Loss of gut microbial diversity in the cultured, agastric fish, Mexican pike silverside (Chirostoma estor: Atherinopsidae)

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Microbiology

Main article text

 

Introduction

Materials & Methods

Sample collection

DNA extraction and sequencing

Bioinformatics

Statistical analysis

Predictive functional analysis by PICRUSt2

Results

Bacterial diversity in the gut of C. estor

Environmental influence on microbial communities

Core microbiota analysis

Differential abundance of taxonomic groups

Functional metabolic prediction using PICRUSt2

Discussion

Conclusions

Supplemental Information

Chirostoma estor weight and length measurements

Minimum, maximum, average, and standard deviation values of body or gut weight and length of Chirostoma estor harvested from each environment including Lake Patzcuaro, Intensive Culture, and Extensive Culture.

DOI: 10.7717/peerj.13052/supp-1

Prevalent phyla in C. estor guts

Total mean relative abundance (%) (first column) ±SE and mean relative abundance ±SE of the 9 most prevalent phyla and 2 Classes of Proteobacteria found in intestinal components (D, A and P) samples of C. estor of three environments (LP, C, and E). Statistical comparisons are separated by intestinal components (digesta, D; anterior intestine, A; posterior intestine, P) and environments (Lake Patzcuaro, LP; Intensive Culture, C; Extensive Culture, E). Different letters indicate a statistically significant (p ¡ 0.05) difference between taxonomic group abundances per row.

DOI: 10.7717/peerj.13052/supp-2

Microbial alpha diversity in C. estor guts

Observed, richness Chao and Shannon diversity mean relative abundance (%) ±SD of intestinal microbiota compared between environments (Lake Patzcuaro, LP; Intensive Culture, C; Extensive Culture, E), intestinal components (Digesta, D; Anterior intestine, A; Posterior intestine, P) and all 9 sample groups (environment by intestinal component). Digesta of Lake Patzcuaro, DLP; Digesta of Intensive Culture, DC; Digesta of Extensive Culture, DE; Anterior intestine of Lake Patzcuaro, ALP; Anterior intestine of Intensive Culture, AC; Anterior intestine of Extensive Culture, AE; Posterior intestine of Lake Patzcuaro, PLP; Posterior intestine of Intensive Culture, PC; Posterior Intestine of Extensive Culture, PE. In parenthesis the n number of samples. Different letters indicate statistical significance between groups (p <0.05).

DOI: 10.7717/peerj.13052/supp-3

Beta diversity per environment

Analysis of similarity (ANOSIM) and Permutational multivariate analysis of variance (Adonis) of intestinal microbiota data of environments.

DOI: 10.7717/peerj.13052/supp-4

Beta diversity per intestinal component

Analysis of similarity (ANOSIM) and Permutational multivariate analysis of variance (Adonis) of data of intestinal microbiota between intestinal components.

DOI: 10.7717/peerj.13052/supp-5

Core microbiota

Forty-two OTUs were annotated at the genus level using the SILVA database. There were a total of core 133 OTUs found in the UpSet plot of intestinal components and environments samples (Fig. 3E). In bold are genera present in the core microbiota above the threshold of 80% occupancy (Figs. 3A3D).

DOI: 10.7717/peerj.13052/supp-6

Chirostoma estor gut

Intestinal sections of Chirostoma estor were separated in the anterior and posterior gut.

DOI: 10.7717/peerj.13052/supp-7

Microbiota genera core

UpSet plot showing the core of microbial genera above a threshold of 80% (above) and below the threshold cutoff of 80% (below). Group set size is plotted as blue horizontal bars. Bars show the number of genera or OTUs that are unique within a specified group (in at least 80% of the samples) and dark circles with connecting bars indicate shared OTUs between multiple samples. Legends: DC, digesta of intensive culture; PC, posterior intestine of intensive culture; DLP, digesta of Lake Patzcuaro fish; PLP, posterior intestine of Lake Patzcuaro fish; ALP, anterior intestine of Lake Patzcuaro fish; AE, anterior intestine of extensive culture; PE, posterior intestine of extensive culture; DE, digesta of extensive culture; AC, anterior intestine of intensive culture.

DOI: 10.7717/peerj.13052/supp-8

Heatmap of the 60 most abundant functional pathways inferred by PICRUSt2 in all 9 sample groupings

Red color represents higher value and blue color lower value. The top color bars indicate the environment and intestinal component groups. Blue bars LP, Lake Patzcuaro; black bars C, Intensive culture; green bars E, Extensive culture; cyan bars D, Digesta; brown bars A, Anterior gut; orange bars P, Posterior gut.

DOI: 10.7717/peerj.13052/supp-9

Statistical differences between the 9 sample groups and their inferred PICRUSt2 KOs pathways

Displayed as extended error bar plots of mean proportional difference between KOs pathways of PICRUSt2 in pairwise groupings by environments or intestinal components of Chirostoma estor. Corrected p values are shown at right. The legend groups are shown: DLP, digesta/Lake Patzcuaro; ALP, anterior intestine/Lake Patzcuaro; PLP, posterior intestine/Lake Patzcuaro; DC, digesta/intensive culture; AC, anterior intestine/intensive culture; PC, posterior intestine/intensive culture; DE, digesta/extensive culture; AE, anterior intestine/extensive culture; PE, posterior intestine/extensive culture.

DOI: 10.7717/peerj.13052/supp-10

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Jesús Mateo Amillano-Cisneros performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Perla T. Hernández-Rosas performed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft.

Bruno Gomez-Gil and Pamela Navarrete-Ramírez conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

María Gisela Ríos-Durán and David Johnston-Monje analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Carlos Cristian Martínez-Chávez conceived and designed the experiments, performed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Carlos Antonio Martínez-Palacios conceived and designed the experiments, performed the experiments, analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Luciana Raggi conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Animal Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

Consejo Nacional de Ciencia y Tecnologia (CONACYT), Mexico, provided full approval for this research (2018-294826).

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The sequence data are available at the NCBI BioProject: PRJNA750495.

Data Availability

The following information was supplied regarding data availability:

Raw sequence data are available at the NCBI Sequence Read Archive (SRA) (SRX11596261 to SRX11596334).

Funding

This study was supported by Laboratorio Nacional de Nutrigenómica y Microbiómica Digestiva Animal and Consejo Nacional de Ciencia y Tecnología (projects No. 315841 and 315209), Coordinación de la Investigación Científica-UMSNH, and CONACYT doctoral scholarship 701910. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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