Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice

Study information

Reviewed Marked as Reviewed by Svetlana up on 2024-6-25

study design

laboratory experiment

Citation

PMID PubMed identifier for scientific articles.

38171017

DOI Digital object identifier for electronic documents.

https://doi.org/10.1128/spectrum.02037-23

URI

Authors

Matějková T, Dodoková A, Kreisinger J, Stopka P, Stopková R

Journal

Microbiology spectrum

Year

2024

Keywords:

16S RNA sequencing, Mus musculus, Pasteurellaceae, estrous cycle, estrus, microbiome, oral, proteome, saliva, vaginal

Symbiotic microbial communities affect the host immune system and produce molecules contributing to the odor of an individual. In many mammalian species, saliva and vaginal fluids are important sources of chemical signals that originate from bacterial metabolism and may act as honest signals of health and reproductive status. In this study, we aimed to define oral and vaginal microbiomes and their dynamics throughout the estrous cycle in wild house mice. In addition, we analyzed a subset of vaginal proteomes and metabolomes to detect potential interactions with microbiomes. 16S rRNA sequencing revealed that both saliva and vagina are dominated by Firmicutes and Proteobacteria but differ at the genus level. The oral microbiome is more stable during the estrous cycle and most abundant bacteria belong to the genera Gemella and Streptococcus, while the vaginal microbiome shows higher bacterial diversity and dynamics during the reproductive cycle and is characterized by the dominance of Muribacter and Rodentibacter. These two genera cover around 50% of the bacterial community during estrus. Proteomic profiling of vaginal fluids revealed specific protein patterns associated with different estrous phases. Highly expressed proteins in estrus involve the keratinization process thus providing estrus markers (e.g., Hrnr) while some proteins are downregulated such as immune-related proteins that limit bacterial growth (Camp, Clu, Elane, Lyz2, and Ngp). The vaginal metabolome contains volatile compounds potentially involved in chemical communication, for example, ketones, aldehydes, and esters of carboxylic acids. Data integration of all three OMICs data sets revealed high correlations, thus providing evidence that microbiomes, host proteomes, and metabolomes may interact.IMPORTANCEOur data revealed dynamic changes in vaginal, but not salivary, microbiome composition during the reproductive cycle of wild mice. With multiple OMICs platforms, we provide evidence that changes in microbiota in the vaginal environment are accompanied by changes in the proteomic and metabolomics profiles of the host. This study describes the natural microbiota of wild mice and may contribute to a better understanding of microbiome-host immune system interactions during the hormonal and cellular changes in the female reproductive tract. Moreover, analysis of volatiles in the vaginal fluid shows particular substances that can be involved in chemical communication and reproductive behavior.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-6-25

Curated date: 2024/03/18

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, Scholastica

Subjects

Location of subjects: Czechia

Host species Species from which microbiome was sampled. Contact us to have more species added.: Mus musculus

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Vagina , Saliva Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae,Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Microbiome measurement Microbiome measurement,microbiome measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Oral (saliva)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Vagina

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Vaginal samples of lived-trapped females of Mus musculus musculus mice

Group 0 sample size Number of subjects in the control (unexposed) group: 18

Group 1 sample size Number of subjects in the case (exposed) group: 18

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): None

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: centered log-ratio

Statistical test: ANCOM

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Richness Number of species: decreased

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-6-25

Curated date: 2024/03/20

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, Scholastica

Source: Figure 3B

Description: Bacterial taxa identified by ANCOM exhibiting significant abundance in oral compared to vaginal samples

Abundance in Group 1: increased abundance in Vagina

NCBI	Quality Control	Links
Enterococcus
Muribaculaceae

Revision editor(s): Omojokunoluwatomisin, Scholastica

Signature 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-6-25

Curated date: 2024/03/20

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, Scholastica

Source: Figure 3B

Description: Bacterial taxa identified by ANCOM exhibiting significant abundance in oral compared to vaginal samples

Abundance in Group 1: decreased abundance in Vagina

NCBI	Quality Control	Links
Gemella
Streptococcus
Corynebacterium
Lactobacillus
Methylobacterium
Bradyrhizobium
Muribacter

Revision editor(s): Omojokunoluwatomisin, Scholastica

Experiment 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-6-25

Curated date: 2024/03/20

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, Scholastica

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Vagina Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Vaginal microbiome measurement vaginal flora measurement,vaginal microbiota measurement,Vaginal microbiome measurement,vaginal microbiome measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Vaginal estrus samples

Group 1 name Corresponds to the case (exposed) group for case-control studies: Vaginal metestrus samples

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Vaginal samples collected during the metestrus phase