Comprehensive functional core microbiome comparison in genetically obese and lean hosts under the same environment

Correlated Responses to Selection for Intramuscular Fat on the Gut Microbiome in Rabbits

Intramuscular fat (IMF) content is important for meat production and human health, where the host genetics and its microbiome greatly contribute to its variation. The aim of this study is to describe the consequences of the genetic modification of IMF by selecting the taxonomic composition of the microbiome, using rabbits from the 10th generation of a divergent selection experiment for IMF (high (H) and low (L) lines differ by 3.8 standard deviations). The selection altered the composition of the gut microbiota. Correlated responses were better distinguished at the genus level (51 genera) than at the phylum level (10 phyla). The H-line was enriched in Hungateiclostridium, Limosilactobacillus, Legionella, Lysinibacillus, Phorphyromonas, Methanosphaera, Desulfovibrio, and Akkermansia, while the L-line was enriched in Escherichia, Methanobrevibacter, Fonticella, Candidatus Amulumruptor, Methanobrevibacter, Exiguobacterium, Flintibacter, and Coprococcus, among other genera with smaller line differences. A microbial biomarker generated from the abundance of four of these genera classified the lines with 78% accuracy in a logit regression. Our results demonstrate different gut microbiome compositions in hosts with divergent IMF genotypes. Furthermore, we provide a microbial biomarker to be used as an indicator of hosts genetically predisposed to accumulate muscle lipids, which opens up the opportunity for research to develop probiotics or microbiome-based breeding strategies targeting IMF.

Plasma metabolomic profiling in two rabbit lines divergently selected for intramuscular fat content

This study provides a thorough comparison of the plasma metabolome of two rabbit lines divergently selected for intramuscular fat content (IMF). The divergent selection led to a correlated response in the overall adiposity, turning these lines into a valuable animal material to study also the genetics of obesity. Over 900 metabolites were detected, and the adjustment of multivariate models, both discriminant and linear, allowed to identify 322 with differential abundances between lines, which also adjusted linearly to the IMF content. The most affected pathways were those of lipids and amino acids, with differences between lines ranging from 0.23 to 6.04 standard deviations, revealing a limited capacity of the low-IMF line to obtain energy from lipids, and a greater branched-chain amino acids catabolism in the high-IMF line related to its increased IMF content. Additionally, changes in metabolites derived from microbial activity supported its relevant role in the lipid deposition. Future research will focus on the analysis of the metabolomic profile of the cecum content, and on the integration of the several -omics datasets available for these lines, to help disentangle the host and microbiome biological mechanisms involved in the IMF deposition.

Gut microbiome-based strategies for host health and disease

Host health and disease are influenced by changes in the abundance and structure of intestinal flora. Current strategies are focused on regulating the structure of intestinal flora to ensure host health by alleviating disease. However, these strategies are limited by multiple factors, such as host genotype, physiology (microbiome, immunity, and gender), intervention, and diet. Accordingly, we reviewed the prospects and limitations of all strategies regulating the structure and abundance of microflora, including probiotics, prebiotics, diet, fecal microbiota transplantation, antibiotics, and phages. Some new technologies that can improve these strategies are also introduced. Compared with other strategies, diets and prebiotics are associated with reduced risk and high security. Besides, phages have the potential for application in the targeted regulation of intestinal microbiota due to their high specificity. Notably, the variability in individual microflora and their metabolic response to different interventions should be considered. Future studies should use artificial intelligence combined with multi-omics to investigate the host genome and physiology based on factors, such as blood type, dietary habits, and exercise, in order to develop individualized intervention strategies to improve host health.

Different microbial genera drive methane emissions in beef cattle fed with two extreme diets

The ratio of forage to concentrate in cattle feeding has a major influence on the composition of the microbiota in the rumen and on the mass of methane produced. Using methane measurements and microbiota data from 26 cattle we aimed to investigate the relationships between microbial relative abundances and methane emissions, and identify potential biomarkers, in animals fed two extreme diets - a poor quality fresh cut grass diet (GRASS) or a high concentrate total mixed ration (TMR). Direct comparisons of the effects of such extreme diets on the composition of rumen microbiota have rarely been studied. Data were analyzed considering their multivariate and compositional nature. Diet had a relevant effect on methane yield of +10.6 g of methane/kg of dry matter intake for GRASS with respect to TMR, and on the centered log-ratio transformed abundance of 22 microbial genera. When predicting methane yield based on the abundance of 28 and 25 selected microbial genera in GRASS and TMR, respectively, we achieved cross-validation prediction accuracies of 66.5 ± 9% and 85 ± 8%. Only the abundance of Fibrobacter had a consistent negative association with methane yield in both diets, whereas most microbial genera were associated with methane yield in only one of the two diets. This study highlights the stark contrast in the microbiota controlling methane yield between animals fed a high concentrate diet, such as that found on intensive finishing units, and a low-quality grass forage that is often found in extensive grazing systems. This contrast must be taken into consideration when developing strategies to reduce methane emissions by manipulation of the rumen microbial composition.

Intramuscular Fat Selection in Rabbits Modifies the Fatty Acid Composition of Muscle and Liver Tissues

Simple Summary

Intramuscular fat content improves the juiciness, tenderness, and flavor of meat, but it can also affect its nutritional quality. A divergent selection experiment for intramuscular fat content was performed on rabbits for 10 generations to study the metabolism of the selected and correlated traits. The direct response to selection and the correlated responses in the meat fatty acid content, in the liver fat and its fatty acid content, and in plasma metabolic markers related to liver metabolism were studied. Increasing intramuscular fat content led to higher fat deposition in the carcass, but not in the liver. The fatty acid contents of Longissimus thoracis et lumborum muscle and liver were modified after selection, for which the microbiome composition also played an important role. A higher concentration of plasma lipids was found in the low-IMF line, probably due to a lower uptake by the muscle and adipose tissue.

Abstract

This study was conducted on two rabbit lines divergently selected for intramuscular fat (IMF) content in the Longissimus thoracis et lumborum (LTL) muscle. The aim was to estimate the direct response to selection for IMF after 10 generations, and the correlated responses in carcass quality traits, meat fatty acid content, liver fat and its fatty acid content, and in plasma metabolic markers related to liver metabolism. Selection for IMF content was successful, showing a direct response equivalent to 3.8 SD of the trait after 10 generations. The high-IMF line (H) showed a greater dissectible fat percentage than the low-IMF line (L), with a relevant difference (D_H-L = 0.63%, P_r = 1). No difference was found in liver fat content (D_H-L = −0.04, P₀ = 0.62). The fatty acid content of both LTL muscle and liver was modified after selection. The LTL muscle had greater saturated (SFA; D_H-L = 5.05, P_r = 1) and monounsaturated fatty acids (MUFA; D_H-L = 5.04, P_r = 1) contents in the H line than in the L line. No relevant difference was found in polyunsaturated fatty acids content (PUFA; P_r = 0.05); however, greater amounts of C18:2n6 (D_H-L = 3.03, P_r = 1) and C18:3n3 (D_H-L = 0.56, P_r = 1) were found in the H than in the L line. The liver presented greater MUFA (D_H-L = 1.46) and lower PUFA (D_H-L = −1.46) contents in the H than in the L line, but the difference was only relevant for MUFA (P_r = 0.86). The odd-chain saturated fatty acids C15:0 and C17:0 were more abundant in the liver of the L line than in the liver of the H line (D_H-L = −0.04, P_r = 0.98 for C15:0; D_H-L = −0.09, P_r = 0.92 for C17:0). Greater concentrations of plasma triglycerides (D_H-L = −34) and cholesterol (D_H-L = −3.85) were found in the L than in the H line, together with greater plasma concentration of bile acids (D_H-L = −2.13). Nonetheless, the difference was only relevant for triglycerides (P_r = 0.98).

Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development

Animal microbiomes are occasionally considered as an extension of host anatomy, physiology, and even their genomic architecture. Their compositions encompass variable and constant portions when examined across multiple hosts. The latter, termed the core microbiome, is viewed as more accommodated to its host environment and suggested to benefit host fitness. Nevertheless, discrepancies in its definitions, characteristics, and importance to its hosts exist across studies. We survey studies that characterize the core microbiome, detail its current definitions and available methods to identify it, and emphasize the crucial need to upgrade and standardize the methodologies among studies. We highlight ruminants as a case study and discuss the link between the core microbiome and host physiology and genetics, as well as potential factors that shape it. We conclude with main directives of action to better understand the host-core microbiome axis and acquire the necessary insights into its controlled modulation. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.