Dominance network analysis of the healthy human vaginal microbiome not dominated by Lactobacillus species
Although Lactobacillus dominance is one of the commonest characteristics of many healthy vaginal microbiomes, a significant proportion of healthy women lack an appreciable amount of Lactobacillus in their microbiome. Indeed, the vaginal microbiomes of many BV (bacterial vaginosis) patients lack the...
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| Format: | Article |
| Language: | English |
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Elsevier
2020-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037020304554 |
| _version_ | 1818560858738917376 |
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| author | Wendy Li Zhanshan (Sam) Ma |
| author_facet | Wendy Li Zhanshan (Sam) Ma |
| author_sort | Wendy Li |
| collection | DOAJ |
| description | Although Lactobacillus dominance is one of the commonest characteristics of many healthy vaginal microbiomes, a significant proportion of healthy women lack an appreciable amount of Lactobacillus in their microbiome. Indeed, the vaginal microbiomes of many BV (bacterial vaginosis) patients lack the dominance by Lactobacillus. One would wonder what are special with those healthy non-Lactobacillus dominated vaginal microbiomes (nLDVM)? Here we re-analyzed the vaginal microbiome datasets of 1107 postpartum women in rural Malawi Doyle et al. (2018) using species dominance network (SDN) analysis. We discovered that: (i) The DN of the nLDVM is predominantly mutualistic, where most competitive (negative) relationships were from bacterial vaginosis-associated bacteria (BVAB), >60% occurred between BVAB and non-BVAB genera. Gardnerella was inhibited by a mutualistic combination of 23 genera, and Lactobacillus by 15 genera. These may be possible mechanisms by which the microbiome maintains high diversity but avoids dominance by Gardnerella or Lactobacillus. Gardnerella and Lactobacillus were only cooperated with a few genera, but they were positively connected with each other. The suppressed Lactobacillus species positively associated with Gardnerella was Lactobacillus iners, indicating that L. iners might act as an “enemy” in the Lactobacillus-poor vaginal microbiome, and inhibition of Gardnerella and L. iners might be a self-protective mechanism to maintain stability and health of this microbiome. (ii) We identified skeletons of the DNs and separate pathways consisting of high salience skeletons. Finegoldia species and Staphylococcus epidermidis were the hubs of the skeleton network. The roles that they play in the nLDVM deserve more attention of future studies. |
| first_indexed | 2024-12-14T00:43:35Z |
| format | Article |
| id | doaj.art-1ac46de9017644c7ab5e4fd82dcc1a50 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-12-14T00:43:35Z |
| publishDate | 2020-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-1ac46de9017644c7ab5e4fd82dcc1a502022-12-21T23:24:14ZengElsevierComputational and Structural Biotechnology Journal2001-03702020-01-011834473456Dominance network analysis of the healthy human vaginal microbiome not dominated by Lactobacillus speciesWendy Li0Zhanshan (Sam) Ma1Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Sciences, University of Chinese Academy of Sciences, ChinaComputational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Sciences, University of Chinese Academy of Sciences, China; Corresponding author at: Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.Although Lactobacillus dominance is one of the commonest characteristics of many healthy vaginal microbiomes, a significant proportion of healthy women lack an appreciable amount of Lactobacillus in their microbiome. Indeed, the vaginal microbiomes of many BV (bacterial vaginosis) patients lack the dominance by Lactobacillus. One would wonder what are special with those healthy non-Lactobacillus dominated vaginal microbiomes (nLDVM)? Here we re-analyzed the vaginal microbiome datasets of 1107 postpartum women in rural Malawi Doyle et al. (2018) using species dominance network (SDN) analysis. We discovered that: (i) The DN of the nLDVM is predominantly mutualistic, where most competitive (negative) relationships were from bacterial vaginosis-associated bacteria (BVAB), >60% occurred between BVAB and non-BVAB genera. Gardnerella was inhibited by a mutualistic combination of 23 genera, and Lactobacillus by 15 genera. These may be possible mechanisms by which the microbiome maintains high diversity but avoids dominance by Gardnerella or Lactobacillus. Gardnerella and Lactobacillus were only cooperated with a few genera, but they were positively connected with each other. The suppressed Lactobacillus species positively associated with Gardnerella was Lactobacillus iners, indicating that L. iners might act as an “enemy” in the Lactobacillus-poor vaginal microbiome, and inhibition of Gardnerella and L. iners might be a self-protective mechanism to maintain stability and health of this microbiome. (ii) We identified skeletons of the DNs and separate pathways consisting of high salience skeletons. Finegoldia species and Staphylococcus epidermidis were the hubs of the skeleton network. The roles that they play in the nLDVM deserve more attention of future studies.http://www.sciencedirect.com/science/article/pii/S2001037020304554Non-Lactobacillus dominated vaginal microbiome (nLDVM)Dominance network (DN)GardnerellaLactobacillus inersCore-periphery networkHigh salience skeleton network |
| spellingShingle | Wendy Li Zhanshan (Sam) Ma Dominance network analysis of the healthy human vaginal microbiome not dominated by Lactobacillus species Computational and Structural Biotechnology Journal Non-Lactobacillus dominated vaginal microbiome (nLDVM) Dominance network (DN) Gardnerella Lactobacillus iners Core-periphery network High salience skeleton network |
| title | Dominance network analysis of the healthy human vaginal microbiome not dominated by Lactobacillus species |
| title_full | Dominance network analysis of the healthy human vaginal microbiome not dominated by Lactobacillus species |
| title_fullStr | Dominance network analysis of the healthy human vaginal microbiome not dominated by Lactobacillus species |
| title_full_unstemmed | Dominance network analysis of the healthy human vaginal microbiome not dominated by Lactobacillus species |
| title_short | Dominance network analysis of the healthy human vaginal microbiome not dominated by Lactobacillus species |
| title_sort | dominance network analysis of the healthy human vaginal microbiome not dominated by lactobacillus species |
| topic | Non-Lactobacillus dominated vaginal microbiome (nLDVM) Dominance network (DN) Gardnerella Lactobacillus iners Core-periphery network High salience skeleton network |
| url | http://www.sciencedirect.com/science/article/pii/S2001037020304554 |
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