Understanding and interpreting community sequencing measurements of the vaginal microbiome

Berman, Hanna; McLaren, Michael R.; Callahan, Benjamin J.

doi:10.1111/1471-0528.15978

Cited by 19 publications

(20 citation statements)

References 90 publications

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“…This sequencing method extracts all actively transcribed genes, not all existing genes, because some genes may not be sufficiently active at the time of sampling [56], and describes gene expression in microbial communities. This provides stronger evidence for the functional activity of genes than DNA-based community sequencing methods because many genes are conditionally expressed [57].…”

Section: Metatranscriptomicsmentioning

confidence: 99%

The Relationship Between the Gut Microbiome and Neurodegenerative Diseases

Xiao-hong

Lou

et al. 2021

Neurosci. Bull.

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Many recent studies have shown that the gut microbiome plays important roles in human physiology and pathology. Also, microbiome-based therapies have been used to improve health status and treat diseases. In addition, aging and neurodegenerative diseases, including Alzheimer's disease and Parkinson's disease, have become topics of intense interest in biomedical research. Several researchers have explored the links between these topics to study the potential pathogenic or therapeutic effects of intestinal microbiota in disease. But the exact relationship between neurodegenerative diseases and gut microbiota remains unclear. As technology advances, new techniques for studying the microbiome will be developed and refined, and the relationship between diseases and gut microbiota will be revealed. This article summarizes the known interactions between the gut microbiome and neurodegenerative diseases, highlighting assay techniques for the gut microbiome, and we also discuss the potential therapeutic role of microbiome-based therapies in diseases.

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Section: Metatranscriptomicsmentioning

confidence: 99%

The Relationship Between the Gut Microbiome and Neurodegenerative Diseases

Xiao-hong

Lou

et al. 2021

Neurosci. Bull.

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“…Studies continue to examine and analyze samples more precisely. Recent studies have reported microbial community sequencing, including amplicon and shotgun metagenomic sequencing, for vaginal microbiome analysis (Berman et al, 2020). It is important to distinguish the different microbial species, since Lactobacillus and Gardnerella are the predominant genera in most of the vaginal microbiome in normal healthy women, especially when vaginal fluid is used as evidence (Ghemrawi et al, 2021).…”

Section: Sequencing Platformsmentioning

confidence: 99%

Forensic Analysis of Human Microbiome in Skin and Body Fluids Based on Geographic Location

Cho

Eom

2021

Front. Cell. Infect. Microbiol.

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High-throughput DNA sequencing technologies have facilitated the in silico forensic analysis of human microbiome. Specific microbial species or communities obtained from the crime scene provide evidence of human contacts and their body fluids. The microbial community is influenced by geographic, ethnic, lifestyle, and environmental factors such as urbanization. An understanding of the effects of these external stressors on the human microbiome and determination of stable and changing elements are important in selecting appropriate targets for investigation. In this study, the Forensic Microbiome Database (FMD) (http://www.fmd.jcvi.org) containing the microbiome data of various locations in the human body in 35 countries was used. We focused on skin, saliva, vaginal fluid, and stool and found that the microbiome distribution differed according to the body part as well as the geographic location. In the case of skin samples, Staphylococcus species were higher than Corynebacterium species among Asians compared with Americans. Holdemanella and Fusobacterium were specific in the saliva of Koreans and Japanese populations. Lactobacillus was found in the vaginal fluids of individuals in all countries, whereas Serratia and Enterobacter were endemic to Bolivia and Congo, respectively. This study is the first attempt to collate and describe the observed variation in microbiomes from the forensic microbiome database. As additional microbiome databases are reported by studies worldwide, the diversity of the applications may exceed and expand beyond the initial identification of the host.

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“…Presently, the vaginal microbiome is typically studied via two DNA-based approaches and one RNA-based strategy: metabarcoding (DNA), metagenomics (DNA) and, to a lesser extent, metatranscriptomics (RNA, not discussed further) 25 . Metabarcoding (also known as metataxonomics or amplicon sequencing) is the most commonly used technique for microbiome analysis, partly due to its simplicity, but primarily because of the low cost (typically <$100 per sample) and well established analysis pipelines (e.g.…”

Section: Introductionmentioning

confidence: 99%

“…Amplicon sequencing involves the PCR amplification of a small hypervariable region or regions (250-500 bp) of the taxonomically informative 16S rRNA gene expressed in all bacterial species. Typically, microbiome specialists would design primers that can amplify a set of variable regions that allow the taxonomic discrimination and identification of bacterial generain some cases to the species level; this is necessary for CST profiling, although bias can be introduced through primer design, the selected 16S rRNA gene region and its coverage 25 . To eliminate obvious bias, primers may need to be redesigned to increase the species detection within the same taxonomic kingdom, or if separate domains are to be targeted, such as when characterising the prokaryotes, fungi and microeukaryotes communities present in the human vaginal tracts 25,26 .…”

Section: Introductionmentioning

confidence: 99%

Vaginal microbial profiling in a preterm birth high-risk cohort using shallow shotgun metagenomics

2021

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Preterm birth (PTB) is a significant health problem globally, with an estimate of 15 million cases annually. Approximately 10% of neonates born early will die prematurely, while a subset will develop severe life-long morbidities. Unfortunately, preterm birth’s syndromic nature has evaded prevention strategies, and it continues to impose a high burden on healthcare systems and families. The role of vaginal bacteria in triggering biomolecular causes of PTB has been recognised for years. However, translating this knowledge to practical diagnostic and therapeutic strategies has remained elusive. New techniques in high-throughput sequencing have improved our understanding of the nature and role of the vaginal microbiome during pregnancy. Several multi-ethnic and multi-geographical studies into the vaginal microbiome have identified five distinct bacterial profiles termed community state types (CSTs), one of which is positively associated with dysbiosis and increased risk of PTB. In a small pilot study of first-trimester vaginal microbial DNA obtained from pregnant women at high-risk of PTB, we compared the CST profiles generated using standard 16S amplicon sequencing with shallow shotgun metagenomics (SSM). Both methods identified the presence of the five CSTs as has been reported previously, although the metagenomic data showed greater taxonomic resolution and more accurate CST assignation. These findings suggest that SSM is a cost-effective and potentially superior alternative to 16S sequencing for vaginal microbiome analysis.

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Understanding and interpreting community sequencing measurements of the vaginal microbiome

Cited by 19 publications

References 90 publications

The Relationship Between the Gut Microbiome and Neurodegenerative Diseases

The Relationship Between the Gut Microbiome and Neurodegenerative Diseases

Forensic Analysis of Human Microbiome in Skin and Body Fluids Based on Geographic Location

Vaginal microbial profiling in a preterm birth high-risk cohort using shallow shotgun metagenomics

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