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Article

Asymmetry Evaluation of Sea Cucumber (Apostichopus japonicus) Gut and Its Surrounding Environment in the Bacterial Community

by
Jingjing Zhang
1,
Yeqing Zhou
1,
Luo Wang
1,*,
Yanxia Liu
1,
Zhiping Lin
1,
Zhenlin Hao
1,
Jun Ding
1,2 and
Yaqing Chang
1
1
Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
2
Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
*
Author to whom correspondence should be addressed.
Symmetry 2022, 14(6), 1199; https://doi.org/10.3390/sym14061199
Submission received: 29 March 2022 / Revised: 24 May 2022 / Accepted: 25 May 2022 / Published: 10 June 2022
(This article belongs to the Special Issue Asymmetric and Symmetric Study on Molecular Biology)
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Abstract

:
Animals are not only regulated by their own genes but also influenced by symbiotic bacteria, most of which are colonized in the gut. The gut bacterial community is involved in plenty of physiological processes; therefore, intestinal colonization by commensal microbiota is essential to the health of the host animal. Here, metagenome sequencing of the A. japonicus gut, surrounding water, and feed was performed to explore the structural and functional characteristics of the colonized bacteria in the gut of A. japonicus. Results showed that Bacteroidetes and Proteobacteria were the main dominant phyla of the A. japonicus gut, and Formosa, Vibrio, and Lactobacillus were the dominant genera. There was asymmetry between the A. japonicus gut and its surrounding environment in the bacterial community. In terms of the top 50 abundant genera, those colonized in the gut shared a similarity of 26% with those colonized in the surrounding water and a similarity of 30% with those colonized in the feed. According to KEGG annotation, the dominant metabolic pathways in the gut of A. japonicus were glycan biosynthesis and metabolism, nitrogen metabolism, and cysteine and methionine metabolism. This implies that the gut-colonized bacteria of A. japonicus are influenced by the surrounding water and the feed. In addition, the gut-colonized bacteria might be related to the growth and metabolism of A. japonicus.

1. Introduction

Microorganisms play an important role in the energy flow and material cycling of cultured organisms. The gut bacterial community is an important part of many animals, with crucial roles in growth and development, nutrient metabolism, digestion and absorption, and defense against pathogens [1]. Hence, the gut bacterial community must maintain a complex dynamic balance with its host. The sea cucumber Apostichopus japonicus has a simple gastrointestinal tract structure and feeds on sediments containing numerous microorganisms, and bacteria make up a large proportion of the gut of A. japonicus and provide lots of its energy needs [2]. Foreign beneficial bacteria colonized in the host intestine can inhibit colonization by indigenous bacteria [3]. It has been shown that A. japonicus, with a rapidly growing gut bacterial community of Marinobacter and Micrococcus, improved digestion and inhibited colonization of pathogenic bacteria such as Escherichia coli [4]. Zhang et al. [5] found that Bacillus and Cladosporium colonized in the gut of A. japonicus are the main enzyme-producing microorganisms and significantly increase digestive enzyme activity. Chi et al. [6] isolated three potential probiotics from A. japonicus-Shewanella japonica, Pseudoalteromonas elyakovii, and Vibrio tubiashii. When fed back to A. japonicus, an enhanced immune response was observed. Furthermore, environmental microorganisms can have a direct or indirect effect on the gut bacterial community of organisms [7]. Studies have shown that alterations in the structure of marine microorganisms can disrupt the homeostasis of the gut bacterial community of organisms, thereby affecting their healthy growth. In turn, the excrement of organisms can damage the water quality and change the composition of the microbial community of the cultured environment [8].
Among invertebrates, A. japonicus has the unique ability of gut regeneration. They can excrete their gut and connected organs through the cloaca in a ruptured manner when they are threatened by enemies or encounter environmental stressors (such as sudden changes in water temperature, lack of oxygen, dirty water, etc.). When the external conditions are suitable, they regenerate new digestive organs [9]. A previous study showed that the intestinal regeneration of sea cucumber stabilized only after 45 days in terms of the bacterial abundance and diversity [10]. Therefore, the gut regeneration of A. japonicus makes them excellent subjects for studying the colonization characteristics of the gut bacterial community. Most previous studies of this, however, used indoor simulation experiments to explore the effects of single factors on the colonization of the gut bacterial community of A. japonicus, and did not consider the combined effect of multiple factors. Therefore, in this study, we investigated the effects of all environmental factors (water and feed) on A. japonicus growth and gut bacterial colonization in a cage culture mode by stimulating them to excrete their gut.
At present, it is difficult to obtain pure cultures of many microorganisms using traditional media identification methods [11], which do not accurately reflect the microbial community. With technological innovation, high-throughput sequencing has become increasingly useful. High-throughput sequencing can analyze microbial communities efficiently and accurately and has been applied to a variety of ecosystems and microbial diversity studies [12]. Compared with 16S rRNA amplicon sequencing, metagenome sequencing provides genetic information on the microorganisms in the community [13], in addition to exploring all microorganisms in the community. This feature allows metagenome sequencing to explore the structure and function of the microbial community and provide a more comprehensive interpretation than 16S rRNA amplicon sequencing.
Therefore, the goal of the present work was to characterize the structural and functional properties of the colonized bacterial community in the gut of A. japonicus using metagenome sequencing after gut regeneration.

2. Materials and Methods

2.1. Animal Trial

The same pedigree of sea cucumber (Apostichopus japonicus) with normal color and an undamaged body was selected, stimulated to excrete their gut, and then bred in cage culture mode, and fed compound feed during feeding. After two months [10], healthy individuals (body weight of 100 ± 10 g) that had completed gut regeneration were selected for the study of the colonization characteristics of the gut bacterial community.

2.2. Samples Collection

Thirty healthy A. japonicus individuals were randomly selected and divided into three replicate groups of G-1, G-2, and G-3. Each group of A. japonicus contained 10 samples. The body walls of A. japonicus were flushed with sterile seawater, excess water absorbed with paper towel, and incised using a sterile scalpel. The gut surfaces were rinsed with 70% ethanol. The gut contents were placed in 1.5 mL sterile centrifuge tubes and then immediately stored in liquid nitrogen. Then, the tubes were stored in a −80 °C refrigerator for DNA extraction.
Water samples (4 L) were collected using a glass water sampler and brought back to the laboratory immediately under low-temperature conditions. Water samples underwent suction filtration using 0.22 μm cellulose acetate membrane. The filtered samples were loaded into sterile centrifugal tubes; divided into three groups labelled W-1, W-2, and W-3; and stored frozen at −80 °C.
The feed used for the cage cultures of A. japonicus was collected in sterile centrifuge tubes; labelled F-1, F-2, and F-3; and stored frozen at −80 °C.

2.3. DNA Extraction

OMEGA Soil DNA kits (Omega Bio-tek, Norcros, GA, USA) were used to extract the gut DNA of A. japonicus, with the concentration and purity tested with a NanoDrop2000 spectrophotometer. The sample concentration obtained was ≥50 ng/μL and the purity was OD260/280 = 1.8–2.0. The DNA detection in 1% agarose gel electrophoresis showed clear DNA bands and a complete banding pattern without tailing, indicating that the DNA was free of protein contamination and degradation.

2.4. Sequencing

Qualified genomic DNA was firstly fragmented by sonication to a size of 350 bp, and then end-repaired, A-tailed, and adaptor-ligated using the NEBNext® ΜLtra™ DNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) according to the preparation protocol. DNA fragments with lengths of 300–400 bp were enriched by PCR. Finally, the PCR products were purified using an AMPure XP system (Beckman Coulter, Brea, CA, USA) and the size distribution of libraries was analyzed by a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA) and quantified using real-time PCR. Genomic sequencing was performed on the Illumina Novaseq 6000 sequencer using pair-end technology (PE 150).

2.5. Data Processing

Raw data from the Illumina platform were filtered using FASTP software. After filtering, the resulting clean reads were used for genome assembly. Clean reads of each sample were assembled individually using MEGAHIT (Institut Pasteur, Paris, France). Genes were predicted based on the final assembly contigs (>500 bp) using MetaGeneMark (version 3.38, GeneMark, GA, USA). The predicted genes ≥ 300 bp in length from all samples were pooled and combined based on ≥95% identity and 90% reads coverage using CD-HIT (version 4.6, Institut Pasteur, Paris, France). The reads were realigned to predicted genes using Bowtie (version 2.2.5, sourceforge, San Diego, CA, USA) to count read numbers. The final gene catalogue was obtained from non-redundant genes with gene read counts > 2.

2.6. Statistical Analysis

SPSS 25.0 software (SPSS, Inc., Chicago, IL, USA) was used to perform a significance test as the mean of three parallel results (mean ± SD) (n = 3). A significance level of 0.05 was used. Mothur software was used to calculate the samples’ alpha diversity indexes (Shannon, Simpson). Multivariate statistical analyses were conducted based on Bray–Curtis distance matrices, such as principal coordinate analysis (PCoA). Species/functional abundance heat maps were plotted using the R language Pheatmap package. LEfSe analysis was performed using LEfSe software to screen for species with large differences between groups using the nonparametric-factors Kruskal–Wallis (KW) and (unpaired) Wilcoxon rank-sum tests. Then, LDA discriminant analysis was applied to determine the extent to which the different species influenced the differences between groups. The KO numbers and pathway annotation information corresponding to the gene set protein sequences were found in the KEGG database using GhostKOALA software, and the abundance of each functional level of KEGG in each sample was statistically analyzed.

3. Results

3.1. Metagenome Sequencing Results

A total of 411,812,484 reads were obtained from the raw sequencing of the three sets of samples, and 59.41 GB of clean data were obtained after quality control and filtering, of which 97.92% were bases with quality values > Q20 (correct identification rate > 99%). The quality-controlled reads were assembled by splicing to obtain 763,733 long sequences (contigs).

3.2. Diversity Analysis

3.2.1. Alpha Diversity Analysis

Figure 1 shows the Shannon index and the Simpson index among the three groups. The Shannon index was highest in water, moderate in the gut of A. japonicus, and lowest in the feed. The Simpson index was lowest in water, second highest in the gut, and highest in the feed. This indicates that the bacterial community diversity was highest in water, second highest in the gut, and lowest in the feed among all the groups.

3.2.2. Beta Diversity Analysis

The differences in the microbial communities among the three groups of samples was assessed by 3D PCoA (Figure 2). The contributions of the principal coordinates were: first = 54.91%, second = 44.62%, and third = 0.29%. Samples from the same group were clustered closer together than those from different groups. Groups G, W, and F were scattered in different quadrants within the two-dimensional plane of principal components consisting of PCoA1 and PCoA2, with samples from the same group clustered closer together than those from different groups. This indicates good biological reproducibility within the three sample groups and significant differences between groups (p < 0.05).

3.3. Relative Abundance of Bacterial Communities

3.3.1. At the Phylum Level

The structures of the bacterial communities in the water, feed, and gut of A. japonicus are shown in Figure 3a. At the phylum level, 105, 102, and 105 phyla were detected in the G, W, and F groups, respectively. In the gut, Bacteroidetes was the primary dominant phylum (52.81%), followed by Proteobacteria (33.31%), with the remaining relatively dominant phyla being Euryarchaeota, Firmicutes, and Planctomycetes in that order.
Similarities existed between the dominant phyla in the A. japonicus gut and the culture environment. The phyla Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, Euryarchaeota, Firmicutes, and Planctomycetes had high relative abundances in both the surrounding water and gut. The phyla with a high relative abundance in both the feed and gut were Firmicutes, Proteobacteria, Euryarchaeota, and Actinobacteria.

3.3.2. At the Genus Level

At the genus level, 2285, 2308, and 1943 genera were detected in the G, W, and F groups, respectively. The primary dominant genera in the gut of A. japonicus were Formosa (32.15%), followed by Vibrio (10.20%), and then Psychromonas, Lutibacter, Halococcus, and Lactobacillus.
Similarities also existed between the main dominant genera in the gut of A. japonicus and the culture environment (Figure 3b). The genera with a high relative abundance in both the surrounding water and the gut of A. japonicus were Rhodobacteraceae_noname, Gammaproteobacteria_noname, Ruegeria, Phaeobacter, Polaribacter, Halocynthiibacter, and Vibrio. Genera with a high relative abundance in both the feed and gut were Lactobacillus, Vibrio, Oceanibaculum, Psychromonas, Photobacterium, Meiothermus, Rhodobacteraceae_noname, Halococcus, Polaribacter, Pirellula, Formosa, Pediococcus, and Pseudoalteromonas.

3.4. Specific Bacterial Communities

A heat map of the bacterial community structure of the three samples at the genus level is shown in Figure 4. The genera with the greatest variability among the three samples were Formosa and Lactobacillus. The abundance of Formosa was significantly different in the gut of A. japonicus than in the feed and surrounding water (p < 0.05) while Lactobacillus was significantly different in the feed than in the surrounding water and gut (p < 0.05).
The gut-specific genera were Formosa, Vibrio, Psychromonas, Lutibacter, and Ilyobacter. The water-specific genera were Celeribacter, Micr_Candidatus_Aquiluna, Gammaproteobacteria_noname, Rhodobacteraceae_noname, Loktanella, and Planktomarina. The feed-specific genera were Lactobacillus, Psychrobacter, Weissella, and Oceanibaculum.

3.5. Predictive Functional Profiling by KEGG

The KEGG annotation results are shown in Figure 5. In total, 27 pathways showed significant differences among the 3 groups (LDA > 3.5), which can be classified into 3 KEGG A classes and 11 KEGG B classes. In terms of the gut of A. japonicus, the genes annotated for carbohydrate metabolism, amino acid metabolism, glycan biosynthesis and metabolism, nitrogen metabolism, and cysteine and methionine metabolism were the most abundant. As for the bacterial community of water, the most abundant genes were annotated for amino acid metabolism, metabolism of cofactors and vitamins, and xenobiotic biodegradation and metabolism. In the bacterial community of feed, the most abundant genes were annotated for nucleotide metabolism, transport and catabolism, and replication and repair.
Among the KEGG A classes, all three groups accounted for the highest proportion of primary metabolic pathways (metabolism), with the gut bacterial community of A. japonicus being significantly higher than those of the other two groups. In addition, environmental information processing was a primary KEGG A class specific to water while genetic information processing was specific to feed.

4. Discussion

4.1. Structural Characteristics of the A. japonicus Gut Bacterial Community

The gut bacterial community plays important roles in the growth, digestion, and immunity of A. japonicus [14]. Animal gut colonization by a bacterial community is mainly influenced by maternal genetics and environmental and dietary factors [15,16]. To avoid the influence of maternal genetics, A. japonicus with the same pedigree were stimulated to excrete their guts and regenerate them in a cage culture environment in this study. This study mainly focused on the effects of the surrounding environmental bacterial communities on the gut regeneration and colonization of sea cucumber; so, the effects of prenatal gut bacterial communities are not discussed here. Marine microorganisms are diverse and functionally rich, and the marine microbial communities that colonize the gut bacterial community of A. japonicus in the culture environment have an effect on the growth and development of A. japonicus. The results showed that the species of the A. japonicus gut, culture water, and bait bacterial community show some similarities, but there is variation in the abundance of the bacterial community. Proteobacteria and Bacteroidetes were the dominant phyla of the three groups, which was consistent with the reported literature [17,18,19], indicating that they are well colonized under different hosts. Proteobacteria is the largest phylum in the bacterial domain and can be used as a marker of dysbiosis in the gut microecological balance [20]. Bacteroidetes can degrade lots of indigestible plant polysaccharides to provide energy for the host [21,22,23]. The dominant phyla of the gut in A. japonicus were consistent with different culture modes, providing evidence for deterministic host selection of specific microbial consortium.
Moreover, the primary dominant genus of the A. japonicus gut was Formosa, followed by Vibrio, Lactobacillus, Psychromonas, and Lutibacter. This is similar to the previously reported dominant genus in the gut bacterial community of A. japonicus [13,17].
Formosa was the primary dominant genus in the gut of A. japonicus and was one of the gut-specific genera. It is a Gram-negative bacterium that was isolated in 2004 by Ivanova et al. [24] from Hornwort brown algae, which is aerobic and salt-tolerant but has also been found to produce nitrate by anaerobic respiration [25]. Formosa belongs to the Bacteroidetes, which has a polysaccharide utilization site (PUL) and a core cluster of genes associated with polysaccharide degradation [26]; thus, this phylum plays an important role in polysaccharide degradation.
Vibrio is one of the dominant genera in the gut of A. japonicus. As an important group of marine bacteria, this bacterium occupies an important position in the bacterial community of mariculture animals. Vibrio is widely recognized as a common conditional pathogenic bacterium, which has become a focus of aquaculture disease research in recent years. Deng et al. [27] showed that bacteria, especially V. cyclitrophicus and V. splendidus, are the main pathogenic bacteria in A. japonicus and are associated with symptoms such as ulceration of the body wall. However, studies have shown that non-toxic Vibrio have also been used as probiotics [28]. Liu isolated the Vibrio strain V33, which showed strong antagonistic activity against pathogenic V. splendidus Vs. This means that V33 can be used to control pathogenic V. splendidus Vs. in A. japonicus [29]. In addition, this bacterium has been shown to promote amino acid and carbohydrate synthesis [30,31]. Therefore, Vibrio, as a conditionally pathogenic bacterium, is not always detrimental to the growth of A. japonicus. Growth promotion in A. japonicus can be achieved through the selection of appropriate Vibrio strains or the rational use of non-toxic Vibrio.
The present study identified Lactobacillus as the specific genus in the feed bacterial community and the dominant genus in the gut. Lactobacillus is a Gram-positive bacterium that is widely valued for its unique physiological activity and nutritional functions. It can secrete antibacterial compounds such as lactic acid, hydrogen peroxide, and bacteriocins, which inhibit the growth of pathogenic bacteria and sterilize them in vivo by altering the cell membrane permeability, among other things [32]. This bacterium can also protect gut epithelial cells. Yan et al. [33] found that two proteins secreted by Lactobacillus rhamnosus, p75 and p40, both inhibit cytokine-induced apoptosis of epithelial cells and significantly reduce TNF-α-produced intestinal epithelial damage. Furthermore, it can compete with pathogenic bacteria in the gut for nutrients or adhesion sites, thereby inhibiting them. Seven Lactobacillus species, including L. casei Shirota, L. rhamnosus ATCC 53103, and L. bulgaricus, inhibit the growth of the gut pathogenic bacterium V. anguillarum in rainbow trout via nutrient competition [34]. Therefore, the addition of Lactobacillus to feed can improve the digestion, growth, and immunity of A. japonicus.

4.2. Functional Characteristics of the A. japonicus Gut Bacterial Community

According to the KEGG pathway database analysis, the dominant KEGG A class in all the groups was metabolism, which mostly comprised amino acid metabolism, carbohydrate metabolism, and energy metabolism. This is consistent with the results of previous studies and indicates that metabolism is a necessary function for microbial survival [35,36,37]. The specific pathways differed, however, which indicates that different environments lead to differences in the ability of microorganisms to utilize environmental substances. It is speculated that the demand for carbon and nitrogen may differ according to the environments in which the microorganisms are located.
Differential analysis of KEGG B classes showed that glycan biosynthesis and metabolism and carbohydrate metabolic pathway aggregation in the gut of A. japonicus were significantly different from those in the surrounding water and feed (p < 0.05). The growth of A. japonicus requires more carbohydrates than lipids and proteins [38]. Carbohydrates are often present in the form of glycans. As a consequence, the consumption of glycans by A. japonicus reflects their carbohydrate requirements to some extent. Formosa is a dominant and specific genus in the gut bacterial community that can effectively degrade glycan. Silchenko et al. [39] cloned an FFA2 gene from the KMM 3553T strain of Formosa, and its amino acid sequence showed 57% agreement with the known marine fucosidase glycosidase FcnA, which can degrade polysaccharides well. Formosa is the dominant gut-specific genus in A. japonicus, presumably because A. japonicus requires a large amount of carbohydrates for growth, which is reflected in its consumption of glycans. Formosa can degrade glycans to support A. japonicus and, therefore, has a high abundance in its gut.
Nitrogen, methionine, and cysteine metabolism are specific KEGG C classes in the gut of A. japonicus. Nitrogen metabolism is an important metabolic pathway in this organism. In recent years, the presence of excessive ammonia and nitrite in aquaculture water has had serious impacts on enzyme catalysis and cell membrane stability in mariculture animals [40,41]. High nitrite concentrations can affect the transport of oxygen in mariculture animals. A variety of bacteria in the organism can carry out nitrogen metabolism, including Bacillus, Clostridium, and Pseudomonas [42]. These genera occupy a dominant position in the gut of A. japonicus, and it is presumed that the difference in the nitrogen metabolism pathway is related to the above genera. Methionine is the only sulfur-containing amino acid among the essential amino acids. In addition to carrying out protein synthesis, methionine has important antioxidant, immune enhancement, and detoxification roles, and its conversion to S-adenosylmethionine is followed by deamination and hydrolysis to form homocysteine, which can also be followed by deamination and cleavage to produce cysteine [43]. It has been shown that the gut is the main site of the food source methionine [44]. There are many amino acid-metabolizing bacteria in the gut bacterial community of A. japonicus, such as Bacteroides, Clostridium, and Streptococcus [45], which occupy the top 10% relative abundances. It is speculated that the specificity of the cysteine and methionine metabolic pathway is related to these genera.

5. Conclusions

We tracked the characteristics and influencing factors of the A. japonicus gut bacterial community using metagenome sequencing and the excretory gut properties. It was found that the gut bacterial community of A. japonicus was reconstructed, and the bacterial community was influenced by both the surrounding water and the feed. These bacteria might have important effects on A. japonicus. Previous findings have shown that Lactobacillus could inhibit the growth of pathogenic bacteria. Formosa could regulate various metabolic pathways and proper use of non-toxic Vibrio can promote growth.

Author Contributions

J.Z.: Analyzed experimental results and drafted the manuscript. Y.Z.: Conducted the experiment. L.W.: Revised the manuscript and assisted with the experiment. Y.L.: Analyzed the sequencing data. Z.L.: Carried out the experiments. Z.H.: Designed the experiments. Y.C.: Revised the manuscript. J.D.: Designed and supported the study. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Natural Science Foundation of China (31902395), the National Key Research and Development Program of China (2018YFD0901604), Youth Science and Technology Star Project of Dalian (2020RQ115), Liaoning Province “Xingliao Talents Plan” project (XLYC2002107), High-level talent support grant for innovation in Dalian (2020RD03), Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (GML2019ZD0402).

Institutional Review Board Statement

The rearing and treatment of laboratory animals is based on the principles of animal experimentation welfare and ethical management.

Informed Consent Statement

Not applicable.

Data Availability Statement

Not applicable.

Conflicts of Interest

The authors declared that they have no conflict of interest in this work.

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Symmetry 14 01199 g001 550
Figure 1. Richness and diversity of bacterial communities in the gut of Apostichopus japonicus (G), surrounding water (W), and feed (F). The Shannon with higher indices indicates higher sample diversity. On the contrary, a lower Simpson index indicates higher diversity. * represents a p value less than 0.05, indicating a significant difference; ** represents a p value less than 0.01, indicating an extremely significant difference.
Figure 1. Richness and diversity of bacterial communities in the gut of Apostichopus japonicus (G), surrounding water (W), and feed (F). The Shannon with higher indices indicates higher sample diversity. On the contrary, a lower Simpson index indicates higher diversity. * represents a p value less than 0.05, indicating a significant difference; ** represents a p value less than 0.01, indicating an extremely significant difference.
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Figure 2. Beta diversity of bacteria in the gut of Apostichopus japonicus (G), surrounding water (W), and feed (F). Each point represents a sample, with colors indicating groups. Closer points indicate better grouping.
Figure 2. Beta diversity of bacteria in the gut of Apostichopus japonicus (G), surrounding water (W), and feed (F). Each point represents a sample, with colors indicating groups. Closer points indicate better grouping.
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Figure 3. Relative abundance of the dominant bacteria in the gut of Apostichopus japonicus (G), surrounding water (W), and feed (F) at the (a) phylum and (b) genus levels. Tracks are distinguished by different colors and labels, showing the relative abundance of each bacteria in each group, and the relative abundance of each bacteria contained in each group by grouping and bacteria linkage.
Figure 3. Relative abundance of the dominant bacteria in the gut of Apostichopus japonicus (G), surrounding water (W), and feed (F) at the (a) phylum and (b) genus levels. Tracks are distinguished by different colors and labels, showing the relative abundance of each bacteria in each group, and the relative abundance of each bacteria contained in each group by grouping and bacteria linkage.
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Figure 4. Hierarchically clustered heatmap of the bacterial distribution of Apostichopus japonicus (G), surrounding water (W), and feed (F) at the genus level. The relative values for the bacteria are indicated by the color intensity with the legend.
Figure 4. Hierarchically clustered heatmap of the bacterial distribution of Apostichopus japonicus (G), surrounding water (W), and feed (F) at the genus level. The relative values for the bacteria are indicated by the color intensity with the legend.
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Figure 5. Differences in the abundance of KEGG pathways in the bacterial communities of Apostichopus japonicus (G), surrounding water (W), and feed (F) by LefSe analysis. The LDA score indicates the extent of the impact of significantly different pathways among the three groups: the larger the value, the more significant the difference. Different colors represent significant differences.
Figure 5. Differences in the abundance of KEGG pathways in the bacterial communities of Apostichopus japonicus (G), surrounding water (W), and feed (F) by LefSe analysis. The LDA score indicates the extent of the impact of significantly different pathways among the three groups: the larger the value, the more significant the difference. Different colors represent significant differences.
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Zhang, J.; Zhou, Y.; Wang, L.; Liu, Y.; Lin, Z.; Hao, Z.; Ding, J.; Chang, Y. Asymmetry Evaluation of Sea Cucumber (Apostichopus japonicus) Gut and Its Surrounding Environment in the Bacterial Community. Symmetry 2022, 14, 1199. https://doi.org/10.3390/sym14061199

AMA Style

Zhang J, Zhou Y, Wang L, Liu Y, Lin Z, Hao Z, Ding J, Chang Y. Asymmetry Evaluation of Sea Cucumber (Apostichopus japonicus) Gut and Its Surrounding Environment in the Bacterial Community. Symmetry. 2022; 14(6):1199. https://doi.org/10.3390/sym14061199

Chicago/Turabian Style

Zhang, Jingjing, Yeqing Zhou, Luo Wang, Yanxia Liu, Zhiping Lin, Zhenlin Hao, Jun Ding, and Yaqing Chang. 2022. "Asymmetry Evaluation of Sea Cucumber (Apostichopus japonicus) Gut and Its Surrounding Environment in the Bacterial Community" Symmetry 14, no. 6: 1199. https://doi.org/10.3390/sym14061199

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