Microbiota and host最新文献

Stability of Fecal Microbiota during Degradation in Ex Situ Cheetahs in the US 美国原地猎豹粪便微生物群在降解过程中的稳定性

Microbiota and host Pub Date : 2024-03-01 DOI: 10.1530/mah-23-0022

Morgan Maly, Adrienne E Crosier, Mia M. Keady, Reade B Roberts, Matthew Breen, Carly R. Muletz-Wolz

{"title":"Stability of Fecal Microbiota during Degradation in Ex Situ Cheetahs in the US","authors":"Morgan Maly, Adrienne E Crosier, Mia M. Keady, Reade B Roberts, Matthew Breen, Carly R. Muletz-Wolz","doi":"10.1530/mah-23-0022","DOIUrl":"https://doi.org/10.1530/mah-23-0022","url":null,"abstract":"Objective:\u0000\u0000Gut health and its relationship to gut microbiota is an important consideration in the care and well-being of managed endangered species, such as the cheetah (Acinonyx jubatus). Non-invasive fecal sampling as a proxy for gut microbiota is preferred and collecting fresh fecals is the current gold standard. Unfortunately, even in managed facilities, collecting fresh samples from difficult to observe or dangerous animals is challenging. Therefore, we conducted a study to determine the terminal collection timepoint for fecal microbial studies in the cheetah.\u0000\u0000Methods:\u0000\u0000We longitudinally sampled eight freshly deposited fecals every 24 hours for five days and assessed bacterial relative abundance, diversity, and composition changes over time.\u0000\u0000Results:\u0000\u0000Our data indicated that fecal samples up to 24 hours post-defecation provided accurate representations of the fresh fecal microbiome. After 24 hours, major changes in community composition began to occur. By 72 hours, individual cheetah fecal microbiota signatures were lost.\u0000\u0000Conclusions:\u0000\u0000Our findings suggest that cheetah fecal samples should be collected within 24 hours of defecation in humid environments, especially if precipitation occurs, in order to provide a more biologically accurate representation of the gut microbiome, and we provide visual characteristics that can aid researchers in approximating time since defecation.\u0000\u0000Significance:\u0000\u0000These data provide guidelines for researchers investigating cheetah and other large felids and carnivores where the ability to collect fresh fecal deposits is limited.\u0000","PeriodicalId":101417,"journal":{"name":"Microbiota and host","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140271441","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

Deep Learning Enables Early-Stage Prediction of Preterm Birth Using Vaginal Microbiota 深度学习利用阴道微生物群实现早产的早期预测

Microbiota and host Pub Date : 2024-03-01 DOI: 10.1530/mah-23-0024

Kaushik Karambelkar, Mayank Baranwal

{"title":"Deep Learning Enables Early-Stage Prediction of Preterm Birth Using Vaginal Microbiota","authors":"Kaushik Karambelkar, Mayank Baranwal","doi":"10.1530/mah-23-0024","DOIUrl":"https://doi.org/10.1530/mah-23-0024","url":null,"abstract":"Objective: Preterm birth (PTB) is one of the leading issues concerning infant health and is a problem that plagues all parts of the world. Vaginal microbial communities have recently garnered attention in the context of PTB, however, the vaginal microbiome varies greatly from individual to individual, and this variation is more pronounced in racially, ethnically and geographically diverse populations. Additionally, microbial communities have been reported to evolve during the duration of the pregnancy, and capturing such a signature may require higher, more complex modeling paradigms. In this study, we develop a neural controlled differential equations (CDEs) based framework for identifying early PTBs in racially diverse cohorts from irregularly sampled vaginal microbial abundance data. \u0000\u0000Methods: We obtained relative abundances of microbial species within vaginal microbiota using 16S rRNA sequences obtained from vaginal swabs at various stages of pregnancy. We employed a recently introduced deep learning paradigm known as ``Neural CDEs\" to predict PTBs. This method, previously unexplored, analyzes irregularly sampled microbial abundance profiles in a time-series format.\u0000\u0000Results: Our framework is able to identify signatures in the temporally evolving vaginal microbiome during trimester~2 and can predict incidences of PTB (mean test set ROC-AUC = 0.81, accuracy = 0.75, f1 score = 0.71) significantly better than traditional ML classifiers, thus enabling effective early-stage PTB risk assessment. \u0000\u0000Conclusion and Significance: Our method is able to differentiate between term and preterm outcomes with a substantial accuracy, despite being trained using irregularly sampled microbial abundance profiles, thus overcoming the limitations of traditional time-series modeling methods.","PeriodicalId":101417,"journal":{"name":"Microbiota and host","volume":"72 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140282449","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

Metabolomics in the Era of Artificial Intelligence 人工智能时代的代谢组学

Microbiota and host Pub Date : 2024-02-01 DOI: 10.1530/mah-23-0017

Elizabeth A Coler, Wunxuan Chen, Alexey V Melnik, James T Morton, Alexander A Aksenov

{"title":"Metabolomics in the Era of Artificial Intelligence","authors":"Elizabeth A Coler, Wunxuan Chen, Alexey V Melnik, James T Morton, Alexander A Aksenov","doi":"10.1530/mah-23-0017","DOIUrl":"https://doi.org/10.1530/mah-23-0017","url":null,"abstract":"Artificial Intelligence (AI) is rapidly revolutionizing our daily lives, as it automates mundane tasks, enhances productivity, and transforms how we interact with technology. We believe it is inevitable that AI will soon become a crucial tool in common research practices, from data analysis to writing papers. Here we explore how this transition is occurring in the field of mass spectrometry-based metabolomics, a rapidly growing area of science. Metabolomics focuses on studying small molecules in biological systems, offering valuable insights into metabolic processes and their impact on health, diseases, and physiological conditions. With the remarkable advancements in sequencing technologies and the exploration of the microbiome, the combination of sequencing and metabolomics presents profound opportunities to understand biological complexity. Incorporating AI will unlock new possibilities and will, in all likelihood, contribute to scientific discoveries in the future. In this review we discuss the current role of AI in metabolomics. Existing practices are examined and we also provide a perspective on future directions for integrating AI into scientific research.","PeriodicalId":101417,"journal":{"name":"Microbiota and host","volume":"34 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139826618","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

Metabolomics in the Era of Artificial Intelligence 人工智能时代的代谢组学

Microbiota and host Pub Date : 2024-02-01 DOI: 10.1530/mah-23-0017

Elizabeth A Coler, Wunxuan Chen, Alexey V Melnik, James T Morton, Alexander A Aksenov

{"title":"Metabolomics in the Era of Artificial Intelligence","authors":"Elizabeth A Coler, Wunxuan Chen, Alexey V Melnik, James T Morton, Alexander A Aksenov","doi":"10.1530/mah-23-0017","DOIUrl":"https://doi.org/10.1530/mah-23-0017","url":null,"abstract":"Artificial Intelligence (AI) is rapidly revolutionizing our daily lives, as it automates mundane tasks, enhances productivity, and transforms how we interact with technology. We believe it is inevitable that AI will soon become a crucial tool in common research practices, from data analysis to writing papers. Here we explore how this transition is occurring in the field of mass spectrometry-based metabolomics, a rapidly growing area of science. Metabolomics focuses on studying small molecules in biological systems, offering valuable insights into metabolic processes and their impact on health, diseases, and physiological conditions. With the remarkable advancements in sequencing technologies and the exploration of the microbiome, the combination of sequencing and metabolomics presents profound opportunities to understand biological complexity. Incorporating AI will unlock new possibilities and will, in all likelihood, contribute to scientific discoveries in the future. In this review we discuss the current role of AI in metabolomics. Existing practices are examined and we also provide a perspective on future directions for integrating AI into scientific research.","PeriodicalId":101417,"journal":{"name":"Microbiota and host","volume":"36 1-2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139886227","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

Rationale behind phosphate therapy to modulate the gut microbiome and protect against surgery-related infection. 磷酸盐治疗调节肠道微生物组和预防手术相关感染的原理。

Microbiota and host Pub Date : 2023-02-01 Epub Date: 2023-09-11 DOI: 10.1530/mah-23-0011

John C Alverdy

{"title":"Rationale behind phosphate therapy to modulate the gut microbiome and protect against surgery-related infection.","authors":"John C Alverdy","doi":"10.1530/mah-23-0011","DOIUrl":"https://doi.org/10.1530/mah-23-0011","url":null,"abstract":"Despite major advances in infection control and the ever increasing use of broader spectrum antibiotics in surgery, postoperative infections continue to occur under the best of care and in the best institutions. Postoperative infections, also termed \"surgical site infections (SSIs), can range from superficial wound infections to deep organ space infections. SSIs can be superficial and only require medical treatment (i.e antibiotics), whereas others such as deep organ space infections resulting from an anastomotic leak can require multiple surgeries leading to sepsis and occasionally shock and death. Many if not most stakeholders in the field including surgeons, infectious disease specialists, infection control nurses, etc., in general advocate the use of prophylactic antibiotics and the enforcement of greater levels of sterility reasoning that all postoperative infections must arise from some type of direct contamination event. In this piece, the alternative view is presented that today, in the era of mandated asepsis protocols, enhanced recovery programs, and enforcement of prophylactic antibiotics in all cases, many if not most postoperative infections and SSIs occur from pathogens endogenous to the patient not from sources exogenous to the patient. It is also suggested that applying broader antibiotic coverage in elective surgery is neither an evolutionarily stable strategy nor inexorable in the context of emerging knowledge in the field of gut ecology. Here this concept is reviewed and the rationale behind using agents that preserve the gut microbiome and attenuate pathogen virulence in lieu of applying broader spectrum antibiotics and greater levels of sterility.","PeriodicalId":101417,"journal":{"name":"Microbiota and host","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10623387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71491000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Sex hormones, sex chromosomes, and microbiota: Identification of Akkermansia muciniphila as an estrogen-responsive microbiota. 性激素、性染色体和微生物群：粘蛋白阿克曼菌作为雌激素反应性微生物群的鉴定。

Microbiota and host Pub Date : 2023-01-01 Epub Date: 2023-10-09 DOI: 10.1530/mah-23-0010

Anil Sakamuri, Pritam Bardhan, Ramakumar Tummala, Franck Mauvais-Jarvis, Tao Yang, Bina Joe, Benard Ojwang Ogola

{"title":"Sex hormones, sex chromosomes, and microbiota: Identification of Akkermansia muciniphila as an estrogen-responsive microbiota.","authors":"Anil Sakamuri, Pritam Bardhan, Ramakumar Tummala, Franck Mauvais-Jarvis, Tao Yang, Bina Joe, Benard Ojwang Ogola","doi":"10.1530/mah-23-0010","DOIUrl":"10.1530/mah-23-0010","url":null,"abstract":"Microbiota composition is known to be linked to sex. However, separating sex hormones and sex chromosome roles in gut microbial diversity is yet to be determined. To investigate the sex chromosome role independent of sex hormones, we used the four-core genotype mouse model. In this mouse model, males with testes and females with ovaries have XX or XY sex chromosome complement. In gonadectomized four-core genotype mice, we observed a significant decrease in the levels of estradiol (P<0.001) and progesterone (P<0.03) in female and testosterone (P<0.0001) in male mice plasma samples. Independent of sex chromosome complement, microbial α diversity was increased in gonadectomized female but not male mice compared to sex-matched gonad-intact controls. β diversity analysis showed separation between male (P<0.05) but not female XX and XY mice. Importantly, Akkermansia muciniphila was less abundant in gonadectomized compared to gonadal intact female mice (P<0.0001). In the presence of β-estradiol, Akkermansia muciniphila growth exponentially increased, providing evidence for the identification of a female sex hormone-responsive bacterium (P<0.001).","PeriodicalId":101417,"journal":{"name":"Microbiota and host","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10629929/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71491001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0