Microorganisms

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22 pages, 3235 KiB

Open AccessArticle

Changes in Lake Sturgeon Gut Microbiomes Relative to Founding Origin and in Response to Chemotherapeutant Treatments

by Shairah Abdul Razak, John M. Bauman, Terence L. Marsh and Kim T. Scribner

Microorganisms 2022, 10(5), 1005; https://doi.org/10.3390/microorganisms10051005 - 10 May 2022

Cited by 4 | Viewed by 2269

Abstract

Antibiotics, drugs, and chemicals (collectively referred to as chemotherapeutants) are widely embraced in fish aquaculture as important tools to control or prevent disease outbreaks. Potential negative effects include changes in microbial community composition and diversity during early life stages, which can reverse the [...] Read more.

Antibiotics, drugs, and chemicals (collectively referred to as chemotherapeutants) are widely embraced in fish aquaculture as important tools to control or prevent disease outbreaks. Potential negative effects include changes in microbial community composition and diversity during early life stages, which can reverse the beneficial roles of gut microbiota for the maintenance of host physiological processes and homeostatic regulation. We characterized the gut microbial community composition and diversity of an ecologically and economically important fish species, the lake sturgeon (Acipenser fulvescens), during the early larval period in response to weekly treatments using chemotherapeutants commonly used in aquaculture (chloramine-T, hydrogen peroxide, and NaCl₂ followed by hydrogen peroxide) relative to untreated controls. The effects of founding microbial community origin (wild stream vs. hatchery water) were also evaluated. Gut communities were quantified using massively parallel next generation sequencing based on the V4 region of the 16S rRNA gene. Members of the phylum Firmicutes (principally unclassified Clostridiales and Clostridium_sensu_stricto) and Proteobacteria were the dominant taxa in all gut samples regardless of treatment. The egg incubation environment (origin) and its interaction with chemotherapeutant treatment were significantly associated with indices of microbial taxonomic diversity. We observed large variation in the beta diversity of lake sturgeon gut microbiota between larvae from eggs incubated in hatchery and wild (stream) origins based on nonmetric dimensional scaling (NMDS). Permutational ANOVA indicated the effects of chemotherapeutic treatments on gut microbial community composition were dependent on the initial source of the founding microbial community. Influences of microbiota colonization during early ontogenetic stages and the resilience of gut microbiota to topical chemotherapeutic treatments are discussed. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals 2.0)

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14 pages, 3258 KiB

Open AccessArticle

Gut Microbial Composition of Pacific Salmonids Differs across Oregon River Basins and Hatchery Ancestry

by Nicole S. Kirchoff, Trevan Cornwell, Staci Stein, Shaun Clements and Thomas J. Sharpton

Microorganisms 2022, 10(5), 933; https://doi.org/10.3390/microorganisms10050933 - 29 Apr 2022

Cited by 3 | Viewed by 2032

Abstract

The gut microbiome may represent a relatively untapped resource in the effort to manage and conserve threatened or endangered fish populations, including wild and hatchery-reared Pacific salmonids. To clarify this potential, we defined how steelhead trout gut microbiome composition varies across watersheds and [...] Read more.

The gut microbiome may represent a relatively untapped resource in the effort to manage and conserve threatened or endangered fish populations, including wild and hatchery-reared Pacific salmonids. To clarify this potential, we defined how steelhead trout gut microbiome composition varies across watersheds and as a function of ancestry. First, we measured this variation across watersheds using wild steelhead trout sampled from nine locations spanning three river basins. While gut microbial composition differs across basins, there exist bacterial clades that are ubiquitous across all populations. Correlating the phylogenetic composition of clades with geographic distance reveals 395 clades of bacteria whose ecological distribution implicates their co-diversification with steelheads. Second, we quantified how microbiome composition varies between first generation hatchery-reared steelhead and traditional hatchery-reared steelhead. Despite being subject to the same hatchery management strategies, fish bred from wild parents carry distinct microbiomes from those bred from hatchery broodstock, implicating the role of genotype on microbiome composition. Finally, we integrated all data from both studies to reveal two distinct, yet robust clusters of community composition. Collectively, our study documents for the first time how the steelhead gut microbiome varies by geography or broodstock and uncovers microbial taxa that may indicate the watershed or hatchery from which an individual was sourced. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals 2.0)

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15 pages, 2153 KiB

Open AccessArticle

Evaluating Methods of Preserving Aquatic Invertebrates for Microbiome Analysis

by Stephanie N. Vaughn and Colin R. Jackson

Microorganisms 2022, 10(4), 811; https://doi.org/10.3390/microorganisms10040811 - 13 Apr 2022

Cited by 3 | Viewed by 2576

Abstract

Research on the microbiomes of animals has increased substantially within the past decades. More recently, microbial analyses of aquatic invertebrates have become of increased interest. The storage method used while collecting aquatic invertebrates has not been standardized throughout the scientific community, and the [...] Read more.

Research on the microbiomes of animals has increased substantially within the past decades. More recently, microbial analyses of aquatic invertebrates have become of increased interest. The storage method used while collecting aquatic invertebrates has not been standardized throughout the scientific community, and the effects of common storage methods on the microbial composition of the organism is unknown. Using crayfish and dragonfly nymphs collected from a natural pond and crayfish maintained in an aquarium, the effects of two common storage methods, preserving in 95% ethanol and freezing at −20 °C, on the invertebrate bacterial microbiome was evaluated. We found that the bacterial community was conserved for two sample types (gut and exoskeleton) of field-collected crayfish stored either in ethanol or frozen, as was the gut microbiome of aquarium crayfish. However, there were significant differences between the bacterial communities found on the exoskeleton of aquarium crayfish stored in ethanol compared to those that were frozen. Dragonfly nymphs showed significant differences in gut microbial composition between species, but the microbiome was conserved between storage methods. These results demonstrate that preserving field-collected specimens of aquatic invertebrates in 95% ethanol is likely to be a simple and effective sample preservation method for subsequent gut microbiome analysis but is less reliable for the external microbiome. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals 2.0)

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11 pages, 2927 KiB

Open AccessArticle

Gut Microbial Characterization of Melon-Headed Whales (Peponocephala electra) Stranded in China

by Shijie Bai, Peijun Zhang, Xianfeng Zhang, Zixin Yang and Songhai Li

Microorganisms 2022, 10(3), 572; https://doi.org/10.3390/microorganisms10030572 - 6 Mar 2022

Cited by 13 | Viewed by 2582

Abstract

Although gut microbes are regarded as a significant component of many mammals and play a very important role, there is a paucity of knowledge around marine mammal gut microbes, which may be due to sampling difficulties. Moreover, to date, there are very few, [...] Read more.

Although gut microbes are regarded as a significant component of many mammals and play a very important role, there is a paucity of knowledge around marine mammal gut microbes, which may be due to sampling difficulties. Moreover, to date, there are very few, if any, reports on the gut microbes of melon-headed whales. In this study, we opportunistically collected fecal samples from eight stranded melon-headed whales (Peponocephala electra) in China. Using high-throughput sequencing technology of partial 16S rRNA gene sequences, we demonstrate that the main taxa of melon-headed whale gut microbes are Firmicutes, Fusobacteriota, Bacteroidota, and Proteobacteria (Gamma) at the phylum taxonomic level, and Cetobacterium, Bacteroides, Clostridium sensu stricto, and Enterococcus at the genus taxonomic level. Meanwhile, molecular ecological network analysis (MENA) shows that two modules (a set of nodes that have strong interactions) constitute the gut microbial community network of melon-headed whales. Module 1 is mainly composed of Bacteroides, while Module 2 comprises Cetobacterium and Enterococcus, and the network keystone genera are Corynebacterium, Alcaligenes, Acinetobacter, and Flavobacterium. Furthermore, by predicting the functions of the gut microbial community through PICRUSt2, we found that although there are differences in the composition of the gut microbial community in different individuals, the predicted functional profiles are similar. Our study gives a preliminary inside look into the composition of the gut microbiota of stranded melon-headed whales. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals 2.0)

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23 pages, 3636 KiB

Open AccessArticle

Is the Intestinal Bacterial Community in the Australian Rabbitfish Siganus fuscescens Influenced by Seaweed Supplementation or Geography?

by Valentin Thépot, Joel Slinger, Michael A. Rimmer, Nicholas A. Paul and Alexandra H. Campbell

Microorganisms 2022, 10(3), 497; https://doi.org/10.3390/microorganisms10030497 - 23 Feb 2022

Cited by 1 | Viewed by 2317

Abstract

We recently demonstrated that dietary supplementation with seaweed leads to dramatic improvements in immune responses in S. fuscescens, a candidate species for aquaculture development in Asia. Here, to assess whether the immunostimulatory effect was facilitated by changes to the gut microbiome, we [...] Read more.

We recently demonstrated that dietary supplementation with seaweed leads to dramatic improvements in immune responses in S. fuscescens, a candidate species for aquaculture development in Asia. Here, to assess whether the immunostimulatory effect was facilitated by changes to the gut microbiome, we investigated the effects of those same seaweed species and four commercial feed supplements currently used in aquaculture on the bacterial communities in the hindgut of the fish. Since we found no correlations between the relative abundance of any particular taxa and the fish enhanced innate immune responses, we hypothesised that S. fuscescens might have a core microbiome that is robust to dietary manipulation. Two recently published studies describing the bacteria within the hindgut of S. fuscescens provided an opportunity to test this hypothesis and to compare our samples to those from geographically distinct populations. We found that, although hindgut bacterial communities were clearly and significantly distinguishable between studies and populations, a substantial proportion (55 of 174 taxa) were consistently detected across all populations. Our data suggest that the importance of gut microbiota to animal health and the extent to which they can be influenced by dietary manipulations might be species-specific or related to an animals’ trophic level. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals 2.0)

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17 pages, 5746 KiB

Open AccessArticle

Commensal and Opportunistic Bacteria Present in the Microbiota in Atlantic Cod (Gadus morhua) Larvae Differentially Alter the Hosts’ Innate Immune Responses

by Ragnhild Inderberg Vestrum, Torunn Forberg, Birgit Luef, Ingrid Bakke, Per Winge, Yngvar Olsen and Olav Vadstein

Microorganisms 2022, 10(1), 24; https://doi.org/10.3390/microorganisms10010024 - 24 Dec 2021

Cited by 4 | Viewed by 3156

Abstract

The roles of host-associated bacteria have gained attention lately, and we now recognise that the microbiota is essential in processes such as digestion, development of the immune system and gut function. In this study, Atlantic cod larvae were reared under germ-free, gnotobiotic and [...] Read more.

The roles of host-associated bacteria have gained attention lately, and we now recognise that the microbiota is essential in processes such as digestion, development of the immune system and gut function. In this study, Atlantic cod larvae were reared under germ-free, gnotobiotic and conventional conditions. Water and fish microbiota were characterised by 16S rRNA gene analyses. The cod larvae’s transcriptional responses to the different microbial conditions were analysed by a custom Agilent 44 k oligo microarray. Gut development was assessed by transmission electron microscopy (TEM). Water and fish microbiota differed significantly in the conventional treatment and were dominated by different fast-growing bacteria. Our study indicates that components of the innate immune system of cod larvae are downregulated by the presence of non-pathogenic bacteria, and thus may be turned on by default in the early larval stages. We see indications of decreased nutrient uptake in the absence of bacteria. The bacteria also influence the gut morphology, reflected in shorter microvilli with higher density in the conventional larvae than in the germ-free larvae. The fact that the microbiota alters innate immune responses and gut morphology demonstrates its important role in marine larval development. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals 2.0)

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19 pages, 2250 KiB

Open AccessArticle

Isolation and Identification of Bacteria with Surface and Antibacterial Activity from the Gut of Mediterranean Grey Mullets

by Rosanna Floris, Gabriele Sanna, Laura Mura, Myriam Fiori, Jacopo Culurgioni, Riccardo Diciotti, Carmen Rizzo, Angelina Lo Giudice, Pasqualina Laganà and Nicola Fois

Microorganisms 2021, 9(12), 2555; https://doi.org/10.3390/microorganisms9122555 - 10 Dec 2021

Cited by 4 | Viewed by 7410

Abstract

Fish gut represents a peculiar ecological niche where bacteria can transit and reside to play vital roles by producing bio-compounds with nutritional, immunomodulatory and other functions. This complex microbial ecosystem reflects several factors (environment, feeding regimen, fish species, etc.). The objective of the [...] Read more.

Fish gut represents a peculiar ecological niche where bacteria can transit and reside to play vital roles by producing bio-compounds with nutritional, immunomodulatory and other functions. This complex microbial ecosystem reflects several factors (environment, feeding regimen, fish species, etc.). The objective of the present study was the identification of intestinal microbial strains able to produce molecules called biosurfactants (BSs), which were tested for surface and antibacterial activity in order to select a group of probiotic bacteria for aquaculture use. Forty-two bacterial isolates from the digestive tracts of twenty Mediterranean grey mullets were screened for testing emulsifying (E-24), surface and antibiotic activities. Fifty percent of bacteria, ascribed to Pseudomonas aeruginosa, Pseudomonas sp., P. putida and P. anguilliseptica, P. stutzeri, P. protegens and Enterobacter ludwigii were found to be surfactant producers. Of the tested strains, 26.6% exhibited an antibacterial activity against Staphylococcus aureus (10.0 ± 0.0–14.5 ± 0.7 mm inhibition zone), and among them, 23.3% of isolates also showed inhibitory activity vs. Proteus mirabilis (10.0 ± 0.0–18.5 ± 0.7 mm inhibition zone) and 6.6% vs. Klebsiella pneumoniae (11.5 ± 0.7–17.5 ± 0.7 mm inhibition zone). According to preliminary chemical analysis, the bioactive compounds are suggested to be ascribed to the class of glycolipids. This works indicated that fish gut is a source of bioactive compounds which deserves to be explored. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals 2.0)

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13 pages, 5531 KiB

Open AccessArticle

Lacticaseibacillus casei ATCC 393 Cannot Colonize the Gastrointestinal Tract of Crucian Carp

by Hongyu Zhang, Xiyan Mu, Hongwei Wang, Haibo Wang, Hui Wang, Yingren Li, Yingchun Mu, Jinlong Song and Lei Xia

Microorganisms 2021, 9(12), 2547; https://doi.org/10.3390/microorganisms9122547 - 9 Dec 2021

Cited by 1 | Viewed by 2484

Abstract

Lactic acid bacteria (LAB) are commonly applied to fish as a means of growth promotion and disease prevention. However, evidence regarding whether LAB colonize the gastrointestinal (GI) tract of fish remains sparse and controversial. Here, we investigated whether Lacticaseibacillus casei ATCC 393 (Lc) [...] Read more.

Lactic acid bacteria (LAB) are commonly applied to fish as a means of growth promotion and disease prevention. However, evidence regarding whether LAB colonize the gastrointestinal (GI) tract of fish remains sparse and controversial. Here, we investigated whether Lacticaseibacillus casei ATCC 393 (Lc) can colonize the GI tract of crucian carp. Sterile feed irradiated with ⁶⁰Co was used to eliminate the influence of microbes, and 100% rearing water was renewed at 5-day intervals to reduce the fecal–oral circulation of microbes. The experiment lasted 47 days and was divided into three stages: the baseline period (21 days), the administration period (7 days: day −6 to 0) and the post-administration period (day 1 to 19). Control groups were fed a sterile basal diet during the whole experimental period, whereas treatment groups were fed with a mixed diet containing Lc (1 × 10⁷ cfu/g) and spore of Geobacillus stearothermophilus (Gs, 1 × 10⁷ cfu/g) during the administration period and a sterile basal diet during the baseline and post-administration periods. An improved and highly sensitive selective culture method (SCM) was employed in combination with a transit marker (a Gs spore) to monitor the elimination of Lc in the GI tract. The results showed that Lc (<2 cfu/gastrointestine) could not be detected in any of the fish sampled from the treatment group 7 days after the cessation of the mixed diet, whereas Gs could still be detected in seven out of nine fish at day 11 and could not be detected at all at day 15. Therefore, the elimination speed of Lc was faster than that of the transit marker. Furthermore, high-throughput sequencing analysis combined with SCM was used to reconfirm the elimination kinetics of Lc in the GI tract. The results show that the Lc in the crucian carp GI tract, despite being retained at low relative abundance from day 7 (0.11% ± 0.03%) to 21, was not viable. The experiments indicate that Lc ATCC 393 cannot colonize the GI tract of crucian carp, and the improved selective culture in combination with a transit marker represents a good method for studying LAB colonization of fish. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals 2.0)

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20 pages, 24969 KiB

Open AccessArticle

Microbial Shift in the Enteric Bacteriome of Coral Reef Fish Following Climate-Driven Regime Shifts

by Marie-Charlotte Cheutin, Sébastien Villéger, Christina C. Hicks, James P. W. Robinson, Nicholas A. J. Graham, Clémence Marconnet, Claudia Ximena Ortiz Restrepo, Yvan Bettarel, Thierry Bouvier and Jean-Christophe Auguet

Microorganisms 2021, 9(8), 1711; https://doi.org/10.3390/microorganisms9081711 - 11 Aug 2021

Cited by 8 | Viewed by 3513

Abstract

Replacement of coral by macroalgae in post-disturbance reefs, also called a “coral-macroalgal regime shift”, is increasing in response to climate-driven ocean warming. Such ecosystem change is known to impact planktonic and benthic reef microbial communities but few studies have examined the effect on [...] Read more.

Replacement of coral by macroalgae in post-disturbance reefs, also called a “coral-macroalgal regime shift”, is increasing in response to climate-driven ocean warming. Such ecosystem change is known to impact planktonic and benthic reef microbial communities but few studies have examined the effect on animal microbiota. In order to understand the consequence of coral-macroalgal shifts on the coral reef fish enteric bacteriome, we used a metabarcoding approach to examine the gut bacteriomes of 99 individual fish representing 36 species collected on reefs of the Inner Seychelles islands that, following bleaching, had either recovered to coral domination, or shifted to macroalgae. While the coral-macroalgal shift did not influence the diversity, richness or variability of fish gut bacteriomes, we observed a significant effect on the composition (R2 = 0.02; p = 0.001), especially in herbivorous fishes (R2 = 0.07; p = 0.001). This change is accompanied by a significant increase in the proportion of fermentative bacteria (Rikenella, Akkermensia, Desulfovibrio, Brachyspira) and associated metabolisms (carbohydrates metabolism, DNA replication, and nitrogen metabolism) in relation to the strong turnover of Scarinae and Siganidae fishes. Predominance of fermentative metabolisms in fish found on macroalgal dominated reefs indicates that regime shifts not only affect the taxonomic composition of fish bacteriomes, but also have the potential to affect ecosystem functioning through microbial functions. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals 2.0)

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24 pages, 7818 KiB

Open AccessArticle

Probiotics Improve Eating Disorders in Mandarin Fish (Siniperca chuatsi) Induced by a Pellet Feed Diet via Stimulating Immunity and Regulating Gut Microbiota

by Xiaoli Chen, Huadong Yi, Shuang Liu, Yong Zhang, Yuqin Su, Xuange Liu, Sheng Bi, Han Lai, Zeyu Zeng and Guifeng Li

Microorganisms 2021, 9(6), 1288; https://doi.org/10.3390/microorganisms9061288 - 12 Jun 2021

Cited by 28 | Viewed by 4551

Abstract

Eating disorders are directly or indirectly influenced by gut microbiota and innate immunity. Probiotics have been shown to regulate gut microbiota and stimulate immunity in a variety of species. In this study, three kinds of probiotics, namely, Lactobacillus plantarum, Lactobacillus rhamnosus and [...] Read more.

Eating disorders are directly or indirectly influenced by gut microbiota and innate immunity. Probiotics have been shown to regulate gut microbiota and stimulate immunity in a variety of species. In this study, three kinds of probiotics, namely, Lactobacillus plantarum, Lactobacillus rhamnosus and Clostridium butyricum, were selected for the experiment. The results showed that the addition of three probiotics at a concentration of 10⁸ colony forming unit/mL to the culture water significantly increased the ratio of the pellet feed recipients and survival rate of mandarin fish (Siniperca chuatsi) under pellet-feed feeding. In addition, the three kinds of probiotics reversed the decrease in serum lysozyme and immunoglobulin M content, the decrease in the activity of antioxidant enzymes glutathione and catalase and the decrease in the expression of the appetite-stimulating regulator agouti gene-related protein of mandarin fish caused by pellet-feed feeding. In terms of intestinal health, the three probiotics reduced the abundance of pathogenic bacteria Aeromonas in the gut microbiota and increased the height of intestinal villi and the thickness of foregut basement membrane of mandarin fish under pellet-feed feeding. In general, the addition of the three probiotics can significantly improve eating disorders of mandarin fish caused by pellet feeding. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals 2.0)

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12 pages, 1475 KiB

Open AccessArticle

Does the Composition of the Gut Bacteriome Change during the Growth of Tuna?

by Elsa Gadoin, Lucile Durand, Aurélie Guillou, Sandrine Crochemore, Thierry Bouvier, Emmanuelle Roque, Laurent Dagorn, Jean-Christophe Auguet, Antoinette Adingra, Christelle Desnues and Yvan Bettarel

Microorganisms 2021, 9(6), 1157; https://doi.org/10.3390/microorganisms9061157 - 27 May 2021

Cited by 8 | Viewed by 3627

Abstract

In recent years, a growing number of studies sought to examine the composition and the determinants of the gut microflora in marine animals, including fish. For tropical tuna, which are among the most consumed fish worldwide, there is scarce information on their enteric [...] Read more.

In recent years, a growing number of studies sought to examine the composition and the determinants of the gut microflora in marine animals, including fish. For tropical tuna, which are among the most consumed fish worldwide, there is scarce information on their enteric bacterial communities and how they evolve during fish growth. In this study, we used metabarcoding of the 16S rDNA gene to (1) describe the diversity and composition of the gut bacteriome in the three most fished tuna species (skipjack, yellowfin and bigeye), and (2) to examine its intra-specific variability from juveniles to larger adults. Although there was a remarkable convergence of taxonomic richness and bacterial composition between yellowfin and bigeyes tuna, the gut bacteriome of skipjack tuna was distinct from the other two species. Throughout fish growth, the enteric bacteriome of yellowfin and bigeyes also showed significant modifications, while that of skipjack tuna remained relatively homogeneous. Finally, our results suggest that the gut bacteriome of marine fish may not always be subject to structural modifications during their growth, especially in species that maintain a steady feeding behavior during their lifetime. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals 2.0)

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16 pages, 577 KiB

Open AccessArticle

Effects of a Bioprocessed Soybean Meal Ingredient on the Intestinal Microbiota of Hybrid Striped Bass, Morone chrysops x M. saxatilis

by Emily Celeste Fowler, Prakash Poudel, Brandon White, Benoit St-Pierre and Michael Brown

Microorganisms 2021, 9(5), 1032; https://doi.org/10.3390/microorganisms9051032 - 11 May 2021

Cited by 9 | Viewed by 3124

Abstract

The hybrid striped bass (Morone chrysops x M. saxatilis) is a carnivorous species and a major product of US aquaculture. To reduce costs and improve resource sustainability, traditional ingredients used in fish diets are becoming more broadly replaced by plant-based products; [...] Read more.

The hybrid striped bass (Morone chrysops x M. saxatilis) is a carnivorous species and a major product of US aquaculture. To reduce costs and improve resource sustainability, traditional ingredients used in fish diets are becoming more broadly replaced by plant-based products; however, plant meals can be problematic for carnivorous fish. Bioprocessing has improved nutritional quality and allowed higher inclusions in fish diets, but these could potentially affect other systems such as the gut microbiome. In this context, the effects of bioprocessed soybean meal on the intestinal bacterial composition in hybrid striped bass were investigated. Using high-throughput sequencing of amplicons targeting the V1–V3 region of the 16S rRNA gene, no significant difference in bacterial composition was observed between fish fed a control diet, and fish fed a diet with the base bioprocessed soybean meal. The prominent Operational Taxonomic Unit (OTU) in these samples was predicted to be a novel species affiliated to Peptostreptococcaceae. In contrast, the intestinal bacterial communities of fish fed bioprocessed soybean meal that had been further modified after fermentation exhibited lower alpha diversity (p < 0.05), as well as distinct and more varied composition patterns, with OTUs predicted to be strains of Lactococcus lactis, Plesiomonas shigelloides, or Ralstonia pickettii being the most dominant. Together, these results suggest that compounds in bioprocessed soybean meal can affect intestinal bacterial communities in hybrid striped bass. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals 2.0)

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Review

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21 pages, 1173 KiB

Open AccessReview

Research Progress of the Gut Microbiome in Hybrid Fish

by Xinyuan Cui, Qinrong Zhang, Qunde Zhang, Yongyong Zhang, Hua Chen, Guoqi Liu and Lifeng Zhu

Microorganisms 2022, 10(5), 891; https://doi.org/10.3390/microorganisms10050891 - 24 Apr 2022

Cited by 24 | Viewed by 5087

Abstract

Fish, including hybrid species, are essential components of aquaculture, and the gut microbiome plays a vital role in fish growth, behavior, digestion, and immune health. The gut microbiome can be affected by various internal and/or external factors, such as host development, diet, and [...] Read more.

Fish, including hybrid species, are essential components of aquaculture, and the gut microbiome plays a vital role in fish growth, behavior, digestion, and immune health. The gut microbiome can be affected by various internal and/or external factors, such as host development, diet, and environment. We reviewed the effects of diet and dietary supplements on intestinal microorganisms in hybrid fish and the difference in the gut microbiome between the hybrid and their hybrids that originate. Then, we summarized the role of the gut microbiome in the speciation and ecological invasion of hybrid fish. Finally, we discussed possible future studies on the gut microbiome in hybrid fish, including the potential interaction with environmental microbiomes, the effects of the gut microbiome on population expansion, and fish conservation and management. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals 2.0)

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14 pages, 730 KiB

Open AccessReview

Methods to Evaluate Bacterial Motility and Its Role in Bacterial–Host Interactions

by Victoria Palma, María Soledad Gutiérrez, Orlando Vargas, Raghuveer Parthasarathy and Paola Navarrete

Microorganisms 2022, 10(3), 563; https://doi.org/10.3390/microorganisms10030563 - 4 Mar 2022

Cited by 26 | Viewed by 10611

Abstract

Bacterial motility is a widespread characteristic that can provide several advantages for the cell, allowing it to move towards more favorable conditions and enabling host-associated processes such as colonization. There are different bacterial motility types, and their expression is highly regulated by the [...] Read more.

Bacterial motility is a widespread characteristic that can provide several advantages for the cell, allowing it to move towards more favorable conditions and enabling host-associated processes such as colonization. There are different bacterial motility types, and their expression is highly regulated by the environmental conditions. Because of this, methods for studying motility under realistic experimental conditions are required. A wide variety of approaches have been developed to study bacterial motility. Here, we present the most common techniques and recent advances and discuss their strengths as well as their limitations. We classify them as macroscopic or microscopic and highlight the advantages of three-dimensional imaging in microscopic approaches. Lastly, we discuss methods suited for studying motility in bacterial–host interactions, including the use of the zebrafish model. Full article

(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals 2.0)

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