Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México
Background The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the us...
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PeerJ Inc.
2022-07-01
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| Online Access: | https://peerj.com/articles/13235.pdf |
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| author | David Ramirez-Delgado Francesco Cicala Ricardo A. Gonzalez-Sanchez Rosalia Avalos-Tellez Elena Solana-Arellano Alexei Licea-Navarro |
| author_facet | David Ramirez-Delgado Francesco Cicala Ricardo A. Gonzalez-Sanchez Rosalia Avalos-Tellez Elena Solana-Arellano Alexei Licea-Navarro |
| author_sort | David Ramirez-Delgado |
| collection | DOAJ |
| description | Background The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities. Methods We employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses. Results As hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6–V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6–V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features. |
| first_indexed | 2024-03-09T06:28:22Z |
| format | Article |
| id | doaj.art-ece1765a6b984fe6aaaa857f75710b36 |
| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-09T06:28:22Z |
| publishDate | 2022-07-01 |
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| spelling | doaj.art-ece1765a6b984fe6aaaa857f75710b362023-12-03T11:14:36ZengPeerJ Inc.PeerJ2167-83592022-07-0110e1323510.7717/peerj.13235Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, MéxicoDavid Ramirez-Delgado0Francesco Cicala1Ricardo A. Gonzalez-Sanchez2Rosalia Avalos-Tellez3Elena Solana-Arellano4Alexei Licea-Navarro5Marine Ecology Department, CICESE, Ensenada, Baja California, MéxicoBiomedical Innovation Department, CICESE, Ensenada, Baja California, MéxicoBiomedical Innovation Department, CICESE, Ensenada, Baja California, MéxicoComisión Nacional de Areas Naturales Protegidas, Secretaría de Medio Ambiente y Recursos Naturales, Bahia de los Angeles, Baja California, MéxicoMarine Ecology Department, CICESE, Ensenada, Baja California, MéxicoBiomedical Innovation Department, CICESE, Ensenada, Baja California, MéxicoBackground The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities. Methods We employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses. Results As hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6–V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6–V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features.https://peerj.com/articles/13235.pdfMicrobiomePinnipedBacterial consortiumZalophus californianusGulf of California |
| spellingShingle | David Ramirez-Delgado Francesco Cicala Ricardo A. Gonzalez-Sanchez Rosalia Avalos-Tellez Elena Solana-Arellano Alexei Licea-Navarro Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México PeerJ Microbiome Pinniped Bacterial consortium Zalophus californianus Gulf of California |
| title | Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México |
| title_full | Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México |
| title_fullStr | Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México |
| title_full_unstemmed | Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México |
| title_short | Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México |
| title_sort | multi locus evaluation of gastrointestinal bacterial communities from zalophus californianus pups in the gulf of california mexico |
| topic | Microbiome Pinniped Bacterial consortium Zalophus californianus Gulf of California |
| url | https://peerj.com/articles/13235.pdf |
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