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JOURNAL ARTICLE
Hyejung Han, Hyo-Jung Lee, Keun-Suh Kim, Jin Chung, Hee Sam Na
OBJECTIVE: Next generation sequencing is commonly used to characterize the microbiome structure. MiSeq is most commonly used to analyze the microbiome due to its relatively long read length. Illumina also introduced the 250 × 2 chip for NovaSeq. The purpose of this study was to compare the performance of MiSeq and NovaSeq in the context of oral microbiome study. METHODS: Total read count, read quality score, relative bacterial abundance, community diversity, and correlation between two platforms were analyzed...
2024: Journal of Oral Microbiology
#2
JOURNAL ARTICLE
Jeffry M Gaston, Eric J Alm, An-Ni Zhang
BACKGROUND: Accurate identification of genetic variants, such as point mutations and insertions/deletions (indels), is crucial for various genetic studies into epidemic tracking, population genetics, and disease diagnosis. Genetic studies into microbiomes often require processing numerous sequencing datasets, necessitating variant identifiers with high speed, accuracy, and robustness. RESULTS: We present QuickVariants, a bioinformatics tool that effectively summarizes variant information from read alignments and identifies variants...
April 22, 2024: BMC Biology
#3
JOURNAL ARTICLE
Ernestina Hauptfeld, Nikolaos Pappas, Sandra van Iwaarden, Basten L Snoek, Andrea Aldas-Vargas, Bas E Dutilh, F A Bastiaan von Meijenfeldt
Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks...
April 20, 2024: Nature Communications
#4
REVIEW
Brook E Santangelo, Madison Apgar, Angela Sofia Burkhart Colorado, Casey G Martin, John Sterrett, Elena Wall, Marcin P Joachimiak, Lawrence E Hunter, Catherine A Lozupone
Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease...
2024: Frontiers in Microbiology
#5
JOURNAL ARTICLE
Adrienne B Narrowe, Johanna M S Lemons, Karley K Mahalak, Jenni Firrman, Pieter Van den Abbeele, Aurélien Baudot, Stef Deyaert, Yanfang Li, Liangli Lucy Yu, LinShu Liu
The genus Senna contains globally distributed plant species of which the leaves, roots, and seeds have multiple traditional medicinal and nutritional uses. Notable chemical compounds derived from Senna spp. include sennosides and emodin which have been tested for antimicrobial effects in addition to their known laxative functions. However, studies of the effects of the combined chemical components on intact human gut microbiome communities are lacking. This study evaluated the effects of Juemingzi ( Senna sp...
2024: Frontiers in Cellular and Infection Microbiology
#6
JOURNAL ARTICLE
Zainab M A Al Radi, Femke M Prins, Valerie Collij, Arnau Vich Vila, Eleonora A M Festen, Gerard Dijkstra, Rinse K Weersma, Marjolein A Y Klaassen, Ranko Gacesa
BACKGROUND: Inflammatory bowel diseases (IBDs) pose a significant challenge due to their diverse, often debilitating, and unpredictable clinical manifestations. The absence of prognostic tools to anticipate the future complications that require therapy intensification presents a substantial burden to patient private life and health. We aimed to explore whether the gut microbiome is a potential biomarker for future therapy intensification in a cohort of 90 IBD patients. METHODS: We conducted whole-genome metagenomics sequencing on fecal samples from these patients, allowing us to profile the taxonomic and functional composition of their gut microbiomes...
April 18, 2024: Inflammatory Bowel Diseases
#7
JOURNAL ARTICLE
Nicola J Wyatt, Hannah Watson, Carl A Anderson, Nicholas A Kennedy, Tim Raine, Tariq Ahmad, Dean Allerton, Michelle Bardgett, Emma Clark, Dawn Clewes, Cristina Cotobal Martin, Mary Doona, Jennifer A Doyle, Katherine Frith, Helen C Hancock, Ailsa L Hart, Victoria Hildreth, Peter M Irving, Sameena Iqbal, Ciara Kennedy, Andrew King, Sarah Lawrence, Charlie W Lees, Robert Lees, Laura Letchford, Trevor Liddle, James O Lindsay, Rebecca H Maier, John C Mansfield, Julian R Marchesi, Naomi McGregor, Rebecca E McIntyre, Jasmin Ostermayer, Tolulope Osunnuyi, Nick Powell, Natalie J Prescott, Jack Satsangi, Shriya Sharma, Tara Shrestha, Ally Speight, Michelle Strickland, James Ms Wason, Kevin Whelan, Ruth Wood, Gregory R Young, Xinyue Zhang, Miles Parkes, Christopher J Stewart, Luke Jostins-Dean, Christopher A Lamb
INTRODUCTION: Characterised by chronic inflammation of the gastrointestinal tract, inflammatory bowel disease (IBD) symptoms including diarrhoea, abdominal pain and fatigue can significantly impact patient's quality of life. Therapeutic developments in the last 20 years have revolutionised treatment. However, clinical trials and real-world data show primary non-response rates up to 40%. A significant challenge is an inability to predict which treatment will benefit individual patients...
April 17, 2024: BMJ Open
#8
JOURNAL ARTICLE
Jacqueline Gottwald, Jens Balke, Johannes Stellmacher, Kira van Vorst, Fereshteh Ghazisaeed, Marcus Fulde, Ulrike Alexiev
The integrity of the protective mucus layer as a primary defense against pathogen invasion and microbial leakage into the intestinal epithelium can be compromised by the effects of antibiotics on the commensal microbiome. Changes in mucus integrity directly affect the solvent viscosity in the immediate vicinity of the mucin network, i.e., the nanoviscosity, which in turn affects both biochemical reactions and selective transport. To assess mucus nanoviscosity, a reliable readout via the viscosity-dependent fluorescence lifetime of the molecular rotor dye Cy3 is established and nanoviscosities from porcine and murine ex vivo mucus are determined...
April 16, 2024: Macromolecular Bioscience
#9
JOURNAL ARTICLE
Wenxin Wang, Yiyuan Liu, Zhikai Yao, Dengbo Chen, Yue Tang, Jingwei Cui, Jiangjiang Zhang, Hong Liu, Zikai Hao
The diverse commensal microbiome of the human intestine has been considered to play a central role in depression. However, no host-microbiota co-culture system has been developed for depression, which hinders the controlled study of the interaction between depression and gut microbiota. We designed and manufactured a microfluidic-based gut-on-a-chip model containing the gut microbiota of patients with depression (depression-on-gut-chip, DoGC), which enables the extended co-culture of viable aerobic human intestinal epithelial cells and anaerobic gut microbiota, and allows the direct study of interactions between human gut microbiota and depression...
April 16, 2024: Lab on a Chip
#10
JOURNAL ARTICLE
Shoumi Sarkar, Samuel Anyaso-Samuel, Peihua Qiu, Somnath Datta
Urban environments, characterized by bustling mass transit systems and high population density, host a complex web of microorganisms that impact microbial interactions. These urban microbiomes, influenced by diverse demographics and constant human movement, are vital for understanding microbial dynamics. We explore urban metagenomics, utilizing an extensive dataset from the Metagenomics & Metadesign of Subways & Urban Biomes (MetaSUB) consortium, and investigate antimicrobial resistance (AMR) patterns...
April 15, 2024: Statistics in Medicine
#11
JOURNAL ARTICLE
Aleksandra Jatkowska, Konstantinos Gkikas, Ben Nichols, Bryn Short, Vasiliki-Konstantina Rizou, Panagiotis Kapranos, Jennifer Klein Gunnewiek, Edelyn Christina, Vaios Svolos, Christopher Quince, Konstantinos Gerasimidis
INTRODUCTION: Enteral nutrition (EN) involves replacing all or part of a person's habitual diet with a nutritional formula. The impact of varying doses of EN on the gut microbiome remains understudied. METHODS: Healthy adults replaced all (100% EN) or part (85% EN, 50% EN and 20% EN) of their energy requirements with EN for 7 days. Faecal samples were collected before and on day 7 of interventions. Faecal pH, short chain fatty acids (SCFAs), branched-chain fatty acids (BCFAs) and 16S rRNA sequencing were performed...
April 9, 2024: Clinical Nutrition
#12
JOURNAL ARTICLE
Lindsay M Leonard, Abigayle M R Simpson, Shiyu Li, Lavanya Reddivari, Tzu-Wen L Cross
The implications of soy consumption on human health have been a subject of debate, largely due to the mixed evidence regarding its benefits and potential risks. The variability in responses to soy has been partly attributed to differences in the metabolism of soy isoflavones, compounds with structural similarities to estrogen. Approximately one-third of humans possess gut bacteria capable of converting soy isoflavone daidzein into equol, a metabolite produced exclusively by gut microbiota with significant estrogenic potency...
April 6, 2024: Nutrients
#13
JOURNAL ARTICLE
Zhongzhi Sun, Zhibin Ning, Daniel Figeys
The human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substantial microbial diversity and functional potential of the human gut microbiome, few studies have summarized and studied the human gut microbiome landscape revealed with metaproteomics...
April 10, 2024: Molecular & Cellular Proteomics: MCP
#14
REVIEW
Inoli Shennon, Brooke C Wilson, Anna H Behling, Theo Portlock, Rashidul Haque, Terrence Forrester, Charles A Nelson, Justin M O'Sullivan
Malnutrition affects 195 million children under the age of five worldwide with long term effects that include impaired cognitive development. Brain development occurs rapidly over the first 36 months of life. Whilst seemingly independent, changes to the brain and gut microbiome are linked by metabolites, hormones, and neurotransmitters as part of the gut-brain axis. In the context of severe malnutrition, the composition of the gut microbiome and the repertoire of biochemicals exchanged via the gut-brain axis vary when compared to healthy individuals...
April 4, 2024: Clinical Nutrition
#15
REVIEW
Siyao Wang, Xu Gong, Fei Xiao, Yun Yang
Microbial communities in the human gut play a significant role in regulating host gene expression, influencing a variety of biological processes. To understand the molecular mechanisms underlying host-microbe interactions, tools that can dissect signaling networks are required. In this review, we discuss recent advances in molecular tools used to study this interplay, with a focus on those that explore how the microbiome regulates host gene expression. These tools include CRISPR-based whole-body genetic tools for deciphering host-specific genes involved in the interaction process, Cre- loxP based tissue/cell-specific gene editing approaches, and in vitro models of host-derived organoids...
2024: Frontiers in Microbiology
#16
JOURNAL ARTICLE
Inmaculada Pérez-Prieto, Aida Rodríguez-Santisteban, Signe Altmäe
PURPOSE OF REVIEW: The analysis of microbiome in association with female health is today a "hot topic" with the main focus on microbes in the female reproductive tract. Nevertheless, recent studies are providing novel information of the possible influence of the gut microbiome on gynecological health outcomes, especially as we start to understand that the gut microbiome is an extended endocrine organ influencing female hormonal levels. This review summarizes the current knowledge of the gut microbes in association with gynecological health...
April 9, 2024: Current Opinion in Clinical Nutrition and Metabolic Care
#17
REVIEW
Exploring the role of the human microbiome in forensic identification: opportunities and challenges.
Lorenzo Franceschetti, Giorgia Lodetti, Alberto Blandino, Alberto Amadasi, Valentina Bugelli
Forensic microbiology is rapidly emerging as a novel tool for human identification. The human microbiome, comprising diverse microbial communities including fungi, bacteria, protozoa, and viruses, is unique to each individual, offering a new dimension to forensic investigations. While traditional identification methods primarily rely on DNA profiling and fingerprint analysis, they face limitations when complete DNA or fingerprints profiles are unattainable or degraded. In this context, the microbial signatures of the human skin microbiome present a promising alternative due to their resilience to environmental stresses and individual-specific composition...
April 10, 2024: International Journal of Legal Medicine
#18
JOURNAL ARTICLE
Karl L Ocius, Sree H Kolli, Saadman S Ahmad, Jules M Dressler, Mahendra D Chordia, Brandon L Jutras, Melanie R Rutkowski, Marcos M Pires
The role of the intestinal microbiota in host health is increasingly revealed in its contributions to disease states. The host-microbiome interaction is multifactorial and dynamic. One of the factors that has recently been strongly associated with host physiological responses is peptidoglycan from bacterial cell walls. Peptidoglycan from gut commensal bacteria activates peptidoglycan sensors in human cells, including the nucleotide-binding oligomerization domain-containing protein 2. When present in the gastrointestinal tract, both the polymeric form (sacculi) and depolymerized fragments can modulate host physiology, including checkpoint anticancer therapy efficacy, body temperature and appetite, and postnatal growth...
April 9, 2024: Bioconjugate Chemistry
#19
REVIEW
Shanchana Srinivasan, Apoorva Jnana, Thokur Sreepathy Murali
Microbial interactions function as a fundamental unit in complex ecosystems. By characterizing the type of interaction (positive, negative, neutral) occurring in these dynamic systems, one can begin to unravel the role played by the microbial species. Towards this, various methods have been developed to decipher the function of the microbial communities. The current review focuses on the various qualitative and quantitative methods that currently exist to study microbial interactions. Qualitative methods such as co-culturing experiments are visualized using microscopy-based techniques and are combined with data obtained from multi-omics technologies (metagenomics, metabolomics, metatranscriptomics)...
April 8, 2024: Microbial Ecology
#20
JOURNAL ARTICLE
David Felipe Garcia Mendez, Siobhon Egan, Julien Wist, Elaine Holmes, Janeth Sanabria
Understanding the intricate ecological interactions within the gut microbiome and unravelling its impact on human health is a challenging task. Bioreactors are valuable tools that have contributed to our understanding of gut microbial ecology. However, there is a lack of studies describing and comparing the microbial diversity cultivated in these models. This knowledge is crucial for refining current models to reflect the gastrointestinal microbiome accurately. In this study, we analysed the microbial diversity of 1512 samples from 18 studies available in public repositories that employed cultures performed in batches and various bioreactor models to cultivate faecal microbiota...
April 8, 2024: Microbial Ecology
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