Multiomic Approach to Analyze Infant Gut Microbiota: Experimental and Analytical Method Optimization

Overview

Journal Biomolecules

Publisher MDPI

Specialties Biochemistry
Molecular Biology

Date 2021 Aug 6

PMID 34356622

Citations 2

Authors

Helena Torrell

Adria Cereto-Massague

Polina Kazakova

Lorena Garcia

Hector Palacios

Nuria Canela

Affiliations

Soon will be listed here.

Abstract

Background: The human intestinal microbiome plays a central role in overall health status, especially in early life stages. 16S rRNA amplicon sequencing is used to profile its taxonomic composition; however, multiomic approaches have been proposed as the most accurate methods for study of the complexity of the gut microbiota. In this study, we propose an optimized method for bacterial diversity analysis that we validated and complemented with metabolomics by analyzing fecal samples.

Methods: Forty-eight different analytical combinations regarding (1) 16S rRNA variable region sequencing, (2) a feature selection approach, and (3) taxonomy assignment methods were tested. A total of 18 infant fecal samples grouped depending on the type of feeding were analyzed by the proposed 16S rRNA workflow and by metabolomic analysis.

Results: The results showed that the sole use of V4 region sequencing with ASV identification and VSEARCH for taxonomy assignment produced the most accurate results. The application of this workflow showed clear differences between fecal samples according to the type of feeding, which correlated with changes in the fecal metabolic profile.

Conclusion: A multiomic approach using real fecal samples from 18 infants with different types of feeding demonstrated the effectiveness of the proposed 16S rRNA-amplicon sequencing workflow.

Citing Articles

Gut Microbiome and Small RNA Integrative-Omic Perspective of Meconium and Milk-FED Infant Stool Samples.

Kazakova P, Abasolo N, de Cripan S, Marques E, Cereto-Massague A, Garcia L Int J Mol Sci. 2023; 24(9).

PMID: 37175775 PMC: 10179101. DOI: 10.3390/ijms24098069.

Enduring Effect of Antibiotic Timentin Treatment on Tobacco In Vitro Shoot Growth and Microbiome Diversity.

Tamosiune I, Andriunaite E, Vinskiene J, Stanys V, Rugienius R, Baniulis D Plants (Basel). 2022; 11(6).

PMID: 35336713 PMC: 8954828. DOI: 10.3390/plants11060832.

References

Kuczynski J, Lauber C, Walters W, Parfrey L, Clemente J, Gevers D . Experimental and analytical tools for studying the human microbiome. Nat Rev Genet. 2011; 13(1):47-58. PMC: 5119550. DOI: 10.1038/nrg3129. View

Ozarda Ilcol Y, Ozbek R, Hamurtekin E, Ulus I . Choline status in newborns, infants, children, breast-feeding women, breast-fed infants and human breast milk. J Nutr Biochem. 2005; 16(8):489-99. DOI: 10.1016/j.jnutbio.2005.01.011. View

Schloss P, Handelsman J . Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol. 2005; 71(3):1501-6. PMC: 1065144. DOI: 10.1128/AEM.71.3.1501-1506.2005. View

Guirro M, Costa A, Gual-Grau A, Mayneris-Perxachs J, Torrell H, Herrero P . Multi-omics approach to elucidate the gut microbiota activity: Metaproteomics and metagenomics connection. Electrophoresis. 2018; 39(13):1692-1701. DOI: 10.1002/elps.201700476. View

Sun Y, Cai Y, Liu L, Yu F, Farrell M, McKendree W . ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res. 2009; 37(10):e76. PMC: 2691849. DOI: 10.1093/nar/gkp285. View

DAmore R, Zeeshan Ijaz U, Schirmer M, Kenny J, Gregory R, Darby A . A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genomics. 2016; 17:55. PMC: 4712552. DOI: 10.1186/s12864-015-2194-9. View

Pfleiderer A, Lagier J, Armougom F, Robert C, Vialettes B, Raoult D . RETRACTED ARTICLE: Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample. Eur J Clin Microbiol Infect Dis. 2013; 32(11):1471-81. DOI: 10.1007/s10096-013-1900-2. View

Milani C, Hevia A, Foroni E, Duranti S, Turroni F, Lugli G . Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol. PLoS One. 2013; 8(7):e68739. PMC: 3711900. DOI: 10.1371/journal.pone.0068739. View

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

10.

Amir A, McDonald D, Navas-Molina J, Kopylova E, Morton J, Xu Z . Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns. mSystems. 2017; 2(2). PMC: 5340863. DOI: 10.1128/mSystems.00191-16. View

11.

Kim O, Cho Y, Lee K, Yoon S, Kim M, Na H . Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol. 2011; 62(Pt 3):716-721. DOI: 10.1099/ijs.0.038075-0. View

12.

Huse S, Dethlefsen L, Huber J, Welch D, Relman D, Sogin M . Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet. 2008; 4(11):e1000255. PMC: 2577301. DOI: 10.1371/journal.pgen.1000255. View

13.

Caio G, Volta U, Sapone A, Leffler D, De Giorgio R, Catassi C . Celiac disease: a comprehensive current review. BMC Med. 2019; 17(1):142. PMC: 6647104. DOI: 10.1186/s12916-019-1380-z. View

14.

Shaufi M, Sieo C, Chong C, Gan H, Wan Ho Y . Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses. Gut Pathog. 2015; 7:4. PMC: 4372169. DOI: 10.1186/s13099-015-0051-7. View

15.

Clemente J, Ursell L, Parfrey L, Knight R . The impact of the gut microbiota on human health: an integrative view. Cell. 2012; 148(6):1258-70. PMC: 5050011. DOI: 10.1016/j.cell.2012.01.035. View

16.

Tilocca B, Pieroni L, Soggiu A, Britti D, Bonizzi L, Roncada P . Gut-Brain Axis and Neurodegeneration: State-of-the-Art of Meta-Omics Sciences for Microbiota Characterization. Int J Mol Sci. 2020; 21(11). PMC: 7312636. DOI: 10.3390/ijms21114045. View

17.

Prodan A, Tremaroli V, Brolin H, Zwinderman A, Nieuwdorp M, Levin E . Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing. PLoS One. 2020; 15(1):e0227434. PMC: 6964864. DOI: 10.1371/journal.pone.0227434. View

18.

Callahan B, McMurdie P, Rosen M, Han A, Johnson A, Holmes S . DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016; 13(7):581-3. PMC: 4927377. DOI: 10.1038/nmeth.3869. View

19.

Yang T, Santisteban M, Rodriguez V, Li E, Ahmari N, Carvajal J . Gut dysbiosis is linked to hypertension. Hypertension. 2015; 65(6):1331-40. PMC: 4433416. DOI: 10.1161/HYPERTENSIONAHA.115.05315. View

20.

Schloss P, Westcott S, Ryabin T, Hall J, Hartmann M, Hollister E . Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009; 75(23):7537-41. PMC: 2786419. DOI: 10.1128/AEM.01541-09. View