Category Archives: Water microbiome

November 28, 2023

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Pregnancy and early life

[PREPRINT]Delivery mode impacts gut bacteriophage colonization during infancy – Subramanian et al. – medRxiv

Human oral microbiome

Oral microbiota analyses of paediatric Saudi population reveals signatures of dental caries – Alyousef et al. – BMC Oral Health

Human gut microbiome

Gastric coinfection with thiopeptide-positive Cutibacterium acnes decreases FOXM1 and pro-inflammatory biomarker expression in a murine model of Helicobacter pylori-induced gastric cancer – Lunger et al. – Microbiology Spectrum

[REVIEW]Butterflies in the gut: the interplay between intestinal microbiota and stress – Lai et al. – Journal of Biomedical Science

[REVIEW]Genetics, Nutrition, and Health: A New Frontier in Disease Prevention – Agrawal et al. – Journal of the American Nutrition Association

Age-dependent changes in the gut microbiota and serum metabolome correlate with renal function and human aging – Sun et al. – Aging Cell

The changes of gut microbiota and metabolites in different drug-induced liver injuries – Zhu et al. – Journal of Medical Microbiology

[PREPRINT]The differing prevalences of propionate and butyrate producing bacteria in the human gut microbiota – Christensen et al. – bioRxiv

[PREPRINT]The Parkinson’s drug entacapone disrupts gut microbiome homeostasis via iron sequestration – Pereira et al. – bioRxiv

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

Mutual modulation of gut microbiota and the immune system in type 1 diabetes models – Rosell-Mases et al. – Nature Communications

[PREPRINT]Microbiota-dependent early life programming of gastrointestinal motility – Frith et al. – bioRxiv

Horizontal transmission of gut microbiota attenuates mortality in lung fibrosis – Gurczynski et al. – JCI insight

High-altitude and low-altitude adapted chicken gut-microbes have different functional diversity – Bhagat et al. – Scientific Reports

Animal microbiome (for animals in the wild)

Introducing an environmental microbiome to axenic Aedes aegypti mosquitoes documents bacterial responses to a blood meal – LaReau et al. – Applied and Environmental Microbiology

Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer – Zhuang et al. – Microbiology Spectrum

Plant, root, and soil microbiome

[PREPRINT]Global patterns in gene content of soil microbiomes emerge from microbial interactions – Crocker et al. – bioRxiv

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

Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India – Brar et al. – Journal of Genetic Engineering and Biotechnology

Bioinformatics

mb-PHENIX: Diffusion and Supervised Uniform Manifold Approximation for denoising microbiota data – Padron-Manrique et al. – Bioinformatics

Facilitating bioinformatics reproducibility with QIIME 2 provenance Replay – Keefe et al. – PLOS Computational Biology

Techniques

High-throughput identification and quantification of bacterial cells in the microbiota based on 16S rRNA sequencing with single-base accuracy using BarBIQ – Jin, Yamamoto & Shiroguchi

November 10, 2023

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Read about new species discovered in the female genitourinary tract Lactobacillus isalae, Gardnerella pickettii and Gardnerella greenwoodii, and important UTI and other latest microbiome science news.
Happy Friday! And see you next week at MVIF!

Urinary microbiome

A human urothelial microtissue model reveals shared colonization and survival strategies between uropathogens and commensals – Carlos Flores – Science Advances

Gardnerella pickettii sp. nov. (formerly Gardnerella genomic species 3) and Gardnerella greenwoodii sp. nov. (formerly Gardnerella genomic species 8) isolated from female urinary microbiome – Márcia Sousa – International Journal of Systematic and Evolutionary Microbiology

Vaginal microbiome

Lactobacillus isalae sp. nov., isolated from the female reproductive tract – Tom Eilers – International Journal of Systematic and Evolutionary Microbiology

Identification of a DNA-cytosine methyltransferase that impacts global transcription to promote group B streptococcal vaginal colonization – Haider S. Manzer – mBio

Gut microbiome

Aggression: A gut reaction? The effects of the gut microbiome on aggression – Atara Uzan-Yulzari – bioRxiv

Oral microbiome

Establishment of tongue microbiota by 18 months of age and determinants of its microbial profile – Shinya Kageyama – mBio

Animal microbiome

Pet cats may shape the antibiotic resistome of their owner’s gut and living environment – Yiwen Yang – Microbiome

The impact of kit, environment and sampling contamination on the observed microbiome of bovine milk – Christopher J Dean – bioRxiv

Animal experiments

Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease – Lola Holcomb – mSystems

Daily fluctuation of colonic microbiome in response to nutrient substrates in a pig model – Hongyu Wang – npj Biofilms and Microbiomes

Water microbiome

Assessing the impact of anti-microbial showerheads on the prevalence and abundance of opportunistic pathogens in shower water and shower water-associated aerosols – Sarah Pitell, Sarah-Jane Haig – Frontiers in Microbiomes

Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants – Huifeng Hu – bioRxiv

Technique

A high-throughput and low-waste viability assay for microbes – Christian T. Meyer – Nature Microbiology

Bioinformatics

Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses – Saioa Manzano-Morales – Genome Biology

ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool – Hoon Je Seong – Briefings in Bioinformatics


October 18, 2023

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Human gut microbiome

Association between gut microbiota and influenza: a bidirectional two-sample mendelian randomization study – Xu et al. – BMC Infectious Diseases

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

LACC1 regulates changes in the intestinal flora in a mouse model of inflammatory bowel disease – Xu & Wang – BMC Gastroenterology

Animal microbiome (for animals in the wild)

[PREPRINT]Sex-specific gut bacteria manipulation impacts offspring production in the honeybee parasite small hive beetle, Aethina tumida Murray – Biswas et al. – bioRxiv

Selective enrichment of founding reproductive microbiomes allows extensive vertical transmission in a fungus-farming termite – Sinotte et al. – Proc. R. Soc. B

Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing – Klinsawat et al. – Scientific Reports

Temporal and spatial variations in body mass and thermogenic capacity associated with alterations in the gut microbiota and host transcriptome in mammalian herbivores – Ren et al. – Science of The Total Environment

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

Metagenome sequencing and recovery of 444 metagenome-assembled genomes from the biofloc aquaculture system – Rajeev et al. – Scientific Data

Net-spinning caddisflies create denitrifier-enriched niches in the stream microbiome – Bertagnolli et al. – ISME Communications

Parasites, Phages and viruses

Effects of heat tolerance on the gut microbiota of Sarcophaga peregrina (Diptera: Sarcophagidae) and impacts on the life history traits – Ren et al. – Parasites & Vectors

Bioinformatics / Techniques

[PREPRINT]Comprehensive Identification of Pathogenic Microbes and Antimicrobial Resistance Genes in Food Products Using Nanopore Sequencing-Based Metagenomics – Wing-Tung et al. – bioRxiv

Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses – Hertel et al. – Cell Reports Methods

Rank selection for non-negative matrix factorization – Cai, Gu & Kenney

September 20, 2023

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General microbiome

Frequency of change determines effectiveness of microbial response strategies – Li et al. – The ISME Journal

Human gut microbiome

Social and psychological adversity are associated with distinct mother and infant gut microbiome variations – Warner et al. – Nature Communications

Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua – Mills et al. – Microbiome

Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts – Hansen et al. – Scientific Reports

The Impacts of Fecal Microbiota Transplantation from Same Sex on the Symptoms of Ulcerative Colitis Patients – Shang et al. – Polish Journal of Microbiology

Animal microbiome (for animals in the wild)

Transcriptomic, 16S ribosomal ribonucleic acid and network pharmacology analyses shed light on the anticoccidial mechanism of green tea polyphenols against Eimeria tenella infection in Wuliangshan black-boned chickens – Song et al. – Parasites & Vectors

Dityrosine Aggravates Hepatic Insulin Resistance in Obese Mice by Altering Gut Microbiota and the LPS/TLR4/NF-κB Inflammatory Pathway – Ding et al. – Molecular Nutrition & Food Research

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

[REVIEW]Microbiome-assisted restoration of degraded marine habitats: a new nature-based solution? – Corinaldesi et al. – Frontiers in Marine Science

Bioinformatics

[PREPRINT]Comparison of computational methods for host removal and classification of mycobacteria from clinical metagenomic data – Hall & Coin – bioRxiv

September 15, 2023

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Today’s digest features the BugSigDB, AMPSphere and more. Also, you can check out my tips for online conferencing and how to do it better. See you at #MVIF next week!

Respiratory microbiome

The landscape of antibiotic resistance genes in the nasopharynx of preterm infants: Prolonged signature of hospitalization and effects by antibiotics – Achal Dhariwal – bioRxiv

Breast cancer microbiome

Integrating current analyses of the breast cancer microbiome – Sidra Sohail and Michael B. Burns – Plos One

Vaginal microbiome

Diet influences community dynamics following vaginal group B Streptococcus colonization – Christina J. Megli – bioRxiv

Gut microbiome

Gut microbes exacerbate systemic inflammation and behavior disorders in neurologic disease CADASIL – Sheng Liu – Microbiome

Water microbiome

Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean – Mirna Vázquez Rosas Landa – mSystems

Insect microbiome

Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions – Francesca De Filippis – Microbiome

Animal experiment

Enhancing Recovery from Gut Microbiome Dysbiosis and Alleviating DSS-Induced Colitis in Mice with a Consortium of Rare Short-Chain Fatty Acid-Producing Bacteria – Achuthan Ambat – bioRxiv

Bioinformatics

BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures – Ludwig Geistlinger – Nature Biotechnology

Computational exploration of the global microbiome for antibiotic discovery – Célio Dias Santos-Júnior – bioRxiv

June 16, 2023

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Thank you for answering my question above.

Today’s digest features indigenous chicken in Ethiopia, drug effects on gut microbiome, beach water microbial risk assessment, and more. See you at #MVIF next week!

Microbial ecology

Guild and Niche Determination Enable Targeted Alteration of the Microbiome – Oriane Moyne – bioRxiv

Genital microbiome

Interaction of genital microbiota in infertile couples – David Baud – bioRxiv

Gut microbiome

Emergence of community behaviors in the gut microbiota upon drug treatment – Sarela Garcia-Santamarina – bioRxiv

Skin microbiome

Skin microbiome differentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons – Marcus H. Y. Leung – Microbiome

Animal microbiome

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia – Laura Glendinning – bioRxiv

Animal experiments

Effects of fenbendazole on fecal microbiome in BPH/5 mice, a model of hypertension and obesity, a brief report – Kalie F. Beckers – Plos One

Gut microbiota and cognitive development in infant mice: Quantity and source of potable water – Chong-Su Kim and Dong-Mi Shin – Plos One

Plant microbiome

Globally consistent response of plant microbiome diversity across hosts and continents to soil nutrients and herbivores – Eric W. Seabloom – Nature Communications

Methodology

Processing and Storage Methods Affect Oral and Gut Microbiome Composition – Dorothy K. Superdock – bioRxiv

QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification – Yu Yang – Water Research

Bioinformatics

ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics – Rémi Gschwind – Nucleic Acids Research

June 13, 2023

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Today’s microbiome digest includes quite a few host-microbe studies, including one published by my colleague and highlighted below which focuses on the hindgut microbiome of the American cockroach.

Human gut microbiome

Gut microbiota interspecies interactions shape the response of Clostridioides difficile to clinically relevant antibiotics – Hromada – and Venturelli – PLOS Biology

Construction of model animals to explore intestinal microbiome for detection of breast cancer – Ji et al. – PLOS One

Animal experiments

**Disentangling hindgut metabolism in the American cockroach through single-cell genomics and metatranscriptomics – Dukes et al. – Frontiers in Microbiology

Evaluation of microbial and vancomycin treatments in ulcerative colitis in murine models – Hasan and Yang – PLOS One

Animal microbiome

Geography, not lifestyle, explains the population structure of free-living and host-associated deep-sea hydrothermal vent snail symbionts – Hauer et al. – Microbiome

Insect phylogeny structures the bacterial communities in the microbiome of psyllids (Hemiptera: Psylloidea) in Aotearoa New Zealand – Martoni et al. – PLOS One

Water and extremophile microbiome

In the right place, at the right time: the integration of bacteria into the Plankton Ecology Group model – Park et al. – Microbiome

Phages and viruses

Beyond pathogenesis: Detecting the full spectrum of ecological interactions in the virosphere – Jurburg et al. – PLOS Biology

Phage therapy and the public: Increasing awareness essential to widespread use – McCammon et al. – PLOS One

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

April 26, 2023

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General microbiome

[PREPRINT]Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance? – Klümper et al. – bioRxiv

Pregnancy and early life

First-Day-of-Life Rectal Swabs Fail To Represent Meconial Microbiota Composition and Underestimate the Presence of Antibiotic Resistance Genes – Graspeuntner et al. – Microbiology Spectrum

Human gut microbiome

Mucin-microbiome signatures shape the tumor microenvironment in gastric cancer – Oosterlinck et al. – Microbiome

[REVIEW]Fecal microbiota transplantation for recurrent C. difficile infection in patients with inflammatory bowel disease: A systematic review and meta-analysis – Porcari et al. – Journal of Autoimmunity

[REVIEW]Alcohol, the gut microbiome, and liver disease – Jew & Hsu – JGH

[REVIEW]Microbial metabolites in colorectal tumorigenesis and cancer therapy – Liu et al. – Gut Microbes

Human biliary microbiome

Neoadjuvant therapy does not impact the biliary microbiome in patients with pancreatic cancer – Behrens et al. – Journal of Surgical Oncology

Animal microbiome (for animals in the wild)

Indirect maternal effects via nest microbiome composition drive gut colonization in altricial chicks – Diez-Mendez et al. – Molecular Ecology

The gut microbiome of solitary bees is mainly affected by pathogen assemblage and partially by land use – de Landa et al. – Environmental Microbiome

Spatial Succession Underlies Microbial Contribution to Food Digestion in the Gut of an Algivorous Sea Urchin – Masasa et al. – Microbiology Spectrum

The microbiota in feces of domestic pigeons in Seoul, Korea – Oh et al. – Heliyon

Plant, root, and soil microbiome

Characterization of the Rhizosphere Bacterial Microbiome and Coffee Bean Fermentation in the Castillo-Tambo and Bourbon Varieties in the Popayán-Colombia Plateau – Solis Pino et al. – BMC Plant Biology

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

Hydrochemical and Seasonally Conditioned Changes of Microbial Communities in the Tufa-Forming Freshwater Network Ecosystem – Cackovic et al. – mSphere

Bioinformatics

[PREPRINT]ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization – Yang et al. – arXiv