bioRxiv - Genomics最新文献_第7页

Efficiently Constructing Complete Genomes with CycloneSEQ to Fill Gaps in Bacterial Draft Assemblies 利用 CycloneSEQ 高效构建完整基因组，填补细菌草案组装的空白

bioRxiv - Genomics Pub Date : 2024-09-07 DOI: 10.1101/2024.09.05.611410

Hewei Liang, Mengmeng Wang, Tongyuan Hu, Haoyu Wang, Wenxin He, Yanmei Ju, Ruijin Guo, Junyi Chen, Fei Guo, Tao Zeng, Yuliang Dong, Bo Wang, Chuanyu Liu, Xin Jin, Wenwei Zhang, Yuanqiang Zou, Xun Xu, Liang Xiao

{"title":"Efficiently Constructing Complete Genomes with CycloneSEQ to Fill Gaps in Bacterial Draft Assemblies","authors":"Hewei Liang, Mengmeng Wang, Tongyuan Hu, Haoyu Wang, Wenxin He, Yanmei Ju, Ruijin Guo, Junyi Chen, Fei Guo, Tao Zeng, Yuliang Dong, Bo Wang, Chuanyu Liu, Xin Jin, Wenwei Zhang, Yuanqiang Zou, Xun Xu, Liang Xiao","doi":"10.1101/2024.09.05.611410","DOIUrl":"https://doi.org/10.1101/2024.09.05.611410","url":null,"abstract":"Current microbial sequencing relies on short-read platforms like Illumina and DNBSEQ, favored for their low cost and high accuracy. However, these methods often produce fragmented draft genomes, hindering comprehensive bacterial function analysis. CycloneSEQ, a novel long-read sequencing platform developed by BGI-Research, its sequencing performance and assembly improvements has been evaluated. Using CycloneSEQ long-read sequencing, the type strain produced long reads with an average length of 11.6 kbp and an average quality score of 14.4. After hybrid assembly with short-read data, the assembled genome exhibited an error rate of only 0.04 mismatches and 0.08 indels per 100 kbp compared to the reference genome. This method was validated across 9 diverse species, successfully assembling complete circular genomes. Hybrid assembly significantly enhances genome completeness by using long reads to fill gaps and accurately assemble multi-copy rRNA genes, which unable be achieved by short reads solely. Through data subsampling, we found that over 500 Mbp of short-read data combined with 100 Mbp of long-read data can result in a high-quality circular assembly. Additionally, using CycloneSEQ long reads effectively improves the assembly of circular complete genomes from mixed microbial communities. CycloneSEQ's read length is sufficient for circular bacterial genomes, but its base quality needs improvement. Integrating DNBSEQ short reads improved accuracy, resulting in complete and accurate assemblies. This efficient approach can be widely applied in microbial sequencing.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dynamics and determinants of the gut mobilome in early life 生命早期肠道移动组的动态和决定因素

bioRxiv - Genomics Pub Date : 2024-09-07 DOI: 10.1101/2024.09.06.611692

Asier Fernandez-Pato, Trishla Sinha, Sanzhima Garmaeva, Anastasia Gulyaeva, Nataliia Kuzub, Simon Roux, Jingyuan Fu, Alexander Kurilshikov, Alexandra Zhernakova

引用次数: 0

Enformation Theory: A Framework for Evaluating Genomic AI 信息论：评估基因组人工智能的框架

bioRxiv - Genomics Pub Date : 2024-09-07 DOI: 10.1101/2024.09.03.611127

Eyes S Robson, Nilah M. Ioannidis

{"title":"Enformation Theory: A Framework for Evaluating Genomic AI","authors":"Eyes S Robson, Nilah M. Ioannidis","doi":"10.1101/2024.09.03.611127","DOIUrl":"https://doi.org/10.1101/2024.09.03.611127","url":null,"abstract":"The nascent field of genomic AI is rapidly expanding with new models, benchmarks, and findings. As the field diversifies, there is an increased need for a common set of measurement tools and perspectives to standardize model evaluation. Here, we present a statistically grounded framework for performance evaluation, visualization, and interpretation using the prominent genomic AI model Enformer as a case study. The Enformer model has been used for a range of applications from mechanism discovery to variant effect prediction, but what makes it better or worse than precedent models at particular tasks? Our goal is not merely to answer these questions for Enformer, but to propose how we should think about new models in general. We start by reporting Enformer's few-shot performance on the GUANinE benchmark, which emphasizes complex genome interpretation tasks, and discuss its gains and deficits compared to precedent models. We follow this analysis with visualizations of Enformer's embeddings in low-dimensional space, where, among other insights, we diagnose features of the embeddings that may limit model generalization to synthetic biology tasks. Finally, we present a novel, theory-backed probe of Enformer embeddings, where variance decomposition allows for holistic interpretation and partial 'backtracking' to explanatory causal features. Through this case study, we illustrate a new framework, Enformation Theory, for analyzing and interpreting genomic AI models.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CRISPRi with barcoded expression reporters dissects regulatory networks in human cells 带有条形码表达报告器的 CRISPRi 可剖析人类细胞中的调控网络

bioRxiv - Genomics Pub Date : 2024-09-06 DOI: 10.1101/2024.09.06.611573

Jinyoung Kim, Ryan Y. Muller, Eliana R Bondra, Nicholas Ingolia

{"title":"CRISPRi with barcoded expression reporters dissects regulatory networks in human cells","authors":"Jinyoung Kim, Ryan Y. Muller, Eliana R Bondra, Nicholas Ingolia","doi":"10.1101/2024.09.06.611573","DOIUrl":"https://doi.org/10.1101/2024.09.06.611573","url":null,"abstract":"Genome-wide CRISPR screens have emerged as powerful tools for uncovering the genetic underpinnings of diverse biological processes. Incisive screens often depend on directly measuring molecular phenotypes, such as regulated gene expression changes, provoked by CRISPR-mediated genetic perturbations. Here, we provide quantitative measurements of transcriptional responses in human cells across genome-scale perturbation libraries by coupling CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). To enable CiBER-seq in mammalian cells, we optimize the integration of highly complex, barcoded sgRNA libraries into a defined genomic context. CiBER-seq profiling of a nuclear factor kappa B (NF-kappaB) reporter delineates the canonical signaling cascade linking the transmembrane TNF- alpha receptor to inflammatory gene activation and highlights cell-type-specific factors in this response. Importantly, CiBER-seq relies solely on bulk RNA sequencing to capture the regulatory circuit driving this rapid transcriptional response. Our work demonstrates the accuracy of CiBER-seq and its potential for dissecting genetic networks in mammalian cells with superior time resolution.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms 从染色质可及性聚合数据推断基因型，揭示遗传调控机制

bioRxiv - Genomics Pub Date : 2024-09-05 DOI: 10.1101/2024.09.04.610850

Brandon M. Wenz, Yuan He, Nae-Chyun Chen, Joseph K. Pickrell, Jeremiah H Li, Max F. Dudek, Taibo Li, Rebecca Keener, Benjamin F. Voight, Christopher D. Brown, Alexis Battle

{"title":"Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms","authors":"Brandon M. Wenz, Yuan He, Nae-Chyun Chen, Joseph K. Pickrell, Jeremiah H Li, Max F. Dudek, Taibo Li, Rebecca Keener, Benjamin F. Voight, Christopher D. Brown, Alexis Battle","doi":"10.1101/2024.09.04.610850","DOIUrl":"https://doi.org/10.1101/2024.09.04.610850","url":null,"abstract":"Background\u0000Understanding the genetic causes for variability in chromatin accessibility can shed light on the molecular mechanisms through which genetic variants may affect complex traits. Thousands of ATAC-seq samples have been collected that hold information about chromatin accessibility across diverse cell types and contexts, but most of these are not paired with genetic information and come from diverse distinct projects and laboratories. Results\u0000We report here joint genotyping, chromatin accessibility peak calling, and discovery of quantitative trait loci which influence chromatin accessibility (caQTLs), demonstrating the capability of performing caQTL analysis on a large scale in a diverse sample set without pre-existing genotype information. Using 10,293 profiling samples representing 1,454 unique donor individuals across 653 studies from public databases, we catalog 23,381 caQTLs in total. After joint discovery analysis, we cluster samples based on accessible chromatin profiles to identify context-specific caQTLs. We find that caQTLs are strongly enriched for annotations of gene regulatory elements across diverse cell types and tissues and are often strongly linked with genetic variation associated with changes in expression (eQTLs), indicating that caQTLs can mediate genetic effects on gene expression. We demonstrate sharing of causal variants for chromatin accessibility and diverse complex human traits, enabling a more complete picture of the genetic mechanisms underlying complex human phenotypes. Conclusions\u0000Our work provides a proof of principle for caQTL calling from previously ungenotyped samples, and represents one of the largest, most diverse caQTL resources currently available, informing mechanisms of genetic regulation of gene expression and contribution to disease.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Frequent genetic exchanges revealed by a pan-mitogenome graph of a fungal plant pathogen 植物真菌病原体的泛基因组图谱揭示了频繁的基因交换

bioRxiv - Genomics Pub Date : 2024-09-05 DOI: 10.1101/2024.06.19.599757

Anouk van Westerhoven, Jelmer Dijkstra, Luis Aznar Palop, Kyran Wissink, Jasper Bell, Gert Kema, Michael F. Seidl

{"title":"Frequent genetic exchanges revealed by a pan-mitogenome graph of a fungal plant pathogen","authors":"Anouk van Westerhoven, Jelmer Dijkstra, Luis Aznar Palop, Kyran Wissink, Jasper Bell, Gert Kema, Michael F. Seidl","doi":"10.1101/2024.06.19.599757","DOIUrl":"https://doi.org/10.1101/2024.06.19.599757","url":null,"abstract":"Mitochondria are present in almost all eukaryotic lineages. The mitochondrial genomes (mitogenomes) evolve separately from nuclear genomes, and they can therefore provide relevant insights into the evolution of their host species. Fusarium oxysporum is a major fungal plant pathogen that is assumed to reproduce clonally. However, horizontal chromosome transfer between strains can occur through heterokaryon formation, and recently signs of sexual recombination have been observed. Similarly, signs of recombination in F. oxysporum mitogenomes challenged the prevailing assumption of clonal reproduction in this species. Here, we construct, to our knowledge, the first fungal pan-mitogenome graph of nearly 500 F. oxysporum mitogenome assemblies to uncover the variation and evolution. In general, the gene order of fungal mitogenomes is not well conserved, yet the mitogenome of F. oxysporum and related species are highly co-linear. We observed two strikingly contrasting regions in the Fusarium oxysporum pan-mitogenome, comprising a highly conserved core mitogenome and a long variable region (6-16 kb in size), of which we identified three distinct types. The pan-mitogenome graph reveals that only five intron insertions occurred in the core mitogenome and that the long variable regions drive the difference between mitogenomes. Moreover, we observed that their evolution is neither concurrent with the core mitogenome nor with the nuclear genome. Our large-scale analysis of long variable regions uncovers frequent recombination between mitogenomes, even between strains that belong to different taxonomic clades. This challenges the common assumption of incompatibility between genetically diverse F. oxysporum strains and provides new insights into the evolution of this fungal species.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"31 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic Epidemiology of SARS-CoV-2 in Norfolk, UK, March 2020 – December 2022 2020 年 3 月至 2022 年 12 月英国诺福克郡 SARS-CoV-2 基因组流行病学研究

bioRxiv - Genomics Pub Date : 2024-09-05 DOI: 10.1101/2024.09.05.611382

Eleanor H Hayles, Andrew J Page, Javier Guitian, Robert A Kingsley, The COVID-19 Genomics UK Consortium, Gemma C Langridge

{"title":"Genomic Epidemiology of SARS-CoV-2 in Norfolk, UK, March 2020 – December 2022","authors":"Eleanor H Hayles, Andrew J Page, Javier Guitian, Robert A Kingsley, The COVID-19 Genomics UK Consortium, Gemma C Langridge","doi":"10.1101/2024.09.05.611382","DOIUrl":"https://doi.org/10.1101/2024.09.05.611382","url":null,"abstract":"Background: In the UK, the COVID-19 Genomics UK Consortium (COG-UK) established a real time national genomic surveillance system during the COVID-19 pandemic, producing centralised data for monitoring SARS-CoV-2. As a COG-UK partner, Quadram Institute Bioscience (QIB) in Norfolk sequenced over 87,000 SARS-CoV-2 genomes, contributing to the region becoming densely sequenced. Retrospective analysis of SARS-CoV-2 lineage dynamics in this region may contribute to preparedness for future pandemics. Methods: 29,406 SARS-CoV-2 whole genome sequences and corresponding metadata from Norfolk were extracted from the COG-UK dataset, sampled between March 2020 and December 2022, representing 9.9% of regional COVID-19 cases. Sequences were lineage typed using Pangolin, and subsequent lineage analysis carried out in R using RStudio and related packages, including graphical analysis using ggplot2. Results: 401 global lineages were identified, with 69.8% appearing more than once and 31.2% over ten times. Temporal clustering identified six lineage communities based on first lineage emergence. Alpha, Delta, and Omicron variants of concern (VOC) accounted for 8.6%, 34.9% and 48.5% of sequences respectively. These formed four regional epidemic waves alongside the remaining lineages which appeared in the early pandemic prior to VOC designation and were termed pre-VOC lineages. Regional comparison highlighted variability in VOC epidemic wave dates dependent on location. Conclusion: This study is the first to assess SARS-CoV-2 diversity in Norfolk across a large timescale within the COVID-19 pandemic. SARS-CoV-2 was both highly diverse and dynamic throughout the Norfolk region between March 2020 – December 2022, with a strong VOC presence within the latter two thirds of the study period. The study also displays the utility of incorporating genomic epidemiological methods into pandemic response.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A genome assembly and annotation for the Australian alpine skink Bassiana duperreyi using long-read technologies 利用长读数技术对澳大利亚高山鼬 Bassiana duperreyi 进行基因组组装和注释

bioRxiv - Genomics Pub Date : 2024-09-05 DOI: 10.1101/2024.09.05.611471

Benjamin J Hanrahan, Kirat Alreja, Andre L. M. Reis, J King Chang, Duminda S. B. Dissanayake, Richard J Edwards, Terry Bertozzi, Jillian M Hammond, Denis O'Meally, Ira W Deveson, Arthur Georges, Paul D. Waters, Hardip Rameshbhai Patel

{"title":"A genome assembly and annotation for the Australian alpine skink Bassiana duperreyi using long-read technologies","authors":"Benjamin J Hanrahan, Kirat Alreja, Andre L. M. Reis, J King Chang, Duminda S. B. Dissanayake, Richard J Edwards, Terry Bertozzi, Jillian M Hammond, Denis O'Meally, Ira W Deveson, Arthur Georges, Paul D. Waters, Hardip Rameshbhai Patel","doi":"10.1101/2024.09.05.611471","DOIUrl":"https://doi.org/10.1101/2024.09.05.611471","url":null,"abstract":"The eastern three-lined skink (Bassiana duperreyi) inhabits the Australian high country in the southwest of the continent including Tasmania. It is an oviparous species that is distinctive because it undergoes sex reversal (from XX genotypic females to phenotypic males) at low incubation temperatures. We present a chromosome-scale genome assembly of a Bassiana duperreyi XY male individual, constructed using a combination of PacBio HiFi and ONT long reads scaffolded using Illumina HiC data. The genome assembly length is 1.57 Gb with a scaffold N50 of 222 Mbp, N90 of 26 Mbp, 200 gaps and 43.10% GC content. Most (95%) of the assembly is scaffolded into 6 macrochromosomes, 8 microchromosomes and the X chromosome, corresponding to the karyotype. Fragmented Y chromosome scaffolds (n=11 ≥1 Mbp) were identified using Y-specific contigs generated by genome subtraction. We identified two novel alpha-satellite repeats of 187 bp and 199 bp in the putative centromeres that did not form higher order repeats. The genome assembly exceeds the standard recommended by the Earth Biogenome Project; 0.02% false expansions, 99.63% kmer completeness, 94.66% complete single copy BUSCO genes and an average 98.42% of transcriptome data mappable to the genome assembly. The mitochondrial genome (17,506 bp) and the model rDNA repeat unit (15,154 bp) were assembled. The B. duperreyi genome assembly has one of the highest completeness levels for a skink and will provide a resource for research focused on sex determination and thermolabile sex reversal, as an oviparous foundation species for studies of the evolution of viviparity, and for other comparative genomics studies of the Scincidae.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"130 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization and bioinformatic filtering of ambient gRNAs in single-cell CRISPR screens using CLEANSER 利用 CLEANSER 对单细胞 CRISPR 筛选中的环境 gRNA 进行表征和生物信息学筛选

bioRxiv - Genomics Pub Date : 2024-09-04 DOI: 10.1101/2024.09.04.611293

Siyan Liu, Marisa C Hamilton, Thomas N Cowart, Alejandro Barrera, Lexi R Bounds, Alexander C Nelson, Richard W Doty, Andrew S Allen, Gregory E Crawford, William H Majoros, Charles A. Gersbach

{"title":"Characterization and bioinformatic filtering of ambient gRNAs in single-cell CRISPR screens using CLEANSER","authors":"Siyan Liu, Marisa C Hamilton, Thomas N Cowart, Alejandro Barrera, Lexi R Bounds, Alexander C Nelson, Richard W Doty, Andrew S Allen, Gregory E Crawford, William H Majoros, Charles A. Gersbach","doi":"10.1101/2024.09.04.611293","DOIUrl":"https://doi.org/10.1101/2024.09.04.611293","url":null,"abstract":"Recent technological developments in single-cell RNA-seq CRISPR screens enable high-throughput investigation of the genome. Through transduction of a gRNA library to a cell population followed by transcriptomic profiling by scRNA-seq, it is possible to characterize the effects of thousands of genomic perturbations on global gene expression. A major source of noise in scRNA-seq CRISPR screens are ambient gRNAs, which are contaminating gRNAs that likely originate from other cells. If not properly filtered, ambient gRNAs can result in an excess of false positive gRNA assignments. Here, we utilize CRISPR barnyard assays to characterize ambient gRNA noise in single-cell CRISPR screens. We use these datasets to develop and train CLEANSER, a mixture model that identifies and filters ambient gRNA noise. This model takes advantage of the bimodal distribution between native and ambient gRNAs and includes both gRNA and cell-specific normalization parameters, correcting for confounding technical factors that affect individual gRNAs and cells. The output of CLEANSER is the probability that a gRNA-cell assignment is in the native distribution over the ambient distribution. We find that ambient gRNA filtering methods impact differential gene expression analysis outcomes and that CLEANSER outperforms alternate approaches by increasing gRNA-cell assignment accuracy.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multiomic Insights into Human Health: Gut Microbiomes of Hunter-Gatherer, Agropastoral, and Western Urban Populations 多组学洞察人类健康：狩猎采集者、农牧民和西方城市人口的肠道微生物组

bioRxiv - Genomics Pub Date : 2024-09-04 DOI: 10.1101/2024.09.03.611095

Harinder Singh, Rosana Wiscovitch-Russo, Claire Kuelbs, Josh Espinoza, Amanda E. Appel, Ruth J. Lyons, Sanjay Vashee, Hagen E.A. Fortsch, Jerome E. Foster, Dan Ramdath, Vanessa M. Hayes, Karen E. Nelson, Norberto Gonzalez-Juarbe

{"title":"Multiomic Insights into Human Health: Gut Microbiomes of Hunter-Gatherer, Agropastoral, and Western Urban Populations","authors":"Harinder Singh, Rosana Wiscovitch-Russo, Claire Kuelbs, Josh Espinoza, Amanda E. Appel, Ruth J. Lyons, Sanjay Vashee, Hagen E.A. Fortsch, Jerome E. Foster, Dan Ramdath, Vanessa M. Hayes, Karen E. Nelson, Norberto Gonzalez-Juarbe","doi":"10.1101/2024.09.03.611095","DOIUrl":"https://doi.org/10.1101/2024.09.03.611095","url":null,"abstract":"Societies with exposure to preindustrial diets exhibit improved markers of health. Our study used a comprehensive multi-omic approach to reveal that the gut microbiome of the Ju/'hoansi hunter-gatherers, one of the most remote KhoeSan groups, exhibit a higher diversity and richness, with an abundance of microbial species lost in the western population. The Ju/'hoansi microbiome showed enhanced global transcription and enrichment of complex carbohydrate metabolic and energy generation pathways. The Ju/'hoansi also show high abundance of short-chain fatty acids that are associated with health and optimal immune function. In contrast, these pathways and their respective species were found in low abundance or completely absent in Western populations. Amino acid and fatty acid metabolism pathways were observed prevalent in the Western population, associated with biomarkers of chronic inflammation. Our study provides the first in-depth multi-omic characterization of the Ju/'hoansi microbiome, revealing uncharacterized species and functional pathways that are associated with health.","PeriodicalId":501161,"journal":{"name":"bioRxiv - Genomics","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0