Changes in Probiotic Lachnospiraceae Genera Across Different Stages of COVID-19: A Meta-Analysis of 16S rRNA Microbial Data
Abstract
1. Introduction
2. Materials and Methods
2.1. Study Selection and Obtaining the Sequencing Datasets
2.2. Sequencing Read Data Processing and Analysis
3. Results
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Autor; Year | Accession Number | Country | Type of Study | NGS Technology | N | Groups |
---|---|---|---|---|---|---|
Albrich et al., 2022 [28] | PRJEB50040 | Switzerland and Ireland | Cohort | MiSeq | 98 | 8 mild, 24 moderate, and 66 severe |
Gaibani et al., 2021 [29] | PRJNA700830 | Italy | Case–control | MiSeq | 69 | COVID-19 |
Galperine et al., 2023 [30] | PRJEB61722 | Switzerland | Cohort | MiSeq | 57 | 42 severe, 15 critical |
Rafiqul Islam et al., 2022 [31] | PRJNA767939 | Bangladesh | Cross-section | MiSeq | 37 | 15 healthy, 22 COVID-19 |
Reinold et al., 2021 [32] | PRJNA747262 | Germany | Cross-section | NovaSeq 6000 | 212 | 95 negative, 44 mild, 35 moderate, 26 severe, 12 critical |
Talukdar et al., 2023 [33] | PRJNA895415 | India | Cohort | MiSeq | 52 | 7 mild, 45 severe |
Wu et al., 2021 [34] | PRJNA684070 | China | Case–control | NovaSeq 6000 | 56 | 32 healthy, 5 mild, 16 moderate, 3 severe |
Genus | Study | Reference Database | Statistical Analysis | p Values | FDR | Healthy | Mild | Moderate | Severe | Critical | LDA Score |
---|---|---|---|---|---|---|---|---|---|---|---|
Blautia | PRJEB50040 | NR | Mann–Whitney | 0.00042096 | - | - | - | - | - | - | - |
Standard Protocol | Silva v. 138 | Lefse | 0.082563 | 0.49618 | - | 528.38 | 568.08 | 324.02 | - | 2.09 | |
PRJEB61722 | EzBioCloud | NBZIMM | - | - | - | - | - | - | - | - | |
Standard Protocol | Silva v. 138 | Lefse | 0.67677 | 0.87127 | 187.86 | 272.73 | 1.64 | ||||
PRJNA747262 | Greengenes 13.8 | Lefse | - | - | - | - | - | - | - | - | |
Standard Protocol | Silva v. 138 | Lefse | 0.27837 | 0.62404 | 1093.1 | 1159.1 | 1336.7 | 852.62 | 1301.8 | 2.39 | |
PRJNA895415 | Silva v. 138 | Lefse | 0.0018892 | 0.027866 | - | - | - | - | - | 5.21 | |
Standard Protocol | Silva v. 138 | Lefse | 0.036234 | 0.37246 | - | 468.71 | - | 168.31 | - | 2.18 | |
PRJNA684070 | Greengenes 13.8 | Lefse | NR | NR | NR | NR | NR | NR | NR | NR | |
Standard Protocol | Silva v. 138 | Lefse | - | - | - | - | - | - | - | - | |
Coprococcus | PRJEB50040 | NR | Mann–Whitney | 0.003043936 | - | - | - | - | - | - | - |
Standard Protocol | Silva v. 138 | Lefse | 0.11478 | 0.54002 | - | 31.5 | 16.417 | 15.909 | - | 0.944 | |
PRJEB61722 | EzBioCloud | NBZIMM | - | - | - | - | - | - | - | - | |
Standard Protocol | Silva v. 138 | Lefse | 0.16682 | 0.66966 | - | - | - | 64.762 | 33 | −1.23 | |
PRJNA747262 | Greengenes 13.8 | Lefse | - | - | - | - | - | - | - | - | |
Standard Protocol | Silva v. 138 | Lefse | 0.22521 | 0.59503 | 122.15 | 216.5 | 199.11 | 152 | 137.83 | 1.68 | |
PRJNA895415 | Silva v. 138 | Lefse | - | - | - | - | - | - | - | - | |
Standard Protocol | Silva v. 138 | Lefse | 0.18663 | 0.7538 | - | 41.429 | - | 23.978 | - | 0.988 | |
PRJNA684070 | Greengenes 13.8 | Lefse | NR | NR | NR | NR | NR | NR | NR | NR | |
Standard Protocol | Silva v. 138 | Lefse | - | - | - | - | - | - | - | - | |
Lachnospira | PRJEB50040 | NR | Mann–Whitney | 7.98309 × 10−5 | - | - | - | - | - | - | - |
Standard Protocol | Silva v. 138 | Lefse | 0.0048226 | 0.1136 | - | 21.875 | 33.083 | 11.455 | - | 1.07 | |
PRJEB61722 | EzBioCloud | NBZIMM | - | - | - | - | - | - | - | - | |
Standard Protocol | Silva v. 138 | Lefse | 0.0057487 | 0.35032 | - | - | - | 146.17 | 22 | −1.8 | |
PRJNA747262 | Greengenes 13.8 | Lefse | - | - | - | - | - | - | - | - | |
Standard Protocol | Silva v. 138 | Lefse | 0.21381 | 0.58498 | 42.895 | 72.091 | 65.114 | 54.346 | 29.083 | 1.35 | |
PRJNA895415 | Silva v. 138 | Lefse | - | - | - | - | - | - | - | - | |
Standard Protocol | Silva v. 138 | Lefse | 0.012363 | 0.21696 | - | 83.714 | - | 10.4 | - | 1.58 | |
PRJNA684070 | Greengenes 13.8 | Lefse | - | - | - | - | - | - | - | - | |
Standard Protocol | Silva v. 138 | Lefse | - | - | - | - | - | - | - | - | |
Roseburia | PRJEB50040 | NR | Mann–Whitney | 0.000113838 | - | - | - | - | - | - | - |
Standard Protocol | Silva v. 138 | Lefse | 0.0087579 | 0.15472 | - | 8.625 | 19.583 | 20.879 | - | 0.853 | |
PRJEB61722 | EzBioCloud | NBZIMM | NR | NR | - | - | - | NR | NR | NR | |
Standard Protocol | Silva v. 138 | Lefse | 0.039976 | 0.58486 | - | - | - | 67.048 | 4.7333 | −1.51 | |
PRJNA747262 | Greengenes 13.8 | Lefse | <0.05 | NR | NR | NR | NR | NR | NR | >3.5 | |
Standard Protocol | Silva v. 138 | Lefse | 0.042058 | 0.27312 | 78.274 | 119.34 | 175.77 | 114.12 | 43.917 | 1.83 | |
PRJNA895415 | Silva v. 138 | Lefse | - | - | - | - | - | - | - | - | |
Standard Protocol | Silva v. 138 | Lefse | 0.25183 | 0.76757 | - | 21.571 | - | 9.3333 | - | 0.852 | |
PRJNA684070 | Greengenes 13.8 | Lefse | - | - | - | - | - | - | - | - | |
Standard Protocol | Silva v. 138 | Lefse | - | - | - | - | - | - | - | - |
Genus | Study | Reference Database | Statistical Analysis | p Values | FDR | Healthy | COVID-19 | LDA Score |
---|---|---|---|---|---|---|---|---|
Blautia | PRJNA767939 | NCBI | Kruskal–Wallis | - | - | - | - | - |
Standard Protocol | Silva v. 138 | LEfSe | 0.81092 | 0.89347 | 18.067 | 36.045 | −1 | |
Coprococcus | PRJNA767939 | NCBI | Kruskal–Wallis | - | - | - | - | - |
Standard Protocol | Silva v. 138 | LEfSe | 0.39419 | 0.57006 | 3.1333 | 2.9091 | 0.0462 | |
Lachnospira | PRJNA767939 | NCBI | Kruskal–Wallis | - | - | - | - | - |
Standard Protocol | Silva v. 138 | LEfSe | 0.035134 | 0.12232 | 9.6 | 13.091 | −0.439 | |
Roseburia | PRJNA767939 | NCBI | Kruskal–Wallis | - | - | - | - | - |
Standard Protocol | Silva v. 138 | LEfSe | 0.001058 | 0.016576 | 3.4 | 0.81818 | 0.36 |
Genus | Study | Reference Database | Statistical Analysis | p Values | FDR | Healthy | Mild | Moderate | Severe | Critical | LDA Score |
---|---|---|---|---|---|---|---|---|---|---|---|
Lachnospiraceae_FCS020_group | PRJEB50040 | Silva v. 138 | Lefse | 0.2352 | 0.65374 | - | 4.5 | 1.2917 | 1.3485 | - | 0.416 |
Lachnospiraceae_FCS020_group | PRJEB61722 | Silva v. 138 | Lefse | 0.27561 | 0.71539 | - | - | - | 1.7619 | 0.8 | −0.171 |
Lachnospiraceae_FCS020_group | PRJNA895415 | Silva v. 138 | Lefse | 0.09367 | 0.61012 | - | - | 2.2857 | 0.84444 | - | 0.236 |
Lachnospiraceae_ge | PRJEB50040 | Silva v. 138 | Lefse | 0.0072566 | 0.14405 | - | 80.125 | 56 | 50.924 | - | 1.19 |
Lachnospiraceae_ge | PRJEB61722 | Silva v. 138 | Lefse | 0.82062 | 0.911 | - | - | - | 157.19 | 126.67 | −1.21 |
Lachnospiraceae_ge | PRJNA747262 | Silva v. 138 | Lefse | 0.094113 | 0.44042 | 249.07 | 307.32 | 392.63 | 357.81 | 640.75 | 2.29 |
Lachnospiraceae_ge | PRJNA895415 | Silva v. 138 | Lefse | 0.012753 | 0.21696 | - | - | 74.857 | 19.733 | - | 1.46 |
Lachnospiraceae_NK3A20_group | PRJNA747262 | Silva v. 138 | Lefse | 0.22463 | 0.59503 | 1.5368 | 1.9773 | 1.0571 | 0.038462 | 0.66667 | 0.294 |
Lachnospiraceae_NK4A136_group | PRJEB61722 | Silva v. 138 | Lefse | 0.0001754 | 0.044201 | - | - | - | 155.52 | 20.267 | −1.84 |
Lachnospiraceae_NK4A136_group | PRJNA747262 | Silva v. 138 | Lefse | 0.00019874 | 0.010158 | 30.895 | 82 | 105.94 | 102.08 | 68 | 1.59 |
Lachnospiraceae_NK4B4_group | PRJNA747262 | Silva v. 138 | Lefse | 0.00020731 | 0.010158 | 0 | 0.22727 | 0.17143 | 1.3462 | 0.41667 | 0.224 |
Lachnospiraceae_XPB1014_group | PRJNA747262 | Silva v. 138 | Lefse | 0.25132 | 0.60649 | 0.021053 | 0.022727 | 0 | 0 | 0.41667 | 0.0822 |
Lachnospiraceae_ND3007_group | PRJEB50040 | Silva v. 138 | Lefse | 0.2958 | 0.68442 | - | 28 | 11.083 | 5.7424 | - | 1.08 |
Lachnospiraceae_ND3007_group | PRJEB61722 | Silva v. 138 | Lefse | 0.34702 | 0.71539 | - | - | - | 7.8333 | 7.0667 | −0.141 |
Lachnospiraceae_ND3007_group | PRJNA747262 | Silva v. 138 | Lefse | 0.7409 | 0.84526 | 41.263 | 51.932 | 35.314 | 41.115 | 35.5 | 0.969 |
Lachnospiraceae_ND3007_group | PRJNA895415 | Silva v. 138 | Lefse | 0.032752 | 0.35878 | - | - | 2.8571 | 0.77778 | - | 0.31 |
Lachnospiraceae_UCG_001 | PRJEB50040 | Silva v. 138 | Lefse | 0.0651 | 0.45349 | - | 1 | 1.2083 | 0.86364 | - | 0.0691 |
Lachnospiraceae_UCG_001 | PRJEB61722 | Silva v. 138 | Lefse | 0.058343 | 0.58486 | - | - | - | 8.5952 | 0.13333 | −0.719 |
Lachnospiraceae_UCG_001 | PRJNA747262 | Silva v. 138 | Lefse | 0.15103 | 0.52394 | 9.1053 | 7.2955 | 6.7429 | 9.1923 | 1.75 | 0.674 |
Lachnospiraceae_UCG_002 | PRJEB61722 | Silva v. 138 | Lefse | 0.016965 | 0.47234 | - | - | - | 0 | 0.46667 | 0.0911 |
Lachnospiraceae_UCG_002 | PRJNA747262 | Silva v. 138 | Lefse | 0.82311 | 0.89087 | 0.021053 | 0.022727 | 0 | 0 | 0 | 0.00491 |
Lachnospiraceae_UCG_003 | PRJEB50040 | Silva v. 138 | Lefse | 0.61272 | 0.86598 | - | 0 | 0 | 0.24242 | - | 0.0497 |
Lachnospiraceae_UCG_004 | PRJEB50040 | Silva v. 138 | Lefse | 0.019059 | 0.20522 | - | 7.875 | 1.75 | 1.5909 | - | 0.617 |
Lachnospiraceae_UCG_004 | PRJEB61722 | Silva v. 138 | Lefse | 0.023851 | 0.47234 | - | - | - | 28.357 | 5.8 | −1.09 |
Lachnospiraceae_UCG_004 | PRJEB61722 | Silva v. 138 | Lefse | 0.023851 | 0.47234 | - | - | - | 28.357 | 5.8 | −1.09 |
Lachnospiraceae_UCG_004 | PRJNA895415 | Silva v. 138 | Lefse | 0.012537 | 0.21696 | - | - | 4.7143 | 1.3333 | - | 0.43 |
Lachnospiraceae_UCG_006 | PRJEB50040 | Silva v. 138 | Lefse | 1.1569 × 10−5 | 0.0024526 | - | 0.5 | 0 | 0 | - | 0.0969 |
Lachnospiraceae_UCG_006 | PRJNA747262 | Silva v. 138 | Lefse | 0.24373 | 0.60649 | 0.042105 | 0.25 | 0.17143 | 0.11538 | 0.75 | 0.132 |
Lachnospiraceae_UCG_010 | PRJEB50040 | Silva v. 138 | Lefse | 0.0004688 | 0.033128 | - | 19.25 | 4.0417 | 3.9848 | - | 0.936 |
Lachnospiraceae_UCG_010 | PRJNA747262 | Silva v. 138 | Lefse | 0.1599 | 0.52394 | 31.411 | 47.409 | 47.514 | 39 | 54.25 | 1.09 |
Lachnospiraceae_unclassified | PRJEB50040 | Silva v. 138 | Lefse | 0.37074 | 0.76342 | - | 397 | 281 | 340.27 | - | 1.77 |
Lachnospiraceae_unclassified | PRJEB61722 | Silva v. 138 | Lefse | 0.05358 | 0.58486 | - | - | - | 404.71 | 137.8 | −2.13 |
Lachnospiraceae_unclassified | PRJNA747262 | Silva v. 138 | Lefse | 0.77331 | 0.86605 | 524.83 | 499.14 | 536.26 | 492.65 | 452.67 | 1.63 |
Lachnospiraceae_unclassified | PRJNA895415 | Silva v. 138 | Lefse | 0.15071 | 0.68777 | - | - | 290.14 | 175.8 | - | 1.76 |
Lachnospiraceae_unclassified | PRJNA684070 | Silva v. 138 | Lefse | 0.0035627 | 0.037853 | - | - | 4001.5 | 4506.3 | 157.67 | 3.34 |
Genus | Study | Reference Database | Statistical Analysis | p Values | FDR | Healthy | COVID-19 | LDA Score |
---|---|---|---|---|---|---|---|---|
Lachnospiraceae_ge | Standard Protocol | Silva v. 138 | LEfSe | 0.48465 | 0.66996 | 0.93333 | 4.0909 | −0.411 |
Lachnospiraceae_NK3A20_group | Standard Protocol | Silva v. 138 | LEfSe | 0.27423 | 0.48637 | 0.93333 | 0.090909 | 0.153 |
Lachnospiraceae_UCG_004 | Standard Protocol | Silva v. 138 | LEfSe | 0.031072 | 0.1211 | 1.1333 | 0 | 0.195 |
Lachnospiraceae_unclassified | Standard Protocol | Silva v. 138 | LEfSe | 0.26464 | 0.47838 | 8.8667 | 147.45 | −1.85 |
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Taufer, C.R.; da Silva, J.; Rampelotto, P.H. Changes in Probiotic Lachnospiraceae Genera Across Different Stages of COVID-19: A Meta-Analysis of 16S rRNA Microbial Data. Microorganisms 2025, 13, 2061. https://doi.org/10.3390/microorganisms13092061
Taufer CR, da Silva J, Rampelotto PH. Changes in Probiotic Lachnospiraceae Genera Across Different Stages of COVID-19: A Meta-Analysis of 16S rRNA Microbial Data. Microorganisms. 2025; 13(9):2061. https://doi.org/10.3390/microorganisms13092061
Chicago/Turabian StyleTaufer, Clarissa Reginato, Juliana da Silva, and Pabulo Henrique Rampelotto. 2025. "Changes in Probiotic Lachnospiraceae Genera Across Different Stages of COVID-19: A Meta-Analysis of 16S rRNA Microbial Data" Microorganisms 13, no. 9: 2061. https://doi.org/10.3390/microorganisms13092061
APA StyleTaufer, C. R., da Silva, J., & Rampelotto, P. H. (2025). Changes in Probiotic Lachnospiraceae Genera Across Different Stages of COVID-19: A Meta-Analysis of 16S rRNA Microbial Data. Microorganisms, 13(9), 2061. https://doi.org/10.3390/microorganisms13092061