Microbiome and Metabolome Analyses in Different Closed-Circulation Aquarium Systems and Their Network Visualization

Abstract

Understanding the causes of microbiome formation and its relationship to environmental conditions is important to properly maintain recirculating aquaculture systems (RASs). Although RAS has been applied to numerous fish types and environmental conditions (e.g., loading intensity), the effects of these environmental conditions (i.e., fish type and loading intensity) on microbiome composition are limitedly known. Therefore, we established three experimental aquarium tanks to explore the effects of fish type, loading intensity, filter pore size, and rearing day on microbiome compositions: (1) a tank for Acanthogobius flavimanus , (2) for Girella punctata , and (3) for G. punctata with higher loading intensity. Multivariate analysis showed that the microbial community composition differed among the tanks, indicating that the fish type and loading intensity significantly affected microbiome formation in rearing water. Some microbes, such as Sediminicola and Glaciecola , were detected at a higher loading intensity, indicating that these microbes might be an indicator of eutrophic conditions in the aquacultural systems. In addition, a partial correlation network revealed a connection between microbes and metabolites in the aquarium tanks. Such a microbe–metabolite network might be a clue to control the microbiome by adjusting the molecule abundance in the aquacultural environment.

An evaluation of homeostatic plasticity for ecosystems using an analytical data science approach

“…Moreover, 1 H NMR and machine learning extreme gradient boosting (XGBoost) has also been used to understand the mechanism of membrane fouling (reduction in membrane permeability), which is a problem in membrane bioreactors (MBRs), an essential part of wastewater treatment operations [99] . Changes in the nature of membrane fouling material as a function of conditions have been investigated using NMR data [100] .…”

Comparison of the gut microbiota and untargeted gut tissue metabolome of Chinese mitten crabs (Eriocheir sinensis) with different shell colors

“…Therefore, many studies have focused on E. sinensis metabolome variations related to food, disease, and the environment ( Chen et al, 2021b ; Guo et al, 2022 ; Jiang et al, 2022 ). In aquatic animals, integrative analysis of the microbiota and metabolome has been utilized to investigate alterations in the physiological status of hosts related to differences in nutrition intake ( Chen et al, 2021b ), habitats ( Chen et al, 2021a ), growth performance ( Uengwetwanit et al, 2020 ; Lan et al, 2023 ), and aquaculture systems ( Ding et al, 2022 ; Yokoyama et al, 2022 ).To our knowledge, there has been no metabolomic study related to the different shell colors of E. sinensis thus far. In this study, we investigated the gut microbiota and metabolomes of the gut tissue of juvenile RH and GH crabs.…”