Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World's Largest Cavefish Diversification (Cyprinidae, Sinocyclocheilus)

The symbiosis between a host and its microbiome is essential for host fitness, and this association is a consequence of the host’s physiology and habitat. Sinocyclocheilus, the largest cavefish diversification of the world, an emerging multi-species model system for evolutionary novelty, provides an excellent opportunity for examining correlates of host evolutionary history, habitat, and gut-microbial community diversity. From the diversification-scale patterns of habitat occupation, major phylogenetic clades (A–D), geographic distribution, and knowledge from captive-maintained Sinocyclocheilus populations, we hypothesize habitat to be the major determinant of microbiome diversity, with phylogeny playing a lesser role. For this, we subject environmental water samples and fecal samples (representative of gut-microbiome) from 24 Sinocyclocheilus species, both from the wild and after being in captivity for 6 months, to bacterial 16S rRNA gene profiling using Illumina sequencing. We see significant differences in the gut microbiota structure of Sinocyclocheilus, reflective of the three habitat types; gut microbiomes too, were influenced by host-related factors. There is no significant association between the gut microbiomes and host phylogeny. However, there is some microbiome related structure at the clade level, with the most geographically distant clades (A and D) being the most distinct, and the two overlapping clades (B and C) showing similarities. Microbes inhabiting water were not a cause for significant differences in fish-gut microbiota, but water quality parameters were. Transferring from wild to captivity, the fish microbiomes changed significantly and became homogenized, signifying plastic changes and highlighting the importance of environmental factors (habitat) in microbiome community assembly. The core microbiome of this group, at higher taxonomic scale, resembled that of other teleost fishes. Our results suggest that divergent natural environments giving rise to evolutionary novelties underlying host adaptations, also includes the microbiome of these fishes.

Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens

The microbial decomposition of animal tissues is an important ecological process that impacts nutrient cycling in natural environments. We studied the microbial decomposition of a common North American fish (rainbow darters) over four time points, combining 16S rRNA gene and shotgun metagenomic sequence data to obtain both taxonomic and functional perspectives. Our data revealed a strong community succession that was reproduced across different fish and environments. Decomposition time point was the main driver of community composition and functional potential; fish environmental origin (upstream or downstream of a wastewater treatment plant) had a secondary effect. We also identified strains related to the putative pathogen Aeromonas veronii as dominant members of the decomposition community. These bacteria peaked early in decomposition and coincided with the metagenomic abundance of hemolytic toxin genes. Our work reveals a strong decomposer succession in wild-caught fish, providing functional and taxonomic insights into the vertebrate necrobiome.

Despite progress understanding microbial communities involved in terrestrial vertebrate decomposition, little is known about the microbial decomposition of aquatic vertebrates from a functional and environmental context. Here, we analyzed temporal changes in the “necrobiome” of rainbow darters, which are common North American fish that are sensitive indicators of water quality. By combining 16S rRNA gene and shotgun metagenomic sequence data from four time points, we studied the progression of decomposers from both taxonomic and functional perspectives. The 16S rRNA gene profiles revealed strong community succession, with early decomposition stages associated with Aeromonas and Clostridium taxa and later stages dominated by members of the Rikenellaceae (i.e., Alistipes/Acetobacteroides genera). These results were reproducible and independent of environmental perturbation, given that exposure to wastewater treatment plant effluent did not substantially influence the necrobiome composition of fish or the associated water sample microbiota. Metagenomic analysis revealed significant changes throughout decomposition in degradation pathways for amino acids, carbohydrates/glycans, and other compounds, in addition to putrefaction pathways for production of putrescine, cadaverine, and indole. Binning of contigs confirmed a predominance of Aeromonas genome assemblies, including those from novel strains related to the pathogen Aeromonas veronii. These bins of Aeromonas genes also encoded known hemolysin toxins (e.g., aerolysin) that were particularly abundant early in the process, potentially contributing to host cell lysis during decomposition. Overall, our results demonstrate that wild-caught fish have a reproducible decomposer succession and that the fish necrobiome serves as a potential source of putative pathogens and toxigenic bacteria.

IMPORTANCE The microbial decomposition of animal tissues is an important ecological process that impacts nutrient cycling in natural environments. We studied the microbial decomposition of a common North American fish (rainbow darters) over four time points, combining 16S rRNA gene and shotgun metagenomic sequence data to obtain both taxonomic and functional perspectives. Our data revealed a strong community succession that was reproduced across different fish and environments. Decomposition time point was the main driver of community composition and functional potential; fish environmental origin (upstream or downstream of a wastewater treatment plant) had a secondary effect. We also identified strains related to the putative pathogen Aeromonas veronii as dominant members of the decomposition community. These bacteria peaked early in decomposition and coincided with the metagenomic abundance of hemolytic toxin genes. Our work reveals a strong decomposer succession in wild-caught fish, providing functional and taxonomic insights into the vertebrate necrobiome.

Community profiling of the intestinal microbial community of juvenile Hammerhead Sharks (Sphyrna lewini) from the Rewa Delta, Fiji

Fourteen juvenile scalloped hammerhead sharks (Sphyrna lewini; SHS) were captured between November and December 2014 in the Rewa Delta in Fiji, and assessed for intestinal microflora characterisation using 16S rRNA amplicon sequencing by Illumina Miseq. The microbial population revealed a fluctuating dominance between the Enterobacteriaceae and Vibrionaceae families, namely Citrobacter and Photobacterium spp. Other related marine operational taxonomic units were closely related to Afipia felis, Chloroflexus aggregans, Psychrobacter oceani, Pontibacter actiniarum and Shigella sonnei. Two sharks had distinctive profiles that were dominated by known pathogens, namely Aeromonas salmonicida and Klebsiella pneumonia. The presence of a Methanosaeta species, and of Shigella and Psychrobacter, would suggest sewage contamination because of a spill that occurred on the 6^th of December 2014. This study successfully establishes a baseline for future research.

Intestinal Methylation and Demethylation of Mercury

Mercury (Hg) is a global pollutant, which is linked with different diseases. The methylation of Hg and demethylation of methylmercury (MeHg) in the environment were extensively studied and summarized; however, the transformation of Hg in the intestine is less presented. In this review, the research progress and the perspectives on the intestinal transformation of Hg were discussed. Studies found that MeHg could be formed when exposed to inorganic Hg by the gut microbiota in aquatic organisms, terrestrial invertebrates, and mammals, etc. hgcAB genes could be used as indicators for predicting Hg methylation potential. In vitro studies using fecal specimen, intestinal contents, and the isolated intestinal microbes confirmed the intestinal demethylation of MeHg. The investigation on the effects of Hg exposure to the abundance and diversity of intestinal microbes and their metabolites could shed light on the mechanism of the toxicity of Hg, especially the neurotoxicity of MeHg, which deserves further study.

Protective effects of the prebiotic on the immunological indicators of rainbow trout (Oncorhynchus mykiss) infected with Aeromonas hydrophila

The aim of this study was to investigate the protective effects of dietary administration of commercial prebiotic, Immunogen, on immunological indicators, enzymatic responses and stress tolerance in juvenile (81.65 ± 1.49) rainbow trout (Oncorhynchus mykiss) following Aeromonas hydrophila infection. The first group of fish was fed with the diet containing 2 g kg(-1) Immunogen whilst the control group received the diet free of Immunogen. There were three replicates per group. After 6 weeks feeding, the control group were divided into two treatments injected with saline buffer (control), and 1.5 × 10(8) CFU A. hydrophila respectively. The fish fed with the Immunogen supplemented diet were also injected with 1.5 × 10(8) CFU A. hydrophila. Our results revealed that dietary Immunogen increased the level of white blood cell (WBC) and percentage of lymphocyte (P < 0.05), however, the level of red blood cell (RBC), Hematocrit (Hct), hemoglobin (Hb) and percent of monocyte decreased in Untreated-Challenged group but unaffected in the group fed with Immunogen (P < 0.05). The level of lysozyme, alternative complement, antiprotease activity, total protein, albumin and globulin decreased in Untreated- Challenged group compared to control group. However, there was an increase in the level of lysozyme, alternative complement, antiprotease activity, bactericidal activity, in the Treated- Challenged group compared to other groups (P < 0.05). Serum alkali phosphatase (ALT) and aspartate aminotransferase, significantly increased fallowing challenge with A. hydrophila but in the Treated-Challenged group, there was no significant difference compared to the control group (P < 0.05). Lactate dehydrogenase (LDH) level was not different between groups (P > 0.05). Serum cortisol and glucose levels were higher in the challenge group, but these levels were lower in fish under challenge that were fed Immunogen-supplemented diet in contrast to the group fed control diet. The stress responses affected by A. hydrophila challenge (P < 0.05). Serum sodium, potassium and calcium concentration decreased by A. hydrophila exposure (P < 0.05), and Immunogen showed protection effect against this change.

Role of peptidases of the intestinal microflora and prey in temperature adaptations of the digestive system in planktivorous and benthivorous fish

Many fish enzymatic systems possess limited adaptations to low temperature; however, little data are available to judge whether enzymes of fish prey and intestinal microbiota can mitigate this deficiency. In this study, the activity of serine peptidases (casein-lytic, mainly trypsin and hemoglobin-lytic, mainly chymotrypsin) of intestinal mucosa, chyme and intestinal microflora in four species of planktivorous (blue bream) and benthivorous (roach, crucian carp, perch) was investigated across a wide temperature range (0-70 °C) to identify adaptations to low temperature. At 0 °C, the relative activity of peptidases of intestinal mucosa (<13%) and usually intestinal microflora (5-12.6%) is considerably less than that of chyme peptidases (up to 40% of maximal activity). The level of peptidase relative activity in crucian carp intestinal microflora was 45% of maximal activity. The shape of t°-function curves of chyme peptidase also differs in fish from different biotopes. Fish from the littoral group are characterized by a higher degree of adaptation of chyme casein-lytic peptidases to functioning at low temperatures as compared to fish from the pelagic group. The role of intestinal microbiota and prey peptidases in digestive system adaptations of planktivorous and benthivorous fish to low temperatures is discussed.

Titanium dioxide nanoparticles enhance mortality of fish exposed to bacterial pathogens

Nano-TiO2 is immunotoxic to fish and reduces the bactericidal function of fish neutrophils. Here, fathead minnows (Pimephales promelas) were exposed to low and high environmentally relevant concentration of nano-TiO2 (2 ng g(-1) and 10 μg g(-1) body weight, respectively), and were challenged with common fish bacterial pathogens, Aeromonas hydrophila or Edwardsiella ictaluri. Pre-exposure to nano-TiO2 significantly increased fish mortality during bacterial challenge. Nano-TiO2 concentrated in the kidney and spleen. Phagocytosis assay demonstrated that nano-TiO2 has the ability to diminish neutrophil phagocytosis of A. hydrophila. Fish injected with TiO2 nanoparticles displayed significant histopathology when compared to control fish. The interplay between nanoparticle exposure, immune system, histopathology, and infectious disease pathogenesis in any animal model has not been described before. By modulating fish immune responses and interfering with resistance to bacterial pathogens, manufactured nano-TiO2 has the potential to affect fish survival in a disease outbreak.

Analysis of immune-related ESTs and differential expression analysis of few important genes in lines of rohu (Labeo rohita) selected for resistance and susceptibility to Aeromonas hydrophila infection

A total of 137,629 contigs generated via de novo transcriptome assembly from resistant and susceptible lines of rohu (first generation) raised against aeromoniasis were further analyzed in terms of defence-related genes. Out of 1,939 contigs showing homology to genes involved in immune processes, 1,866 were further categorised into different functional subgroups. Comparative analysis revealed five genes for the first time in any carp species out of which apolipoprotein h, septin 4 isoform 3 and septin isoform cra_c were identified for the first time in fish. Differential expression analysis of ten genes viz., heat shock proteins (Hsps) (Hsp30, Hsp70 and Hsp90), serum lectin isoform 1 (SLI1), linker histone H1M (LHH1M), NAD(P)H quinone 1 (NQO1), zona pellucida 2 (ZP2) and three unknown genes that were highly up-expressed in first generation resistant line fish from mRNA-seq coverage data, was carried out using susceptible and resistant individuals of the second generation selected populations in eight different tissues viz. liver, kidney, intestine, gill, brain, spleen, skin and muscle using qPCR. Significant up-regulation in Hsp90, NQO1, C_116914 and C_22454 in specific tissues of resistant line and variable expression in Hsp30 and LHH1M genes in different tissues of both lines were noticed. The expression of Hsp70 was lower in many tissues of the resistant line than in susceptible line rohu. The expression of ZP2, SLI1 and C_94589 genes was not significantly different in terms of fold difference between the two lines. Differentially expressed genes need further characterisation to explore their role in resistance to Aeromonas hydrophila infection in rohu.

Intestinal microbiota in fishes: what's known and what's not

High-throughput sequencing approaches have enabled characterizations of the community composition of numerous gut microbial communities, which in turn has enhanced interest in their diversity and functional relationships in different groups of vertebrates. Although fishes represent the greatest taxonomic and ecological diversity of vertebrates, our understanding of their gut microbiota and its functional significance has lagged well behind that of terrestrial vertebrates. In order to highlight emerging issues, we provide an overview of research on fish gut microbiotas and the biology of their hosts. We conclude that microbial community composition must be viewed within an informed context of host ecology and physiology, and that this is of particular importance with respect to research planning and sampling design.

Vulnerability of larval and juvenile white sturgeon to barotrauma: can they handle the pressure?

Techniques were developed to determine which life stages of fish are vulnerable to barotrauma from expansion of internal gases during decompression. Eggs, larvae, and juvenile hatchery-reared white sturgeon (Acipenser transmontanus; up to 91 days post hatch; d.p.h.) were decompressed to assess vulnerability to barotrauma and identify initial swim bladder inflation. Barotrauma-related injury and mortality were first observed 9 d.p.h., on the same day as initial exogenous feeding. However, barotrauma-related injury did not occur again until swim bladder inflation 75 d.p.h. (visible at necropsy and on radiographs). Swim bladder inflation was not consistent among individuals, with only 44% being inflated 91 d.p.h. Additionally, swim bladder inflation did not appear to be size dependent among fish ranging in total length from 61 to 153 mm at 91 d.p.h. The use of a combination of decompression tests and radiography was validated as a method to determine initial swim bladder inflation and vulnerability to barotrauma. Extending these techniques to other species and life-history stages would help to determine the susceptibility of fish to hydro turbine passage and aid in fish conservation.

Influence of pH upon the activity of glycosidases and proteinases of intestinal mucosa, chyme and microbiota in fish

It is shown that amylolytic and proteolytic activity of the intestinal mucosa, the chyme and the intestinal flora in the fishes, zander Zander lucioperca (L.), perch Perca fluviatilis L., bream Abramis brama (L.) and roach Rutilus rutilus (L.), belonging according to their feeding habits to different ecological groups at the same pH values as well as in the pH range from 5.0 to 10.0 considerably varies. The glycosidase pH optimum of the mucosa and intestinal microbiota is 7.0, whereas that of the chyme varies from 6.0 (in roach) to 8.0 (in bream). pH optimum of the mucosa proteinases in all fish species is 10.0, whereas that of the chyme and the bacterial flora can be observed in all the range of pH values.

A unique symbiosis in the gut of tropical herbivorous surgeonfish (acanthuridae: teleostei) from the red sea

Herbivorous surgeonfish (Acanthurus species) in the Red Sea harbor gut symbionts that include bacteria, trichomonadid flagellates, and a peculiar putative protist that attains densities of 20,000 to 100,000 cells per milliliter of gut contents. The structure, mode of reproduction, and within-gut distribution of the latter are described. This may be the first report of an organism of this type and the first evidence of a consistent endosymbiosis in the gut of a herbivorous marine fish.

Digestive enzyme activities and gastrointestinal fermentation in wood-eating catfishes

To determine what capabilities wood-eating and detritivorous catfishes have for the digestion of refractory polysaccharides with the aid of an endosymbiotic microbial community, the pH, redox potentials, concentrations of short-chain fatty acids (SCFAs), and the activity levels of 14 digestive enzymes were measured along the gastrointestinal (GI) tracts of three wood-eating taxa (Panaque cf. nigrolineatus "Marañon", Panaque nocturnus, and Hypostomus pyrineusi) and one detritivorous species (Pterygoplichthys disjunctivus) from the family Loricariidae. Negative redox potentials (-600 mV) were observed in the intestinal fluids of the fish, suggesting that fermentative digestion was possible. However, SCFA concentrations were low (<3 mM in any intestinal region), indicating that little GI fermentation occurs in the fishes' GI tracts. Cellulase and xylanase activities were low (<0.03 U g(-1)), and generally decreased distally in the intestine, whereas amylolytic and laminarinase activities were five and two orders of magnitude greater, respectively, than cellulase and xylanase activities, suggesting that the fish more readily digest soluble polysaccharides. Furthermore, the Michaelis-Menten constants (K(m)) of the fishes' beta-glucosidase and N-acetyl-beta-D-glucosaminidase enzymes were significantly lower than the K(m) values of microbial enzymes ingested with their food, further suggesting that the fish efficiently digest soluble components of their detrital diet rather than refractory polysaccharides. Coupled with rapid gut transit and poor cellulose digestibility, the wood-eating catfishes appear to be detritivores reliant on endogenous digestive mechanisms, as are other loricariid catfishes. This stands in contrast to truly "xylivorous" taxa (e.g., beavers, termites), which are reliant on an endosymbiotic community of microorganisms to digest refractory polysaccharides.

Selected nondigestible carbohydrates and prebiotics support the growth of probiotic fish bacteria mono-cultures in vitro

AIMS

To search for nondigestible but fermentable (NDF) carbohydrates and prebiotics with a potency to promote the growth of selected bacteria in vitro.

METHODS AND RESULTS

The growth of three reference bacteria strains Bacillus subtilis LMG 7135(T), Carnobacterium piscicola LMG 9839, Lactobacillus plantarum LMG 9211 and one candidate probiotic bacteria Lactobacillus delbrueckii subsp. lactis was investigated over a minimum period of 48 h in the presence of beta-glucan, xylo-oligosaccharide, arabinoxylo-oligosaccharide, inulin, oligofructose and glucose. Besides the capability to grow on inulin and oligofructose containing media, a distinct high growth in beta-glucan based substrates and a low growth in (arabino)xylooligosaccharide containing media were evident for most bacteria tested. With the exception of B. subtilis and L. plantarum, other bacteria grew equally well or even better on different substrates than on glucose. The fermentation of studied carbohydrates by these micro-organisms was dominated by the production of acetic acid as the main short chain fatty acid.

CONCLUSIONS

Selected bacteria are able to ferment and grow on NDF and prebiotic carbohydrates but in a substrate dependent manner.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study delivers a first screening of which NDF or prebiotic carbohydrates are the most promising for aquaculture feed supplementations.

Microbial diversity of intestinal contents and mucus in rainbow trout (Oncorhynchus mykiss)

AIMS

The aim of this study was to understand the microbial community of intestinal contents and mucosal layer in the intestine of rainbow trout by means of culture-dependent conventional and independent molecular techniques.

METHODS AND RESULTS

Forty-one culturable microbial phylotypes, and 39 sequences from 16S rRNA and two from 18S rRNA genes, were retrieved. Aeromonadaceae, Enterobacteriaceae and Pseudomonadaceae representatives were the dominant cultured bacteria. Genomic DNA isolated from intestinal contents and mucus was used to generate 104 random clones, which were grouped into 32 phylotypes at 99% minimum similarity, most of which were affiliated with Proteobacteria (>70% of the total). However, unlike library C (intestinal contents), the phyla Bacteroidetes and Fusobacteria were not found in intestinal mucus (library M), indicating that the microbiota in the gut mucus was different from that of the intestinal contents. Twelve sequences were retrieved from denaturing gradient gel electrophoresis analysis, and dominant bands were mostly related to Clostridium.

CONCLUSIONS

Many novel sequences that have not been previously recognized as part of the intestinal flora of rainbow trout were retrieved.

SIGNIFICANCE AND IMPACT OF THE STUDY

The fish gut harbours a larger bacterial diversity than previously recognized, and the diversity of gut mucus is different from that of intestinal contents.

Novel ecological niche of Cetobacterium somerae, an anaerobic bacterium in the intestinal tracts of freshwater fish

AIMS

This study was conducted to clarify the taxonomic status of Bacteroides type A strains with high vitamin B(12)-producing ability that is widely distributed in the intestinal tracts of freshwater fish.

METHODS AND RESULTS

Seventeen strains of Bacteroides type A isolated from five fish species were all rod-shaped and gram-negative. The strains were positive for esculin hydrolysis, nitrate reduction, resistance to bile, acid phosphatase, and negative for the production of catalase and urease and the susceptibility to vancomycin. The G+C content of DNA from the 17 strains was 29 x 1-31 x 9 mol%, and 16S rDNA sequence analysis revealed a close phylogenetic relationship between Bacteroides type A strains and Cetobacterium somerae sharing 99 x 7-100% sequence similarity. In addition, strains were capable of producing vitamin B(12) at a rate of 1 x 82-13 x 98 ng ml(-1) in 48 h.

CONCLUSION

Phenotypic and phylogenetic characteristics indicated that all isolates previously classified as Bacteroides type A strains belong to C. someare.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provided the important finding of novel niche of vancomycin-resistant bacteria such as C. somerae in the intestinal tract of freshwater fish.

Debromination of polybrominated diphenyl ether congeners BDE 99 and BDE 183 in the intestinal tract of the common carp (Cyprinus carpio)

Polybrominated diphenyl ether (PBDE) congener patterns in biota are often enriched in tetra-, penta-, and hexabrominated diphenyl ethers, which is believed to result from the use of the commercial "pentaBDE" formulation. However, our evidence suggests that debromination of PBDEs occurs within fish tissues leading to appreciable accumulation of less brominated congeners. This suggests that PBDE body burdens can reflect both direct uptake from exposure and debromination of more highly brominated congeners. We conducted two independent dietary exposure studies using the common carp (Cyprinus carpio) to trace the fate of 2,2',4,4',5-pentabromodiphenyl ether (BDE 99) and 2,2',3,4,4',5',6-heptabromodiphenyl ether (BDE 183) in fish tissues. Carp were fed food spiked with individual BDE congeners for 62 d, and depuration was monitored during the following 37 d. Significant debromination was observed, converting BDE 99 to 2,2',4,4'-tetrabromodiphenyl ether (BDE47) and BDE 183 to 2,2',4,4',5,6-hexabromodiphenyl ether (BDE 154) and another as yet unidentified hexa-BDE congener. The BDE 99 concentration rapidly declined from 400 +/- 40 ng/g ww in the food to 53 +/- 12 ng/g ww in the gut content material sampled 2.5 +/- 1 h following feeding. At least 9.5 +/- 0.8% of the BDE 99 mass in the gut was debrominated to BDE 47 and assimilated in carp tissues. In the BDE 183 exposure, approximately 17% of the BDE 183 mass was debrominated and accumulated in carp tissues in the form of two hexa-BDE congeners. In both exposure studies, the concentration of the exposure compound decreased significantly in the gut within 2.5 +/- 1 h following ingestion. This rapid decrease in the concentration of the BDE congeners could not be explained entirely by debromination to quantified products or fecal egestion. Reactions occurring within the gut transform BDE congeners to other products that may accumulate or be excreted. Further studies are needed to identify and determine the effects of these BDE metabolites.

Clostridium perfringens toxin types from wild-caught Atlantic cod (Gadus morhua L.), determined by PCR and ELISA

Ninety-five fecal samples from Atlantic cod (Gadus morhua L.), caught along the northern Norwegian coast, were examined bacteriologically for occurrence of C. perfringens. Isolates were examined by polymerase chain reaction (PCR) for genes encoding the four lethal toxins (alpha, beta, epsilon, and iota) for classification into toxin types and for genes encoding enterotoxin and the novel beta2 toxin for further subclassification. In addition, a commercial enzyme-linked immunosorbent assay (ELISA) kit for detection of C. perfringens alpha, beta, and epsilon toxin was used. Clostridium perfringens could be isolated in 37 fecal samples (38.9%) from cod. All isolates were C. perfringens toxin type A (alpha toxin positive) as determined by PCR and also ELISA. In addition, in isolates from two cod (2.1%) the gene encoding for beta2 toxin was found (A, beta2) by PCR. Genes encoding for beta, epsilon, and iota toxins and enterotoxin were not found. This is the first detection of C. perfringens alpha and beta2 toxin in cod and of beta2 toxin in fish in general. The origin of this bacterium in cod is discussed.

Contributions of microbes in vertebrate gastrointestinal tract to production and conservation of nutrients

The vertebrate gastrointestinal tract is populated by bacteria and, in some species, protozoa and fungi that can convert dietary and endogenous substrates into absorbable nutrients. Because of a neutral pH and longer digesta retention time, the largest bacterial populations are found in the hindgut or large intestine of mammals, birds, reptiles, and adult amphibians and in the foregut of a few mammals and at least one species of bird. Bacteria ferment carbohydrates into short-chain fatty acids (SCFA), convert dietary and endogenous nitrogenous compounds into ammonia and microbial protein, and synthesize B vitamins. Absorption of SCFA provides energy for the gut epithelial cells and plays an important role in the absorption of Na and water. Ammonia absorption aids in the conservation of nitrogen and water. A larger gut capacity and longer digesta retention time provide herbivores with additional SCFA for maintenance energy and foregut-fermenting and copoprophagic hindgut-fermenting species with access to microbially synthesized protein and B vitamins. Protozoa and fungi also contribute nutrients to the host. This review discusses the contributions of gut microorganisms common to all vertebrates, the numerous digestive strategies that allow herbivores to maximize these contributions, and the effects of low-fiber diets and discontinuous feeding schedules on these microbial digestive processes.

Characterization and Ecology of Carboxymethylcellulase-Producing Anaerobic Bacterial Communities Associated with the Intestinal Tract of the Pinfish, Lagodon rhomboides

Carboxymethylcellulase (CMCase)-producing obligate anaerobes were isolated from the intestinal tract contents but not the feeding habitat of seagrass-consuming pinfish. Taxonomic characterization of these CMCase-producing strains revealed four taxonomic clusters; three were clostridial and one was of unknown taxonomic affinity. Our results demonstrated that the CMCase-producing obligate anaerobe community from pinfish differed from functionally similar microbial communities in terrestrial herbivores.

Effect of different holding regimens on the intestinal microflora of herring (Clupea harengus) larvae

The aerobic intestinal microflora of 2-week-old herring (Clupea harengus) larvae was characterized by using conventional microbiological methods and electron microscopy. Larvae were hatched and kept in filtered seawater or in seawater with penicillin and streptomycin. The gastrointestinal tract of herring larvae is essentially a straight tube divided into two compartments. Light microscopy revealed bacteria present in a progressively increasing amount throughout the length of the gastrointestinal tract from esophagus to anus. The posterior region of the intestinal lumen appeared completely occluded with bacteria. The intestinal microflora consisted mainly of members of the genera Pseudomonas and Alteromonas in the larvae incubated in filtered seawater, whereas Flavobacterium spp. dominated in larvae exposed to antibiotics. The intestinal microflora of untreated fish larvae was sensitive to all tested antibiotics, whereas multiple resistance was found in the intestinal microflora of the group given antibiotics. Thus, a dramatic change in the microflora resulted from incubation with antibiotics. Nonpigmented yeasts were detected in both larval groups. Ciliated epithelial cells were observed in the midgut, probably propeling bacteria towards the hindgut, where endocytosis of bacteria has been demonstrated. These findings suggest that transport and sequestering mechanisms resembling those of invertebrates may be found in the gut of fish larvae. The possible significance for larval health and nutrition is discussed.

Bacterial flora of fishes: A review

Bacterial floras isolated from eggs, skin, gills, and intestines have been described for a limited number of fish species. Generally, the range of bacterial genera isolated is related to the aquatic habitat of the fish and varies with factors such as the salinity of the habitat and the bacterial load in the water. In many investigations, identification of isolates to the genus level only makes it difficult to determine the precise relationships of aquatic and fish microfloras. Bacteria recovered from the skin and gills may be transient rather than resident on the fish surfaces. Microfloras of fish intestines appear to vary with the complexity of the fish digestive system. The genera present in the gut generally seem to be those from the environment or diet which can survive and multiply in the intestinal tract, although there is evidence for a distinct intestinal microflora in some species. While obligate anaerobes have been recovered from carp and tilapia intestines, low ambient temperatures may prevent colonization by anaerobes in species such as rainbow trout.

The establishment of an intestinal microflora in developing goldfish (Carassius auratus) of culture ponds

The bacterial flora in the intestinal tract of goldfish (Carassius auratus) was investigated at different stages of fish development. The floras of the diets and the water and sediment of a culture pond were also analyzed. The total counts in the intestine ranged from 2.2 × 10(6)-2.1 × 10(8) cells g(-1) wet weight.Aeromonas hydrophila, A. punctata, Pseudomonas, Bacteroidaceae andClostridium species were the common components in the intestinal tract of goldfish from larvae to adult stage.Bacteroides type A appeared at 44 days with a density of 10(3) cells g(-1) and then predominated with densities of 10(5)-10(7) cells g(-1). The intestinal microflora of goldfish become relatively stable after 67 days of hatching. These observations suggest that the intestinal microflora of adult goldfish becomes established approximately 2 months after hatching.

Mercury methylation by fish intestinal contents

A new radiochemical method has been applied to the examination of mercury methylation in fish intestinal contents. Intestinal contents of six freshwater fish species were found capable of converting 203Hg2+ to CH3203Hg+. This activity was observed in fish from five of six lakes tested whether or not there was mercury pollution. Bacterial activity in the intestinal contents is most likely responsible for this methylation. Methylating activity of piscivors increased with decreasing quantity of intestinal contents. Generally, pike and walleye intestinal contents methylated a larger fraction of 203Hg2+ than those of whitefish and suckers. These data contradict the previous general conclusion that there is no mercury methylation in fish.