High Spatial and Temporal Variations of Microbial Community along the Southern Catfish Gastrointestinal Tract: Insights into Dynamic Food Digestion

Abstract

The fish intestinal microbiota is affected by dietary shifts or diet-related seasonal fluctuations making it highly variable and dynamic. It assists with the digestion and absorption of food that is a common, yet dynamic process. However, fundamental dynamics of microbial ecology associated with food digestion in intestine and stomach are poorly understood in fish. We selected the southern catfish, Silurus meridionalis, as the targeted species, owing to its foraging behavior with a large meal that can assure clear periodic rhythms in food digestion, to study spatial variations of the microbial community along the gastrointestinal (GI) tract. We further evaluated temporal microbial dynamics by collecting GI tract samples at time intervals 03, 12, and 24h after feeding. High-throughput sequencing results showed higher microbial diversity in the stomach than in the intestine and distinguishable community structures between stomach and intestine. Firmicutes were dominated by both Clostridium and unclassified Clostridiaceae, which was the most abundant taxon in the stomach, whereas Fusobacteria were dominated by Cetobacterium, which prevailed in the intestine. Firmicutes was significantly increased and Fusobacteria was decreased after feeding. Furthermore, inter-stomach microbial variability was greater than inter-intestine microbial variability. These results demonstrate that GI microbial assemblies are specific per anatomical site and are highly dynamic during food digestion, indicating that digestive status and/or sampling time are factors potentially influencing the microbial compositions. Furthermore, the finding of high spatial and temporal variations of the microbial community along the GI tract suggests limitations of single sampling regime to study food-derived microbial ecology.

Host Age Affects the Development of Southern Catfish Gut Bacterial Community Divergent From That in the Food and Rearing Water

“…This is in line with the result observed in juvenile southern catfish fed on the same diet from 18 to 33 days post-hatching, but differing from that in the adult fish collected from a natural lake (Yan et al, 2016 ). The high abundance of Cetobacterium OTUs was consistently found in the gut of several freshwater fish as well as on-growing zebrafish at the late age (Zac Stephens et al, 2016 ; Zhang et al, 2017 ). The discrepancies among studies further underline the importance and necessity of host developmental context in studying host microbiota and their responses to external factors (Goffredi et al, 2014 ).…”

Dietary Bile Salt Types Influence the Composition of Biliary Bile Acids and Gut Microbiota in Grass Carp

“…The fish were then euthanized, dissected, and gallbladder and hindgut content of each fish collected and stored at -80°C for the downstream use. All the samplings were done between 5 and 6 h after feeding in order to avoid the temporal variation of gut microbiota ( Zhang et al, 2017 ). All animal-handling procedures and experiments were reviewed and approved by the ethics committee of the Institute of Hydrobiology, Chinese Academy of Sciences.…”

“…We discarded seven bile samples which did not have enough bile, so only 56 bile samples (TCA fed group = 6, TCDCA fed group = 8, TUDCA fed group = 9, TLCA fed group = 8, TDCA fed group = 8, Chol = 9, and Ctrl = 8) were successfully processed. Ten BAs, including four primary: CA, taurocholic acid (TCA), chenodeoxycholic acid (CDCA), and taurochenodeoxycholic acid (TCDCA); four secondary: DCA, taurodeoxycholic acid (TDCA), lithocholic acid (LCA), and taurolithocholic acid (TLCA); as well as two non-classified BAs: ursodeoxycholic acid (UDCA) and tauroursodeoxycholic acid (TUDCA) were quantified in the bile samples of grass carp by high-performance liquid chromatography–mass spectrometry (HPLC-MS) as described before ( Zhang et al, 2017 ). Total BAs were calculated as the sum of the concentrations of all 10 measured BAs.…”

“…Grass carp ( Ctenopharyngodon idellus ), the major aquacultured species globally in terms of the total production output ( Faoro, 2015 ), often suffers functional disorder of liver and gallbladder, which is accompanied by the accumulation of lipids in liver and which can result in death ( Ni and Wang, 1999 ). It has also been reported that different diets produce distinct BA pools and gut microbiota profiles in grass carp ( Zhang et al, 2017 ). Herein, five different BS-supplemented diets, as well as one BA-chelating diet and one control diet (no BS added), were used to conduct the grass carp feeding trial.…”

The In Ovo Feeding Administration (Gallus Gallus)—An Emerging In Vivo Approach to Assess Bioactive Compounds with Potential Nutritional Benefits

“…It has been reported that the gut microbiome contains an estimated 3–8 million unique genes, which expands the genetic capacity of humans by >100-fold [ 101 ]. In recent years, it was demonstrated that the gut microbiome community participates in abundant bioactivities, such as the: (1) maturation and regulation of the immune system [ 102 ]; (2) digestion and release of essential nutrients [ 103 ]; (3) improvement of intestinal barrier function [ 90 ]; and the (4) potential inhibition of pathogenic bacteria [ 90 ].…”