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Characterization of Fecal Microbiomes of Osteoporotic Patients in Korea Cover

Characterization of Fecal Microbiomes of Osteoporotic Patients in Korea

Polish Journal of Microbiology
Volume 71 (2022): Issue 4 (December 2022)
By: Asad Ul-Haq,  Hoonhee Seo,  Sujin Jo,  Hyuna Park,  Sukyung Kim,  Youngkyoung Lee,  Saebim Lee,  Je Hoon Jeong and  Ho‑Yeon Song  
Open Access
|Dec 2022

Figures & Tables

Fig. 1

Rarefaction curve for sequence depth. The Faith phylogenetic diversity (Faith_pd) rarefaction curve shows that there is no difference in species abundance and diversity between the healthy control (HC) group and the osteoporotic (OP) patient group.
Rarefaction curve for sequence depth. The Faith phylogenetic diversity (Faith_pd) rarefaction curve shows that there is no difference in species abundance and diversity between the healthy control (HC) group and the osteoporotic (OP) patient group.

Fig. 2

Average taxonomic compositions of healthy controls (normal) and osteoporosis patient groups. The normal group and osteoporosis (OP) patients were further classified at the phylum, class, order, family, and genus levels. Those with relative abundances less than 1% were expressed as ETC. Only the Lachnospira genus showed a significant difference between the two groups among taxa of all ranks. Statistical significance between groups was analyzed using the Wilcoxon rank-sum test. *p < 0.05.
Average taxonomic compositions of healthy controls (normal) and osteoporosis patient groups. The normal group and osteoporosis (OP) patients were further classified at the phylum, class, order, family, and genus levels. Those with relative abundances less than 1% were expressed as ETC. Only the Lachnospira genus showed a significant difference between the two groups among taxa of all ranks. Statistical significance between groups was analyzed using the Wilcoxon rank-sum test. *p < 0.05.

Fig. 3

Alpha diversity indices for stool samples of healthy controls (normal) and osteoporosis (OP) patients. A) Species richness was analyzed with Ace, Chao1, Jackknife, OTUs, and B) Species diversity was analyzed with NPShannon, Shannon, Simpson, and Phylogenetic diversity. The horizontal thick black band represents the median value, and boxplot margins indicate the first and third quartiles.There was no significant difference between the two groups in any analysis results.
Alpha diversity indices for stool samples of healthy controls (normal) and osteoporosis (OP) patients. A) Species richness was analyzed with Ace, Chao1, Jackknife, OTUs, and B) Species diversity was analyzed with NPShannon, Shannon, Simpson, and Phylogenetic diversity. The horizontal thick black band represents the median value, and boxplot margins indicate the first and third quartiles.There was no significant difference between the two groups in any analysis results.

Fig. 4

Principal coordinate analysis (PCoA) of bacterial communities. Clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA). Healthy controls (normal) and osteoporosis (OP) patients were analyzed by A) Jensen-Shannon, B) Bray-Curtis, C) Generalized UniFrac, and D) UniFrac.
Principal coordinate analysis (PCoA) of bacterial communities. Clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA). Healthy controls (normal) and osteoporosis (OP) patients were analyzed by A) Jensen-Shannon, B) Bray-Curtis, C) Generalized UniFrac, and D) UniFrac.

Fig. 5

Clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA). Healthy controls (normal) and osteoporosis (OP) patients were analyzed by A) Jensen-Shannon, B) Bray-Curtis, C) Generalized UniFrac, and D) UniFrac.
Clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA). Healthy controls (normal) and osteoporosis (OP) patients were analyzed by A) Jensen-Shannon, B) Bray-Curtis, C) Generalized UniFrac, and D) UniFrac.

Fig. 6

Distinct taxa identified in healthy controls (normal) and osteoporosis (OP) patients using LEfSe (Linear discriminant analysis Effect Size) analysis. Taxonomic variations with linear discriminant analysis (LDA) scores greater than 2 and significance at α < 0.05 as determined by the Kruskal-Wallis test are presented here. The raw data of the above analysis results are presented in Table SIII.
Distinct taxa identified in healthy controls (normal) and osteoporosis (OP) patients using LEfSe (Linear discriminant analysis Effect Size) analysis. Taxonomic variations with linear discriminant analysis (LDA) scores greater than 2 and significance at α < 0.05 as determined by the Kruskal-Wallis test are presented here. The raw data of the above analysis results are presented in Table SIII.

Fig. 7

The taxonomic abundance of the Lachnospira genus. Among taxa of all ranks, only the Lachnospira genus showed a significant difference in abundance between the two groups. A) Among 16S gene-based metagenomics analysis results, the relative taxonomic abundance of the Lachnospira genus was analyzed, and the Wilcoxon rank-sum test was used for statistical significance, B) this result was verified by real-time PCR. Unpaired Student’s t-test was applied for statistical significance. The quantification cycle (Cq) value of the osteoporosis (OP) group was lower than that of the normal (HC) group, confirming that the osteoporosis (OP) group contained more Lachnospira than the normal group (HC). * p < 0.05; ** p < 0.01
The taxonomic abundance of the Lachnospira genus. Among taxa of all ranks, only the Lachnospira genus showed a significant difference in abundance between the two groups. A) Among 16S gene-based metagenomics analysis results, the relative taxonomic abundance of the Lachnospira genus was analyzed, and the Wilcoxon rank-sum test was used for statistical significance, B) this result was verified by real-time PCR. Unpaired Student’s t-test was applied for statistical significance. The quantification cycle (Cq) value of the osteoporosis (OP) group was lower than that of the normal (HC) group, confirming that the osteoporosis (OP) group contained more Lachnospira than the normal group (HC). * p < 0.05; ** p < 0.01

Fig. 8

Functional differences between OP and HC groups. A total of 11 metabolic pathways varied between the two groups. Tests were conducted at Kyoto Encyclopedia of Genes and Genomes (KEGG) using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUST) and MetaCyc webserver. PCO, photorespiratory carbon oxidation.
Functional differences between OP and HC groups. A total of 11 metabolic pathways varied between the two groups. Tests were conducted at Kyoto Encyclopedia of Genes and Genomes (KEGG) using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUST) and MetaCyc webserver. PCO, photorespiratory carbon oxidation.

Results of beta set-significance analysis_

Pair-wiseSpeciesGenus
Jensen-ShannonN.S. (p = 0.725)N.S. (p = 0.796)
Bray-CurtisN.S. (p = 0.463)N.S. (p = 0.173)
Generalized UniFracN.S. (p = 0.616)N.S. (p = 0.631)
UniFracN.S. (p = 0.757)N.S. (p = 0.732)
DOI: https://doi.org/10.33073/pjm-2022-045 | Journal eISSN: 2544-4646 | Journal ISSN: 1733-1331
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Language: English
Page range: 601 - 613
Submitted on: Jul 11, 2022
Accepted on: Sep 11, 2022
Published on: Dec 21, 2022
Published by: Polish Society of Microbiologists
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year
Keywords:
osteoporosis,
microbiomes,
gut microbiota,
fecal microbiomes,
16S rRNA gene-based metagenomics
Related subjects:
Life sciences,
Microbiology and virology

© 2022 Asad Ul-Haq, Hoonhee Seo, Sujin Jo, Hyuna Park, Sukyung Kim, Youngkyoung Lee, Saebim Lee, Je Hoon Jeong, Ho‑Yeon Song, published by Polish Society of Microbiologists
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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