Field expedient stool collection methods for gut microbiome analysis in deployed military environments.

IF 3.7 2区 生物学 Q2 MICROBIOLOGY
mSphere Pub Date : 2025-06-25 Epub Date: 2025-05-15 DOI:10.1128/msphere.00818-24
Car Reen Kok, James B Thissen, Michele Cerroni, David R Tribble, Anthony Cancio, Sophia Tran, Christina Schofield, Rhonda E Colombo, Tom Troth, Christie Joya, Tahaniyat Lalani, Nicholas A Be
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Abstract

Field expedient devices and protocols for the collection, storage, and shipment of stool samples in deployed settings are needed for the advancement of microbiome research in military health. Relevant assessments include the evaluation of microbiome signatures associated with susceptibility to travelers' diarrhea and recovery of gut function following infection. However, inherent biases in microbial measurements due to preservatives and sampling methods are unclear and should be assessed for an accurate evaluation of the microbiome. We performed shotgun metagenomic sequencing and compared the microbiome composition in paired fecal samples collected using Flinters Technology Associates (FTA) cards and OMNIgene (OG) Gut tubes, prior to and during international travel, from 49 adult participants, 39 of whom remained asymptomatic and 10 experienced travelers' diarrhea. Higher concentrations of nucleic acid and sequencing libraries were observed in OG samples. A majority of genera (82.9%) were detected with both methods, and detections of genera limited to one collection method were not highly prevalent across samples and were present in extremely low relative abundances (<0.01%). Differences in beta diversity were largely explained by inter-individuality of microbiome composition, followed by the effect of collection method and timepoint-disease states. Differential abundance analysis indicated that Corynebacterium and Blautia were consistently higher in abundance across all groups with FTA and OG collection, respectively. The observed differences in microbiome composition between methods suggest the need for consistent and standardized protocols within a study. Overall, the data presented here could help guide the future design of fecal microbiome study protocols in field and military deployment settings.IMPORTANCEThe assessment of field-deployable methods for fecal sample collection and storage is required to reliably capture samples collected in remote and austere locations. This study describes a comparative metagenomics analysis between samples collected by two different commercially available methods in a military-deployed setting. The results presented here are foundational for the future design of fecal microbiome study protocols in an operational context.

部署军事环境中肠道微生物组分析的现场粪便收集方法。
需要在部署环境中收集、储存和运输粪便样本的现场便利设备和协议,以促进军事卫生中的微生物组研究。相关评估包括评估与旅行者腹泻易感性和感染后肠道功能恢复相关的微生物组特征。然而,由于防腐剂和采样方法导致的微生物测量的固有偏差尚不清楚,应该对其进行评估以准确评估微生物组。我们对49名成年参与者进行了鸟枪宏基因组测序,并比较了在国际旅行之前和期间使用flters Technology Associates (FTA)卡和OMNIgene (OG)肠管收集的配对粪便样本中的微生物组组成,其中39人仍然无症状,10人有经验的旅行者腹泻。在OG样品中观察到较高浓度的核酸和测序文库。两种方法均检测到大多数属(82.9%),仅限于一种收集方法的属在样品中并不普遍,并且相对丰度极低(棒状杆菌和蓝芽胞杆菌在FTA和OG收集的所有组中的丰度均一致较高)。观察到的不同方法之间微生物组组成的差异表明,在一项研究中需要一致和标准化的方案。总的来说,这里提供的数据可以帮助指导未来在野外和军事部署环境中设计粪便微生物组研究方案。重要性评估现场可部署的粪便样本收集和储存方法,以可靠地捕获在偏远和恶劣地点收集的样本。本研究描述了在军事部署环境中通过两种不同的商业可用方法收集的样本之间的比较宏基因组学分析。这里提出的结果是基础的粪便微生物组研究方案在操作环境下的未来设计。
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来源期刊
mSphere
mSphere Immunology and Microbiology-Microbiology
CiteScore
8.50
自引率
2.10%
发文量
192
审稿时长
11 weeks
期刊介绍: mSphere™ is a multi-disciplinary open-access journal that will focus on rapid publication of fundamental contributions to our understanding of microbiology. Its scope will reflect the immense range of fields within the microbial sciences, creating new opportunities for researchers to share findings that are transforming our understanding of human health and disease, ecosystems, neuroscience, agriculture, energy production, climate change, evolution, biogeochemical cycling, and food and drug production. Submissions will be encouraged of all high-quality work that makes fundamental contributions to our understanding of microbiology. mSphere™ will provide streamlined decisions, while carrying on ASM''s tradition for rigorous peer review.
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