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Haworth SE, White KS, Côté SD, Shafer ABA. Space, time and captivity: quantifying the factors influencing the fecal microbiome of an alpine ungulate. FEMS Microbiol Ecol 2020; 95:5519850. [PMID: 31210274 DOI: 10.1093/femsec/fiz095] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 06/15/2019] [Indexed: 12/21/2022] Open
Abstract
The community of microorganisms in the gut is affected by host species, diet and environment and is linked to normal functioning of the host organism. Although the microbiome fluctuates in response to host demands and environmental changes, there are core groups of microorganisms that remain relatively constant throughout the hosts lifetime. Ruminants are mammals that rely on highly specialized digestive and metabolic modifications, including microbiome adaptations, to persist in extreme environments. Here, we assayed the fecal microbiome of four mountain goat (Oreamnos americanus) populations in western North America. We quantified fecal microbiome diversity and composition among groups in the wild and captivity, across populations and in a single group over time. There were no differences in community evenness or diversity across groups, although we observed a decreasing diversity trend across summer months. Pairwise sample estimates grouped the captive population distinctly from the wild populations, and moderately grouped the southern wild group distinctly from the two northern wild populations. We identified 33 genera modified by captivity, with major differences in key groups associated with cellulose degradation that likely reflect differences in diet. Our findings are consistent with other ruminant studies and provide baseline microbiome data in this enigmatic species, offering valuable insights into the health of wild alpine ungulates.
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Affiliation(s)
- Sarah E Haworth
- Forensics Program, Trent University, K9J 7B8 Peterborough, Canada.,Environmental and Life Sciences Graduate Program, Trent University, 7K9J 7B8 Peterborough, Canada
| | - Kevin S White
- Division of Wildlife Conservation, Alaska Department of Fish and Game, Juneau, AK 99802, USA
| | - Steeve D Côté
- Département de Biologie and Centre for Northern Studies, Université Laval, Québec G1V 0A6, Canada
| | - Aaron B A Shafer
- Forensics Program, Trent University, K9J 7B8 Peterborough, Canada.,Environmental and Life Sciences Graduate Program, Trent University, 7K9J 7B8 Peterborough, Canada
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52
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Rimoldi S, Gini E, Koch JFA, Iannini F, Brambilla F, Terova G. Effects of hydrolyzed fish protein and autolyzed yeast as substitutes of fishmeal in the gilthead sea bream (Sparus aurata) diet, on fish intestinal microbiome. BMC Vet Res 2020; 16:118. [PMID: 32321508 PMCID: PMC7178574 DOI: 10.1186/s12917-020-02335-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/06/2020] [Indexed: 01/11/2023] Open
Abstract
Background This study evaluated the effects of partial substitution of dietary fishmeal (FM) with either fish protein hydrolysate (FPH) or autolysed dried yeast (HiCell®, Biorigin, Brazil) on intestinal microbiota of gilthead sea bream (Sparus aurata). A total number of 720 fish of 122.18 ± 6.22 g were fed for 92 days with three different diets in triplicate (3 tanks/diet). A diet based on FM/vegetable meal was used as control. The other two diets were formulated by replacing FM with 5% of either FPH or HiCell®. To analyze the gut microbiota associated to autochthonous and allochthonous microbial communities, the Illumina MiSeq platform for sequencing of 16S rRNA gene and QIIME pipeline were used. Results A total number of 102 OTUs (operational taxonomic units) at 97% identity were identified in fish gut samples collected at the end of feeding trial. Fourteen OTUs constituted the core gut microbiota, i.e. those OTUs found in at least nine out of fifteen samples per group and shared regardless of the diet. Eight OTUs were assigned to Firmicutes represented by Lactobacillus, Staphylococcus, and Bacillus genera, and six to Proteobacteria phylum. Dietary dried yeast autolysate modulated the intestinal microbiota by promoting the growth of some beneficial bacteria. At order level, fish fed yeast showed an enrichment in Bacillales and Clostridiales as compared to the control group, whereas fish fed FPH showed a significantly lower amount of bacteria belonging to Alteromonadales and Enterobacteriales than the other two feeding groups. Although we did not observe any effect of 5% FM replacement with alternative nitrogen sources at phylum level, at lower taxonomical levels, the composition of gut microbiota, in terms of relative abundance of specific taxa, was significantly influenced by the dietary treatment. Conclusions The metabarcoding analysis revealed a clearly intestinal microbiota modulation in response to dietary autolyzed yeast. The abundance of some beneficial bacteria, i.e. indigestible carbohydrate degrading- and SCFA producing bacteria, was positively affected. Brewer’s yeast autolysate could be a valid alternative protein source to FM as well as a valid functional ingredient for aquafeed production.
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Affiliation(s)
- S Rimoldi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant, 3, 21100, Varese, Italy
| | - E Gini
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant, 3, 21100, Varese, Italy
| | - J F A Koch
- Biorigin Brazil. Rua XV de Novembro, 865, Lençóis Paulista, São Paulo, 18680-900, Brazil
| | - F Iannini
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant, 3, 21100, Varese, Italy
| | - F Brambilla
- VRM srl Naturalleva, Via Sommacampagna, 63/D, 37137, Verona, Italy
| | - G Terova
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant, 3, 21100, Varese, Italy.
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53
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Rimoldi S, Torrecillas S, Montero D, Gini E, Makol A, Valdenegro V. V, Izquierdo M, Terova G. Assessment of dietary supplementation with galactomannan oligosaccharides and phytogenics on gut microbiota of European sea bass (Dicentrarchus Labrax) fed low fishmeal and fish oil based diet. PLoS One 2020; 15:e0231494. [PMID: 32298317 PMCID: PMC7162502 DOI: 10.1371/journal.pone.0231494] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/24/2020] [Indexed: 11/19/2022] Open
Abstract
There is an increasing interest from the aquafeed industry in functional feeds containing selected additives that improve fish growth performance and health status. Functional feed additives include probiotics, prebiotics, organic acids, and phytogenics (substances derived from plants and their extracts). This study evaluated the effects of dietary inclusion of a mucilage extract rich in galactomannan oligosaccharides (GMOS), a mixture of garlic and labiatae-plants oils (PHYTO), and a combination of them (GMOSPHYTO), on gut microbiota composition of European sea bass (Dicentrarchus labrax) fed with a low fishmeal (FM) and fish oil (FO) diet. Three experimental diets and a control diet (plant-based formulation with 10% FM and 6% FO) were tested in a 63-days feeding trial. To analyze the microbiota associated to feeds and the intestinal autochthonous (mucosa-adhered) and allochthonous (transient) microbial communities, the Illumina MiSeq platform for sequencing of 16S rRNA gene and QIIME2 pipeline were used. Metabarcoding analysis of feed-associated bacteria showed that the microbial communities of control (CTRL) feed deeply differed from those of experimental diets. The number of reads was significantly lower in CTRL feed than in other feeds. The OTU (operational taxonomic unit) number was instead similar between the feeds, ranging from 42 to 50 OTUs. The variation of resident gut microbiota induced by diet was lower than the variation of transient intestinal microbiota, because feedstuffs are a major source of allochthonous bacteria, which can temporarily integrate into the gut transient microbiome. However, the composition of transient bacterial communities was not simply a mirror of feed-borne bacteria. Indeed, the microbial profile of feeds was different from both faecal and mucosa profiles. Our findings suggest that the dietary inclusion of GMOS (0.5%) and PHYTO (0.02%) in a low FM and FO diet induces changes in gut microbiota composition of European sea bass. However, if on allochthonous microbiota the combined inclusion of GMOS and PHYTO showed an antagonistic effect on bactericidal activity against Vibrionales, at mucosa level, only GMOSPHYTO diet increased the relative abundance of Bacteroidales, Lactobacillales, and Clostridiales resident bacterial orders. The main beneficial effects of GMOS and PHYTO on gut microbiota are the reduction of coliforms and Vibrionales bacteria, which include several potentially pathogenic species for fish, and the enrichment of gut microbiota composition with butyrate producer taxa. Therefore, these functional ingredients have a great potential to be used as health-promoting agents in the farming of European sea bass and other marine fish.
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Affiliation(s)
- Simona Rimoldi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Silvia Torrecillas
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Telde, Las Palmas, Canary Islands, Spain
| | - Daniel Montero
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Telde, Las Palmas, Canary Islands, Spain
| | - Elisabetta Gini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Alex Makol
- Delacon Biotechnik GmbH, Steyregg, Austria
| | | | - Marisol Izquierdo
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, Telde, Las Palmas, Canary Islands, Spain
| | - Genciana Terova
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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54
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Pereira SA, Jesus GFA, Pereira GV, Silva BC, Sá LS, Martins ML, Mouriño JLP. The Chelating Mineral on Organic Acid Salts Modulates the Dynamics and Richness of the Intestinal Microbiota of a Silver Catfish Rhamdia quelen. Curr Microbiol 2020; 77:1483-1495. [PMID: 32236647 DOI: 10.1007/s00284-020-01962-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/21/2020] [Indexed: 02/01/2023]
Abstract
The aim of this study was to evaluate the influence of the chelating mineral on propionic acid, calcium or sodium on the composition, dynamics and richness of the intestinal microbiota of a native silver catfish Rhamdia quelen through high-throughput sequencing (HTS). A total of 225 fish (8.43 ± 0.18 g) were distributed in tanks, 15 fish per tank in five groups with three replicates each: Control, Ca-propionate 0.25% (Ca0.25%) Ca-propionate 1% (Ca1%), Na-propionate 0.25% (Na0.25%) and Na-propionate 1% (Na1%). The feed was provided four times a day for 60 days. After experimental period, the fish were fasted for 24 h and the intestine was aseptically collected, pooled by treatment, and fixed in pure absolute ethanol for subsequent DNA extraction and HTS. The HTS showed that the supplementation of the propionic acid chelated to the mineral calcium or sodium in the different concentrations increased the operational taxonomic units and richness in comparison to control group. The main phyla found were Fusobacteria, Firmicutes, Proteobacteria and Bacteroides. Both the fusobacteria and the genus Cetobacterium, especially C. somerae, were positively modulated with Ca0.25% and Na1% supplementation. It can be emphasized that supplementation with calcium or sodium propionate at different concentrations changed the natural microbiota of R. quelen.
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Affiliation(s)
- Scheila A Pereira
- AQUOS - Aquatic Organisms Health Laboratory, Aquaculture Department, Federal University of Santa Catarina (UFSC), Rod. Admar Gonzaga 1346, Florianópolis, SC, 88040-900, Brazil.
| | - Gabriel F A Jesus
- AQUOS - Aquatic Organisms Health Laboratory, Aquaculture Department, Federal University of Santa Catarina (UFSC), Rod. Admar Gonzaga 1346, Florianópolis, SC, 88040-900, Brazil
| | - Gabriella V Pereira
- Fish Nutrition and Health Research Group, School of Biological Sciences, Faculty of Science and Environment, Plymouth University, Plymouth, UK
| | - Bruno C Silva
- EPAGRI - Company of Agricultural Research and Rural Extension of Santa Catarina, Rua Joaquim Garcia, s/n, Camboriú, SC, 88340-000, Brazil
| | - Lúvia S Sá
- AQUOS - Aquatic Organisms Health Laboratory, Aquaculture Department, Federal University of Santa Catarina (UFSC), Rod. Admar Gonzaga 1346, Florianópolis, SC, 88040-900, Brazil
| | - Maurício L Martins
- AQUOS - Aquatic Organisms Health Laboratory, Aquaculture Department, Federal University of Santa Catarina (UFSC), Rod. Admar Gonzaga 1346, Florianópolis, SC, 88040-900, Brazil
| | - José L P Mouriño
- AQUOS - Aquatic Organisms Health Laboratory, Aquaculture Department, Federal University of Santa Catarina (UFSC), Rod. Admar Gonzaga 1346, Florianópolis, SC, 88040-900, Brazil
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Horlick J, Booth MA, Tetu SG. Alternative dietary protein and water temperature influence the skin and gut microbial communities of yellowtail kingfish ( Seriola lalandi). PeerJ 2020; 8:e8705. [PMID: 32219022 PMCID: PMC7085898 DOI: 10.7717/peerj.8705] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/06/2020] [Indexed: 01/21/2023] Open
Abstract
Fish skin and gut microbiomes contribute to host health and growth and are often significantly different in aquaculture-reared fish compared to wild fish. Determining how factors associated with aquaculture, including altered diet and abiotic conditions, affect the microbiome will assist with optimizing farming practices and non-invasively assessing fish health. Here, juvenile yellowtail kingfish (Seriola lalandi) housed at optimal (22 °C) and non-optimal (26 °C) water temperature were fed a fishmeal control diet or the same diet substituted with 30% soy-protein concentrate (SPC) in order to investigate impacts on host health and the microbial community composition of the skin mucosa, gut mucosa and digesta. Each of these sites was observed to have a distinct microbiome composition. The combination of SPC and housing at 26 °C significantly reduced weight gain in yellowtail kingfish and affected immune parameters. The overall microbial composition and relative abundance of specific operational taxonomic units (OTUs) was also significantly altered by inclusion of SPC at 26 °C, with a notable increase in an OTU identified as Photobacterium in the skin mucosa and digesta. Increased relative abundance of Photobacterium sp. was significantly correlated with reduced levels of digesta myeloperoxidase in yellowtail kingfish; a recognized innate immunity defense mechanism. The changes in the microbial communities of yellowtail kingfish fed a diet containing 30% SPC at 26 °C highlights the importance of considering the interactive effects of diet and environmental factors on microbiome health in farmed yellowtail kingfish.
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Affiliation(s)
- Jack Horlick
- Department of Molecular Science, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Mark A Booth
- NSW Department of Primary Industries, Port Stephens Fisheries Institute, Nelson Bay, NSW, Australia
| | - Sasha G Tetu
- Department of Molecular Science, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
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56
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Dulski T, Kozłowski K, Ciesielski S. Habitat and seasonality shape the structure of tench (Tinca tinca L.) gut microbiome. Sci Rep 2020; 10:4460. [PMID: 32157130 PMCID: PMC7064478 DOI: 10.1038/s41598-020-61351-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/26/2020] [Indexed: 02/06/2023] Open
Abstract
Tench (Tinca tinca L.) is one of the most valued species of the Cyprinidae. This species is commercially important and has been intensively domesticated in recent years. To avoid excessive production losses, the health of farm fish must be maintained. Characterization of the tench gut microbiome can help achieve this goal, as the gastrointestinal microbiome plays an important role in host health. As part of this characterization, investigating the influence of the environment and season will help to understand the interrelationship between host and gut microbiota. Therefore, our aim was to use high-throughput 16S rRNA gene amplicon sequencing to profile the gut microbiome of tench. We studied two populations in summer and autumn: wild tench living in a lake and tench living in a pond in a semi-intensive fish farm. We found that, in the gut microbiome of all fish, the most abundant phylum was Proteobacteria, followed by Firmicutes, Bacteroidetes and Actinobacteria. Together, these phyla constituted up to 90% of the microbial communities. The abundance of Candidatus Xiphinematobacter differed significantly between lake and pond fish in summer, but not in autumn. In pond tench, Methylobacterium abundance was significantly lower in summer than in autumn. Mean Shannon, Chao1 indices and observed OTU's indicated that microbial biodiversity was greater in the gut of lake fish than in that of pond fish. Beta-diversity analysis showed significant divergence between groups with both weighted and unweighted UniFrac distance matrices. Principal coordinates analysis revealed that more of the variance in microbial diversity was attributable to environment than to season. Although some of the diversity in lake tench gut microbiota could be attributable to feeding preferences of individual fish, our results suggest that environment is the main factor in determining gut microbiome diversity in tench.
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Affiliation(s)
- Tomasz Dulski
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.
| | - Krzysztof Kozłowski
- Department of Ichthyology and Aquaculture, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Slawomir Ciesielski
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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57
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Huang H, Zhou P, Chen P, Xia L, Hu S, Yi G, Lu J, Yang S, Xie J, Peng J, Ding X. Alteration of the gut microbiome and immune factors of grass carp infected with Aeromonas veronii and screening of an antagonistic bacterial strain (Streptomyces flavotricini). Microb Pathog 2020; 143:104092. [PMID: 32145322 DOI: 10.1016/j.micpath.2020.104092] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 12/11/2022]
Abstract
Aeromonas veronii is a widely distributed novel pathogen that can affect humans and animals, it can cause sepsis in fish with high mortality and serious economic losses to aquaculture. In the study, the gut microbiome of the infected and uninfected grass carp with Aeromonas veronii were analyzed probiotics and pathogenic bacteria by the Miseq high-throughput sequencing, the results showed that the infected fish were significantly higher in Proteobacteria, Firmicutes, Fusobacteria, and the immune factors in liver and kidney were up-regulated by qRT-PCR. In order to effectively inhibit the pathogen, we screened an actinomycete strain and had good antibacterial effect on Aeromonas veronii. The new antagonistic bacteria was named as Streptomyces flavotricini X101, the whole genome sequencing revealed that the metabolic process was most active. After grass carp was inoculated with the minimum inhibitory concentration of 900 μg/mL of the strain's fermentation supernatant, then Aeromonas veronii was injected, we found that the pathological symptoms such as body surface, anus and abdominal congestion were alleviated by H&E staining. Cellular experiments showed that it wasn't toxic to liver cells of grass carp. Overall, this is the first study of changes in intestinal flora, phenotype, and immune factors in grass crap infected with Aeromonas veronii, it had important theoretical significance and application value for immunization and prevention.
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Affiliation(s)
- Haiyan Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Pengji Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Pei Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Liqiu Xia
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Shengbiao Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Ganfeng Yi
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Jiaoyang Lu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Shuqing Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Junyan Xie
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Jinli Peng
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Xuezhi Ding
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
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Characterization of the gut microbiome of black-necked cranes (Grus nigricollis) in six wintering areas in China. Arch Microbiol 2020; 202:983-993. [PMID: 31901964 DOI: 10.1007/s00203-019-01802-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/12/2019] [Accepted: 12/21/2019] [Indexed: 12/18/2022]
Abstract
The black-necked crane (Grus nigricollis) is a vulnerable species, breeding exclusively on the high-altitude wetlands of the Qinghai-Tibet Plateau. Bird species harbor diverse communities of microorganisms within their gastrointestinal tracts, which have important roles in the health, nutrition, and physiology of birds. Hitherto, virtually nothing was known about the gut microbial communities associated with wild black-necked cranes. For the first time, this study characterized the gut microbial community compositions, diversity, and functions of black-necked cranes from six wintering areas in China using the Illumina Miseq platform. The taxonomic results revealed that Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the four most abundant phyla in the gut of black-necked cranes. At the genus level, 11 genera including Lactobacillus, Pseudomonas, Carnobacterium, Pantoea, Enterococcus, Erwinia, Turicibacter, Bacillus, Phenylobacterium, Sanguibacter, and Psychrobacter were dominant. The differences in the gut microbial community alpha and the beta diversities of black-necked cranes among the six wintering areas were investigated. Furthermore, the representative microbial taxa and their predicted functions in each wintering location were also determined. These data represent the first analysis of the gut microbiome of black-necked cranes, providing a baseline for further microbiological studies and a foundation for the conservation of this bird.
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Zheng Y, Hu G, Wu W, Qiu L, Bing X, Chen J. Time-dependent gut microbiota analysis of juvenile Oreochromis niloticus by dietary supplementation of resveratrol. Arch Microbiol 2019; 202:43-53. [PMID: 31463601 DOI: 10.1007/s00203-019-01712-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/24/2019] [Accepted: 07/31/2019] [Indexed: 02/07/2023]
Abstract
To evaluate the changes in bacterial diversity at various time points under resveratrol supplementation, we aimed to investigate the diversification of gut microbiota and the changes in total genetic diversity. We performed 16S rDNA gene sequencing at different time points (15, 30, and 45 days) to analyze the gut microbiota of tilapia. Fusobacteria, Proteobacteria, and Bacteroidetes (15 days) or Cyanobacteria (30 and 45 days) were found to be the three most abundant phyla. Cyanobacteria (15 and 30 days), Proteobacteria (15 days), Firmicutes and Chlamydiae (30 and 45 days), Planctomycetes (30 days), Bacteroidetes, Actinobacteria, and Fusobacteria (45 days) in the 0.05 g/kg RES group increased as compared to that in the controls. Proteobacteria and Cyanobacteria significantly decreased and increased at 30 and 45 days, respectively, while the reverse pattern was observed at 15 days. The Bacteroidetes:Firmicutes and Proteobacteria:Cyanobacteria ratios were significantly increased (15 and 45 days, P < 0.05) and decreased (30 days, P < 0.05). RES supplementation did not affect the richness and diversity of the gut microbiota in tilapia. Our findings may contribute to the development of strategies for the management of diseases.
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Affiliation(s)
- Yao Zheng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, People's Republic of China
| | - Gengdong Hu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, People's Republic of China
| | - Wei Wu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, People's Republic of China
| | - Liping Qiu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, People's Republic of China
| | - Xuwen Bing
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, People's Republic of China.
| | - Jiazhang Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Environmental Factors (Wuxi), Ministry of Agriculture, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, People's Republic of China. .,Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture, Beijing, 100141, People's Republic of China.
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60
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Foysal MJ, Fotedar R, Tay CY, Gupta SK. Dietary supplementation of black soldier fly ( Hermetica illucens) meal modulates gut microbiota, innate immune response and health status of marron ( Cherax cainii, Austin 2002) fed poultry-by-product and fishmeal based diets. PeerJ 2019; 7:e6891. [PMID: 31149398 PMCID: PMC6534111 DOI: 10.7717/peerj.6891] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/01/2019] [Indexed: 12/15/2022] Open
Abstract
The present study aimed to evaluate the dietary supplementary effects of black soldier fly (Hermetia illucens) (BSF) meal on the bacterial communities in the distal gut, immune response and growth of freshwater crayfish, marron (Cherax cainii) fed poultry-by-product meal (PBM) as an alternative protein source to fish meal (FM). A total of 64 marron were randomly distributed into 16 different tanks with a density of four marron per tank. After acclimation, a 60-days feeding trial was conducted on marron fed isonitrogenouts and isocalorific diets containing protein source from FM, PBM, and a combination of FM + BSF and PBM + BSF. At the end of the trial, weight gain and growth of marron were found independent of any dietary treatment, however, the two diets supplemented with BSF significantly (P < 0.05) enhanced haemolymph osmolality, lysozyme activity, total haemocyte counts, and protein and energy contents in the tail muscle. In addition, the analysis of microbiota and its predicted metabolic pathways via 16s rRNA revealed a significantly (P < 0.05) higher bacterial activity and gene function correlated to biosynthesis of protein, energy and secondary metabolites in PBM + BSF than other dietary groups. Diets FM + BSF and PBM + BSF were seen to be associated with an up-regulation of cytokine genes in the intestinal tissue of marron. Overall, PBM + BSF diet proved to be a superior diet in terms of improved health status, gut microbiota and up-regulated expression of cytokine genes for marron culture.
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Affiliation(s)
- Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,Department of Genetic Engineering and Biotechnology, Shahjalal University of Science & Technology, Sylhet, Bangladesh
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Chin-Yen Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Sanjay Kumar Gupta
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
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61
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Gómez B, Munekata PES, Zhu Z, Barba FJ, Toldrá F, Putnik P, Bursać Kovačević D, Lorenzo JM. Challenges and opportunities regarding the use of alternative protein sources: Aquaculture and insects. ADVANCES IN FOOD AND NUTRITION RESEARCH 2019; 89:259-295. [PMID: 31351528 DOI: 10.1016/bs.afnr.2019.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The world population is constantly growing so that the needs of food, including protein sources, will also increase considerably in the coming years. Animal farming has been related to numerous environmental consequences such as soil erosion, exaggerated water consumption, generation of large quantities of waste and accumulation of greenhouse gases. This is a situation that demonstrates the suitability and importance of finding more sustainable protein alternatives without losing the quality and the nutritional benefits of current common protein sources. In this context, it is worth highlighting the potential of insects and products derived from aquaculture. Particularly, farmed aquatic food products can reduce the impact on wild fish stocks, whose overfishing may end up in an ecological collapse, and insects are easy to be reared and efficient in converting feed into biomass. However, there are still several challenges like the need to adapt technologies and methods for the production and well-characterization of the new ingredients, careful evaluation of the introduction of such new proteins in the diet and its safety of use, including potential allergies, and the acceptance by consumers.
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Affiliation(s)
- Belén Gómez
- Centro Tecnológico de la Carne de Galicia, Ourense, Spain
| | - Paulo E S Munekata
- Centro Tecnológico de la Carne de Galicia, Ourense, Spain; Department of Food Engineering, College of Animal Science and Food Engineering, University of São Paulo, São Paulo, Brazil
| | - Zhenzhou Zhu
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Francisco J Barba
- Nutrition and Food Science Area, Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine Department, Faculty of Pharmacy, Universitat de València, València, Spain.
| | - Fidel Toldrá
- Instituto de Agroquímica y Tecnología de Alimentos (CSIC), Valencia, Spain
| | - Predrag Putnik
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | | | - José M Lorenzo
- Centro Tecnológico de la Carne de Galicia, Ourense, Spain.
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The Effects of Dietary Insect Meal from Hermetia illucens Prepupae on Autochthonous Gut Microbiota of Rainbow Trout ( Oncorhynchus mykiss). Animals (Basel) 2019; 9:ani9040143. [PMID: 30987067 PMCID: PMC6523354 DOI: 10.3390/ani9040143] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 01/06/2023] Open
Abstract
This study evaluated the effects of dietary insect meal from Hermetia illucens larvae on autochthonous gut microbiota of rainbow trout (Oncorhynchus mykiss). Three diets, with increasing levels of insect meal inclusion (10%, 20%, and 30%) and a control diet without insect meal were tested in a 12-week feeding trial. To analyze the resident intestinal microbial communities, the Illumina MiSeq platform for sequencing of 16S rRNA gene and QIIME pipeline were used. The number of reads taxonomically classified according to the Greengenes database was 1,514,155. Seventy-four Operational Taxonomic Units (OTUs) at 97% identity were identified. The core of adhered intestinal microbiota, i.e., OTUs present in at least 80% of mucosal samples and shared regardless of the diet, was constituted by three OTUs assigned to Propiobacterinae, Shewanella, and Mycoplasma genera, respectively. Fish fed the insect-based diets showed higher bacterial diversity with a reduction in Proteobacteria in comparison to fish fed the fishmeal diet. Insect-meal inclusion in the diet increased the gut abundance of Mycoplasma, which was attributed the ability to produce lactic and acetic acid as final products of its fermentation. We believe that the observed variations on the autochthonous intestinal microbiota composition of trout are principally due to the prebiotic properties of fermentable chitin.
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63
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Effect of Dietary Carbohydrate-to-Protein Ratio on Gut Microbiota in Atlantic Salmon ( Salmo salar). Animals (Basel) 2019; 9:ani9030089. [PMID: 30862122 PMCID: PMC6466077 DOI: 10.3390/ani9030089] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Carbohydrates, in the form of energy reserve polysaccharides, are major food components that supply low-cost energy in farm animal feed formulation. Most of these compounds are obtained from plant ingredients (i.e., cereal grains). As the aquaculture industry moves towards formulating marine-derived ingredients free diets, the inclusion of plant ingredients is expected to continuously increase, and thus the amount of carbohydrates in aquafeed formulation will increase as well. Carnivorous fish, including salmonids, show a slow blood glucose clearance rate and suboptimal growth performance when fed rich carbohydrate meals. The role of gut microbial communities on carbohydrate utilization has been poorly explored in salmonids. Hence, we conducted an experiment to evaluate the effect of feeding a high carbohydrate diet to Atlantic salmon (Salmo salar) on gut microbiota composition. Our results suggest increasing the level of digestible carbohydrate mostly affects low-abundance bacteria in favor of those capable of using carbohydrates as a major energy-yielding substrate. Further study for a better understanding of the role of gut microbiota in carbohydrate utilization in carnivorous fish is required. Abstract Atlantic salmon (Salmo salar) is a carnivorous fish species whose productive performance tends to be suboptimal when fed low-cost carbohydrate rich meals. It is of interest to study the dynamics of gut microbiota communities in salmonids fed high carbohydrate diets since gut microbes are referred to as key players that influence the metabolism and physiology of the host. A study was conducted to determine the effect of feeding a high carbohydrate diet to Atlantic salmon in gut microbiota communities. A medium carbohydrate (15% wheat starch)/medium protein (MC/MP) diet or a high carbohydrate (30% wheat starch)/low protein (HC/LP) diet was fed to triplicate tanks (28 fish each) during four weeks. We conducted an in-depth characterization of the distal intestine digesta microbiota using high-throughput sequencing of the V4 region of the 16S rRNA gene. Firmicutes, Actinobacteria and Proteobacteria were the major phyla determined in either experimental group. Phylum Planctomycetes, class Planctomycetia, order Planctomycetales and genus Lactococcus were significantly more abundant in fish fed the HC/LP diet compared with fish fed the MC/MP diet. Our study suggests feeding a carbohydrate rich meal to salmon exerts a low impact on the structure of gut microbial communities, affecting mostly low-abundance bacteria capable of metabolizing anaerobically carbohydrates as a major energy-yielding substrate.
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Ringø E, Hoseinifar SH, Ghosh K, Doan HV, Beck BR, Song SK. Lactic Acid Bacteria in Finfish-An Update. Front Microbiol 2018; 9:1818. [PMID: 30147679 PMCID: PMC6096003 DOI: 10.3389/fmicb.2018.01818] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/19/2018] [Indexed: 12/17/2022] Open
Abstract
A complex and dynamic community of microorganisms, play important roles within the fish gastrointestinal (GI) tract. Of the bacteria colonizing the GI tract, are lactic acid bacteria (LAB) generally considered as favorable microorganism due to their abilities to stimulating host GI development, digestive function, mucosal tolerance, stimulating immune response, and improved disease resistance. In early finfish studies, were culture-dependent methods used to enumerate bacterial population levels within the GI tract. However, due to limitations by using culture methods, culture-independent techniques have been used during the last decade. These investigations have revealed the presence of Lactobacillus, Lactococcus, Leuconostoc, Enterococcus, Streptococcus, Carnobacterium, Weissella, and Pediococcus as indigenous species. Numerous strains of LAB isolated from finfish are able to produce antibacterial substances toward different potential fish pathogenic bacteria as well as human pathogens. LAB are revealed be the most promising bacterial genera as probiotic in aquaculture. During the decade numerous investigations are performed on evaluation of probiotic properties of different genus and species of LAB. Except limited contradictory reports, most of administered strains displayed beneficial effects on both, growth-and reproductive performance, immune responses and disease resistance of finfish. This eventually led to industrial scale up and introduction LAB-based commercial probiotics. Pathogenic LAB belonging to the genera Streptococcus, Enterococcus, Lactobacillus, Carnobacterium, and Lactococcus have been detected from ascites, kidney, liver, heart, and spleen of several finfish species. These pathogenic bacteria will be addressed in present review which includes their impacts on finfish aquaculture, possible routes for treatment. Finfish share many common structures and functions of the immune system with warm-blooded animals, although apparent differences exist. This similarity in the immune system may result in many shared LAB effects between finfish and land animals. LAB-fed fish show an increase in innate immune activities leading to disease resistances: neutrophil activity, lysozyme secretion, phagocytosis, and production of pro-inflammatory cytokines (IL-1β, IL-6, IL-8, and TNF-α). However, some LAB strains preferentially induces IL-10 instead, a potent anti-inflammatory cytokine. These results indicate that LAB may vary in their immunological effects depending on the species and hosts. So far, the immunological studies using LAB have been focused on their effects on innate immunity. However, these studies need to be further extended by investigating their involvement in the modulation of adaptive immunity. The present review paper focuses on recent findings in the field of isolation and detection of LAB, their administration as probiotic in aquaculture and their interaction with fish immune responses. Furthermore, the mode of action of probiotics on finfish are discussed.
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Affiliation(s)
- Einar Ringø
- Faculty of Bioscience, Fisheries and Economics, Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Seyed Hossein Hoseinifar
- Department of Fisheries, Faculty of Fisheries and Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Koushik Ghosh
- Aquaculture Laboratory, Department of Zoology, The University of Burdwan, Bardhaman, India
| | - Hien Van Doan
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
| | - Bo Ram Beck
- School of Life Science, Handong University, Pohang, South Korea
| | - Seong Kyu Song
- School of Life Science, Handong University, Pohang, South Korea
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Rimoldi S, Gliozheni E, Ascione C, Gini E, Terova G. Effect of a specific composition of short- and medium-chain fatty acid 1-Monoglycerides on growth performances and gut microbiota of gilthead sea bream ( Sparus aurata). PeerJ 2018; 6:e5355. [PMID: 30083467 PMCID: PMC6074759 DOI: 10.7717/peerj.5355] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 07/07/2018] [Indexed: 01/21/2023] Open
Abstract
In aquaculture research, one important aim of gut microbiota studies is to provide the scientific basis for developing effective strategies to manipulate gut microbial communities through the diet, promoting fish health and improving productivity. Currently, there is an increasing commercial and research interest towards the use of organic acids in aquafeeds, due to several beneficial effects they have on growth performance and intestinal tract's health of farmed fish. Among organic acids, monoglycerides of short-chain fatty acids (SCFAs) and medium-chain fatty acids (MCFAs) have attracted particular research attention also for their bacteriostatic and bactericidal properties. Accordingly, the present study aimed to evaluate the potential beneficial effects of SCFA and MCFA monoglycerides, used as a feed additive, on fish growth performance, and intestinal microbiota composition. For this purpose, a specific combination of short- and medium-chain 1-monoglycerides (SILOhealth 108Z) was tested in 600 juvenile gilthead sea bream (Sparus aurata) of about 60 g mean initial weight that were fed for 90 days with plant-based diets. Two isoproteic and isolipidic diets were formulated. The control fish group received a plant-based diet, whereas the other group received the same control feed, but supplemented with 0.5% of SILOhealth 108Z. The Illumina MiSeq platform for high-throughput amplicon sequencing of 16S rRNA gene and QIIME pipeline were used to analyse and characterize the whole microbiome associated both to feeds and S. aurata intestine. The number of reads taxonomically classified according to the Greengenes database was 394,611. We identified 259 OTUs at 97% identity in sea bream fecal samples; 90 OTUs constituted the core gut microbiota. Firmicutes, Proteobacteria and Actinobacteria represented the dominant phyla in both experimental groups. Among them, relative abundance of Firmicutes and Proteobacteria were positively and negatively affected by dietary SCFA monoglycerides supplementation, respectively. In summary, our findings clearly indicated that SILOhealth 108Z positively modulated the fish intestinal microbiota by increasing the number of beneficial lactic acid bacteria, namely, Lactobacillus, and reducing Gammaproteobacteria, which include several potential pathogenic bacteria. The specific composition of 1-monoglycerides of short- and medium-chain fatty acids contained in SILOhealth 108Z could thus have a great potential as a feed additive in aquaculture.
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Affiliation(s)
- Simona Rimoldi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Emi Gliozheni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Chiara Ascione
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elisabetta Gini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Genciana Terova
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Inter-University Centre for Research in Protein Biotechnologies, “The Protein Factory”, Polytechnic University of Milan and University of Insubria, Varese, Italy
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