Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes

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. Betadiversity 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.

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Habitat and seasonality shape the structure of tench (Tinca tinca L.) gut microbiome

Dulski

Kozłowski

Ciesielski

2020

“…The enriched bacteria at genus level in the probiotic fed marron can be correlated with better growth and immune performance and water quality from previous studies. For instances, Pirellula abundance was found correlated to essential amino acids such as isoleucine, leucine and valine production in grass carp (Ctenopharyngodon idellus) and blunt snout bream (Megalobrama amblycephala) 34 . Another genus Reyranella that is phylogenetically very close to Rhodospirillaceae, also reported to play a crucial role in nitrate reduction from soil and freshwater 60,61 .…”

Section: Discussionmentioning

confidence: 99%

Lactobacillus acidophilus and L. plantarum improve health status, modulate gut microbiota and innate immune response of marron (Cherax cainii)

Foysal

Fotedar

Siddik

et al. 2020

This study aimed to investigate the combined effects of two most potent probiotic bacteria Lactobacillus acidophilus and Lactobacillus plantarum on overall health and immune status of freshwater crayfish, marron under laboratory conditions. A total of 36 marron were distributed into six different tanks and two different feeding groups, control and probiotic-fed group. After acclimation, control group was fed with basal diet while probiotic group was fed 10 9 cfU/mL per kg of bacterial supplemented feed for 60 days. The results showed no significant differences in weight gain, however, probiotic feed significantly enhanced some hemolymph parameters and biochemical composition of tail muscle. Histology data revealed better hepatopancreas health and higher microvilli counts in the marron gut fed probiotic diet. The probiotic bacteria triggered significant shift of microbial communities at different taxa level, mostly those reported as beneficial for crayfish. The probiotic diet also enriched the metabolic functions and genes associated with innate immune response of crayfish. Further correlation analysis revealed significant association of some taxa with increased activity for hemolymph and immune genes. therefore, dietary Lactobacillus supplementation can modulate the overall health and immunity as well as gut microbial composition and interaction network between gut microbiota and immune system in crayfish. Aquaculture has become an important food sector for meeting the overall protein demand for growing population. The global consumption of crustaceans has increased greatly and especially those with live transport abilities are increasingly becoming popular 1-3. Marron (Cherax cainni) is one of the largest freshwater crayfish farmed in Western Australia (WA) that has high nutritive value and widespread consumer preferences 4,5. In addition, long distance live transportation ability of marron further increases its international demand, and thus has become an ideal crayfish species for commercial farming 6,7. However, the production of marron in WA has remained stagnant for a long time 7. Selection of proper diets and maintaining the optimum water quality are the two most crucial factors required for marron farming 5,7. Although no disease outbreaks have yet been reported, the interest and intend of intensification in marron farming can expose marron to possible crayfish pathogens including Vibrio, Aeromonas and Rhodobacter 5,6. In the past, several laboratory based trials have been conducted 3,6-9 , however, finding a suitable diet and identifying the beneficial bacteria that potentially can influence the growth and immune performance of marron has still remained unknown. Towards sustainable development of aquaculture, the use of feed additives including probiotics, prebiotics, synbiotics, parabiotics and phytogenics in crustacean's diet to boost biological indices has gained extensive attention from the researchers and farmers. Probiotics are microorganisms associated with health and immune benefits for the host ...

“…DNA was isolated and purified using an E.Z.N.A. ® Stool DNA Kit (Omega Bio-tek, Norcross, GA, U.S.) according to the manufacturer's protocols 56 . The DNA quality and concentration were checked on a 1.0% agarose gel after electrophoresis and a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, United States), respectively.…”

Section: Dna Extraction and Pcr Amplificationmentioning

confidence: 99%

Distinct microbial communities among different tissues of citrus tree Citrus reticulata cv. Chachiensis

et al. 2020

Plant microbiota colonize all organs of a plant and play crucial roles including supplying nutrients to plants, stimulating seed germination, promoting plant growth, and defending plants against biotic and abiotic stress. Because of the economic importance, interactions between citrus and microbes have been studied relatively extensively, especially citrus-pathogen interactions. However, the spatial distribution of microbial taxa in citrus trees remains under-studied. In this study, Citrus reticulata cv. Chachiensis was examined for the spatial distribution of microbes by sequencing 16S rRNA genes. More than 2.5 million sequences were obtained from 60 samples collected from soil, roots, leaves, and phloem. The dominant microbial phyla from all samples were Proteobacteria, Actinobacteria and Acidobacteria. The composition and structure of microbial communities in different samples were analyzed by PCoA, CAP, Anosim and MRPP methods. Variation in microbial species between samples were analyzed and the indicator microbes of each sample group were identified. Our results suggested that the microbial communities from different tissues varied significantly and the microenvironments of tree tissues could affect the composition of its microbial community.www.nature.com/scientificreports www.nature.com/scientificreports/ trees 23 . Most previous investigation on citrus-associated microbiomes are analyses on huanglongbing-infected, or specially-treated samples [24][25][26][27][28][29] .Citrus reticulata cv. Chachiensis is an important citrus variety widely cultivated around the world and the orange peel of the fruit was regarded as the valuable material which could be processed as food, tea drinks, and seasoning 30 . Besides, the orange peel owned antioxidant properties and extremely high medicinal value was also used as herb-medicine 31 . In China, C. reticulata cv. Chachiensis has grown in Xinhui District, Jiangmen City, Guangdong Province was considered as one of the most important cash crops for locals and the orange peel named genuine Pericarpium Citri Reticulatae (Guang Chen Pi) was admired as the best Chen pi which possesses the excellent clinical efficacy 32 . Plant-related microorganisms could protect the host from pathogens and pests, help plants use nutrients, and improve plant stress resistance 33 , while the microbial community of C. reticulata cv. Chachiensis remains unknown. In this study, endosphere microbiomes in soils, roots, leaves, and phloem of C. reticulata cv. Chachiensis were systematically investigated by sequencing 16S rRNA genes. The composition and structure of the microbial community in different tissues were performed by PCoA, CAP, Anosim and MRPP methods. Variation in microbial compositions among citrus tissues were analyzed and indicator microbes for different samples were identified. Our results suggested that the microbial community from different tissues of C. reticulata cv. Chachiensis in south china varied significantly. Our results laid a foundation for future studies on microbial comm...