode in the golden age of prokaryotic systematics – Diego Javier Jiménez – ISME Journal

Digestive Disease Week 2024 – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Barriers and enablers to the effective implementation of omics research in low- and middle-income countries – Jacus S. Nacis – Nature Biotechnology

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

February 25th, 2023

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Bonjour from Paris, France !

In today’s digest you will find a broad range of amazing preprints and published papers! Fontana and collaborator performed a fascinating meta-analysis of publicly datasets obtained from fecal samples of healthy athletes and healthy sedentary adults and revealed the microbiota changes associated with competitive athletes lifestyle.

Today’s non-microbiology pick is an preprint exploring postdoctoral and PhD student’s career self-efficacy in US biological sciences and showed how women and non US citizen have a significant lower level of career self-efficacy compared to their male and US citizen peers. The authors discuss potential causes for these differences and offer recommendations for increasing trainee career self-efficacy.

Have a great Saturday!

Pregnancy and early life

Preprint: Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition – Li et al. – BioRXiv

Human gut microbiome

The human gut microbiome of athletes: metagenomic and metabolic insights – Fontana et al. – Microbiome

Review: Gut microbiome-based strategies for host health and disease – Wang et al. – Critical Reviews in Food Science and Nutrition

The role of diet in shaping human gut microbiota – Rinninella et al. – Best practive & Research clinical Gastroenterology

Preprint: Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria – Robitaille et al. – BioRXiv

Genetic-Phenotype Analysis of Bifidobacterium bifidum and Its Glycoside Hydrolase Gene Distribution at Different Age Groups – Wei et al. – Foods

Animal microbiome

Preprint: Life stage and vaccination shape the gut microbiome of hatchery-reared Atlantic salmon (Salmo salar) – Andres et al. – BioRXiv

Plant, root, and soil microbiome

Preprint: Short- and long-term effects of continuous compost amendment on soil microbiome community – Kraut-Cohen et al. – BioRXiv

Awaking the Dormant Virome in the Rhizosphere – Braga and Schumacher – Molecular ecology

Water and extremophile microbiome

Preprint: A novel order-level lineage of ammonia-oxidizing Thaumarchaeota is widespread in marine and terrestrial environments – Zheng et al. – BioRXiv

Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics – Dart et al. – Viruses

Food microbiology

Analysis of the core bacterial community associated with consumer-ready Eastern oysters (Crassostrea virginica) – Hines et al. – Plos One

Phages and viruses

Review: The Role of Temperate Phages in Bacterial Pathogenicity – Gummalla et al. – Microorganisms

Bioinformatics

Review: Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses – Ibanez-Lligona et al – Viruses

Non microbiology pick

Preprint: Citizenship status and career self-efficacy: An intersectional study of biomedical trainees in the United States – Chatterjee et al. – BioRXiv

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