Human microbiome: an academic update on human body site specific surveillance and its possible role

Archives of Microbiology, Journal Year: 2020, Volume and Issue: 202(8), P. 2147 - 2167

Published: June 10, 2020

Language: Английский

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Open challenges for microbial network construction and analysis

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(11), P. 3111 - 3118

Published: June 9, 2021

Microbial network construction is a popular explorative data analysis technique in microbiome research. Although large number of microbial tools has been developed to date, there are several issues concerning the and interpretation networks that have received less attention. The purpose this perspective draw attention these underexplored challenges analysis.

Language: Английский

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Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation

Nature Methods, Journal Year: 2022, Volume and Issue: 19(11), P. 1438 - 1448

Published: Oct. 17, 2022

Abstract Advances in microscopy hold great promise for allowing quantitative and precise measurement of morphological molecular phenomena at the single-cell level bacteria; however, potential this approach is ultimately limited by availability methods to faithfully segment cells independent their or optical characteristics. Here, we present Omnipose, a deep neural network image-segmentation algorithm. Unique outputs such as gradient distance field allow Omnipose accurately on which current algorithms, including its predecessor, Cellpose, produce errors. We show that achieves unprecedented segmentation performance mixed bacterial cultures, antibiotic-treated elongated branched morphology. Furthermore, benefits extend non-bacterial subjects, varied imaging modalities three-dimensional objects. Finally, demonstrate utility characterization extreme phenotypes arise during interbacterial antagonism. Our results distinguish powerful tool characterizing diverse arbitrarily shaped cell types from data.

Language: Английский

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Nanopore sequencing and its application to the study of microbial communities

Computational and Structural Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19, P. 1497 - 1511

Published: Jan. 1, 2021

Since its introduction, nanopore sequencing has enhanced our ability to study complex microbial samples through the possibility sequence long reads in real time using inexpensive and portable technologies. The use of allowed address several previously unsolved issues field, such as resolution genomic structures, facilitated access metagenome assembled genomes (MAGs). Furthermore, low cost portability platforms together with development rapid protocols analysis pipelines have featured technology an attractive ever-growing tool for real-time in-field environmental analysis. This review provides up-to-date summary experimental bioinformatic tools communities sequencing, highlighting most important recent research field a major focus on infectious diseases. An overview main approaches including targeted shotgun approaches, metatranscriptomics, epigenomics, epitranscriptomics is provided, outlook challenges perspectives over this studies.

Language: Английский

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A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data

Computational and Structural Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19, P. 6301 - 6314

Published: Jan. 1, 2021

Metagenomic sequencing provides a culture-independent avenue to investigate the complex microbial communities by constructing metagenome-assembled genomes (MAGs). A MAG represents genome group of sequences from assembly with similar characteristics. It enables us identify novel species and understand their potential functions in dynamic ecosystem. Many computational tools have been developed construct annotate MAGs metagenomic sequencing, however, there is prominent gap comprehensively introduce background practical performance. In this paper, we thoroughly investigated designed for both upstream downstream analyses, including metagenome assembly, binning, gene prediction, functional annotation, taxonomic classification, profiling. We categorized commonly used into unique groups based on introduced underlying core algorithms associated information demonstrate comparative outlook. Furthermore, emphasized requisition offered guidance users select most efficient tools. Finally, indicated current limitations, solutions, future perspectives further improving construction annotation. believe that our work consolidated resource stage studies shed light development more effective analysis sequencing.

Language: Английский

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New Insights Into the Cancer–Microbiome–Immune Axis: Decrypting a Decade of Discoveries

Frontiers in Immunology, Journal Year: 2021, Volume and Issue: 12

Published: Feb. 23, 2021

The past decade has witnessed groundbreaking advances in the field of microbiome research. An area where immense implications have been demonstrated is tumor biology. affects initiation and progression through direct effects on cells indirectly manipulation immune system. It can also determine response to cancer therapies predict disease survival. Modulation be harnessed potentiate efficacy immunotherapies decrease their toxicity. In this review, we comprehensively dissect recent evidence regarding interaction anti-tumor machinery outline critical questions which need addressed as further explore dynamic colloquy.

Language: Английский

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Maternal exposures and the infant gut microbiome: a systematic review with meta-analysis

Gut Microbes, Journal Year: 2021, Volume and Issue: 13(1)

Published: Jan. 1, 2021

Early life, including the establishment of intestinal microbiome, represents a critical window growth and development. Postnatal factors affecting mode delivery, feeding type, antibiotic exposure have been widely investigated, but questions remain regarding influence exposures

Language: Английский

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Current understanding of the Alzheimer’s disease-associated microbiome and therapeutic strategies

Experimental & Molecular Medicine, Journal Year: 2024, Volume and Issue: 56(1), P. 86 - 94

Published: Jan. 4, 2024

Abstract Alzheimer’s disease (AD) is a fatal progressive neurodegenerative disease. Despite tremendous research efforts to understand this complex disease, the exact pathophysiology of not completely clear. Recently, anti-Aβ antibodies have been shown remove amyloid from brain and slow clinical progression mild dementia by ~30%. However, exploring alternative strategies crucial understanding developing more effective therapeutic interventions. In recent years, microbiota-gut-brain axis has received significant attention in AD field. Numerous studies suggested that alterations gut microbiota composition are associated with AD, several underlying mechanisms proposed. area still their infancy, many aspects field just beginning be explored understood. Gaining deeper intricate interactions signaling pathways involved microbiota-AD interaction for optimizing targeting positively impact AD. review, we aim summarize current We will discuss existing evidence regarding role pathogenesis, mechanisms, biological factors influencing microbiome-gut-brain remaining questions Last, potential approaches recondition community alleviate progression. An ongoing exploration gut-brain development microbiota-based therapies hold advancing management future.

Language: Английский

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Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis

npj Biofilms and Microbiomes, Journal Year: 2023, Volume and Issue: 9(1)

Published: Sept. 22, 2023

Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir microbial biodiversity, yet majority desert microorganisms remain uncharacterized are seen as "microbial dark matter". Here, we introduce multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, shotgun metagenomic sequencing. The results showed CBM captured amount taxonomic functional diversity missed in direct sequencing by increasing recovery amplicon sequence variants (ASVs) high/medium-quality metagenome-assembled genomes (MAGs). Importantly, allowed post hoc microbes interest (e.g., novel or specific taxa), even those with extremely low abundance culture. Furthermore, strain-level analyses based on revealed soils harbored considerable number bacterial candidates (1941, 51.4%), which 1095 (from CBM) were culturable. However, would not exactly reflect relative true composition pathways situ environment, its use coupled could provide greater insight into microbiomes. Overall, this study exemplifies strategy high-resolution is an ideal way to deeply explore untapped resources soils, substantially expands our knowledge matter hidden vast expanse deserts.

Language: Английский

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Gut microbiota in overweight and obesity: crosstalk with adipose tissue

Nature Reviews Gastroenterology & Hepatology, Journal Year: 2023, Volume and Issue: 21(3), P. 164 - 183

Published: Dec. 8, 2023

Language: Английский

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