Gastrointestinal Microbiome in Animals

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Veterinary Microbiology".

Deadline for manuscript submissions: closed (31 October 2023) | Viewed by 11826

Special Issue Editor


E-Mail Website
Guest Editor
Departments of Microbiology and Cell Biology, and Animal and Range Sciences, Montana State University, Bozeman, MT 59718, USA
Interests: microbiology and microbial ecology associated with animal system; structure and function of host-associated microbial communities

Special Issue Information

Dear Colleagues,

I am pleased to invite you to participate in a Special Issue on our current understanding of the non-human animal gastrointestinal tract microbiome, simply titled ‘Gastrointestinal Microbiome in Animals’. Having dedicated almost 20 years to studying microbial communities of the gastrointestinal and reproductive tracts across a wide variety of animal species, I have been amazed at the numerous similarities in compositional and functional properties and mechanisms that exist across very disparate species, as well as the differences in these traits or their impacts on host health and physiology. While we regularly draw on observations, ideas, and hypotheses developed in studies of human microbial ecosystems, it is important that we remain objective and consider alternative possibilities until evidence supports or refutes our suspicions. Likewise, microbial community properties can vary across and within non-human species. 

This Special Issue aims to provide comprehensive reviews of the current knowledge and methodological best practices in our understanding of the microbes that inhabit the gastrointestinal tract environment of non-human animal species, from insects to primates, along with cutting-edge new developments and insights. Manuscripts that delineate shared properties from unique characteristics of each animal host, assess the versatility and define key decision points in commonly applied analytical approaches, or explicitly and unbiasedly define the contentions in our understandings and next frontiers are strongly encouraged.

In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following: cross-species comparative analyses, analyses of the biases and versatility of common analytical approaches and bioinformatic pipelines, molecular insights into the physical and/or biochemical properties of the gastrointestinal biome and its influence on microbial colonization and compositional flux, routes of colonization and successional dynamics of the gastrointestinal microbiome, interactions with host nutritional, immunological, developmental, or other physiological functions, value and limits of model systems, and novel or under-recognized symbiotic interactions (positive, neutral, or negative).

I look forward to receiving your contributions.

Dr. Carl Yeoman
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbiome
  • microbiota
  • molecular approaches
  • bioinformatics
  • ecology
  • symbiosis
  • gastrointestinal
  • non-human animal
  • model systems

Published Papers (10 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

21 pages, 7428 KiB  
Article
Modulating Gastrointestinal Microbiota in Preweaning Dairy Calves: Dose-Dependent Effects of Milk-Based Sodium Butyrate Supplementation
by Donglin Wu, Zhanhe Zhang, Qifan Song, Yang Jia, Jingwei Qi and Ming Xu
Microorganisms 2024, 12(2), 333; https://doi.org/10.3390/microorganisms12020333 - 05 Feb 2024
Viewed by 801
Abstract
Sodium butyrate (SB), an essential nutritional additive for livestock, has drawn notable interest for its potential for enhancing microbiota development in ruminant animals. This study aimed to assess SB’s effects on ruminal and intestinal microbiota when added to milk for preweaning dairy calves [...] Read more.
Sodium butyrate (SB), an essential nutritional additive for livestock, has drawn notable interest for its potential for enhancing microbiota development in ruminant animals. This study aimed to assess SB’s effects on ruminal and intestinal microbiota when added to milk for preweaning dairy calves nearing 45 days old. We administered SB in the calves’ milk at four levels: 0 g/d (control), 4.4 g/d (low), 8.8 g/d (medium), and 17.6 g/d (high). After a six-week trial with ten replicates per group, ruminal fluid and fecal samples were collected for 16S rRNA sequencing, specifically targeting the V3–V4 regions to analyze microbiota. The results indicated an enhancement in ruminal microbiota, particularly in community richness, with low-level SB supplementation but minimal benefits from medium and high levels of supplementation. Increasing the level of SB supplementation had a negative impact on intestinal microbiota, affecting community richness and some potentially beneficial bacterial genera. However, low SB supplementation could positively adjust the communication between ruminal and intestinal microbiota. Overall, this study suggests feeding milk supplemented with a low level of SB to suckling calves close to an older age to promote ruminal microbiota development. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiome in Animals)
Show Figures

Figure 1

17 pages, 3017 KiB  
Article
Assessing the Probiotic Effects of Pediococcus pentosaceus CACC616 in Weaned Piglets
by Soyeon Park, Jeongsup Song, Mi Ae Park, Hyun-Jun Jang, Seoyun Son, Dae-Hyuk Kim and Yangseon Kim
Microorganisms 2023, 11(12), 2890; https://doi.org/10.3390/microorganisms11122890 - 30 Nov 2023
Viewed by 926
Abstract
During weaning, piglets experience various stressor events that disrupt their gut microbiota and immune balance, decrease growth parameters, and increase mortality rates. In this study, we assessed the efficacy of Pediococcus pentosaceus CACC616 as a probiotic supplement. We characterized this strain and evaluated [...] Read more.
During weaning, piglets experience various stressor events that disrupt their gut microbiota and immune balance, decrease growth parameters, and increase mortality rates. In this study, we assessed the efficacy of Pediococcus pentosaceus CACC616 as a probiotic supplement. We characterized this strain and evaluated its effect on improving growth performance, modulating gut microbiota composition, and reducing noxious odor components in weaned piglets compared to a non-supplementary diet (control). During the 26-day period, 40 crossbred weaned piglets were randomly assigned to pens with 20 animals each in two groups: control and treatment groups with CACC616. On day 26, the treatment group exhibited a lower feed conversion ratio (FCR) and a significant alteration in gut microbial composition, correlating with improved growth parameters and gut health (p < 0.05). The treatment group also exhibited significantly reduced digestibility- and intestinal-environment-related noxious odor components (p < 0.05). The CACC616 strain effectively reduced pathogenic genera numbers, including Campylobacter, Mogibacterium, Escherichia–Shigella, and Desulfovibrio spp., with the treatment group exhibiting lower fecal calprotectin levels than the control group (p < 0.05). Overall, this study revealed that the functional probiotic CACC616 contributes to enhanced FCR and effectively modulates weaned piglets’ inflammation and intestinal microbiota. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiome in Animals)
Show Figures

Figure 1

21 pages, 8774 KiB  
Article
Effects of Varying Levels of Wheat Bran Dietary Fiber on Growth Performance, Fiber Digestibility and Gut Microbiota in Erhualian and Large White Pigs
by Taoran Du, Pinghua Li, Qing Niu, Guang Pu, Binbin Wang, Gensheng Liu, Pinghui Li, Peipei Niu, Zongping Zhang, Chengwu Wu, Liming Hou, Mette Skou Hedemann, Qingbo Zhao and Ruihua Huang
Microorganisms 2023, 11(10), 2474; https://doi.org/10.3390/microorganisms11102474 - 01 Oct 2023
Viewed by 1045
Abstract
To evaluate the tolerance of a high-fiber diet in Erhualian pigs (Er-HL), the present investigation systematically investigated the ramifications of varying wheat bran fiber levels, specified as total dietary fiber (TDF) values of 14.07%, 16.32%, 17.99%, and 18.85%, on growth performance, fiber digestibility [...] Read more.
To evaluate the tolerance of a high-fiber diet in Erhualian pigs (Er-HL), the present investigation systematically investigated the ramifications of varying wheat bran fiber levels, specified as total dietary fiber (TDF) values of 14.07%, 16.32%, 17.99%, and 18.85%, on growth performance, fiber digestibility and gut microbiota in Er-HL, large Large White pigs (L-LW, the same physiological stage as the Er-HL) and small Large White pigs (S-LW, the same body weight as the Er-HL). Our results revealed that fiber levels exerted no discernable impact on growth performance (average daily feed intake (ADFI), and average daily gain (ADG)) of Er-HL (p > 0.05). Conversely, L-LW exhibited a decrease in ADFI and ADG with increasing fiber levels (p < 0.05). Notably, the apparent total tract digestibility (ATTD) of various fiber components, including neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose, TDF and insoluble dietary fiber (IDF), in Er-HL were significantly higher than those in S-LW and L-LW irrespective of diets (p < 0.05). The ATTD of cellulose and hemicellulose in Er-HL significantly decreased with increasing fiber levels (p < 0.05), yet remained statistically indifferent when comparing the 7%-wheat-bran-replaced diet (7% WRB, TDF 16.32%) to the basal diet (TDF 14.07%) (p > 0.05). The cecal microbiota of Er-HL had higher richness estimators (Chao1 and ACE) than those of S-LW and L-LW irrespective of diets (p < 0.01). Breed serves as a pivotal determinant in shaping swine gut microbiota. Thirteen genera were selected as the key bacteria related to high fiber digestibility of Er-HL. Further functional examination of these key genera elucidated an enrichment of pathways pertinent to carbohydrate metabolism in Er-HL samples compared with S-LW and L-LW samples. In summary, Er-HL exhibited high-fiber tolerance both in terms of growth performance and fiber digestibility compared with Large White pigs. Specifically, the ATTD of NDF, ADF, hemicellulose, IDF and TDF were significantly higher in Er-HL compared with L-LW and S-LW, irrespective of diets. Fiber level exerted no discernable impact on growth performance (ADFI, ADG) and the ATTD of fiber (NDF, ADF, IDF and TDF) in Er-HL. The optimum fiber level of the Er-HL was identified as 7% WRB (TDF 16.32%). Thirteen genera were ascertained to significantly contribute to high fiber digestibility of Er-HL, correlating with an enhancement of carbohydrate metabolism pathways. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiome in Animals)
Show Figures

Figure 1

13 pages, 8640 KiB  
Article
Ruminant Salivary Microbes: Passenger or Player in the Rumen?
by Joan E. Edwards, Eun Joong Kim, David R. Davies, Radwa Hanafy and Alison H. Kingston-Smith
Microorganisms 2023, 11(10), 2390; https://doi.org/10.3390/microorganisms11102390 - 25 Sep 2023
Viewed by 951
Abstract
Sampling of ruminant saliva has gained interest as a non-invasive proxy for exploring the structure of the rumen microbiome. However, the subsequent data analysis assumes that bacteria originating from the oral cavity are merely passengers in the rumen and play no active role. [...] Read more.
Sampling of ruminant saliva has gained interest as a non-invasive proxy for exploring the structure of the rumen microbiome. However, the subsequent data analysis assumes that bacteria originating from the oral cavity are merely passengers in the rumen and play no active role. In this study, it was hypothesised that metabolically active oral bacteria present in the salivary microbiome play a role in the ruminal degradation of plant material. In vitro cultivation-based enumeration confirmed that the ruminant oral cavity harbours a significant number of anaerobic and cellulolytic bacteria that are metabolically active under ruminal conditions. Bacterial 16S rRNA gene profiling of in vitro enrichments also confirmed that oral-derived bacteria were capable of colonising plant material. Preliminary analysis of the colonising bacteria indicated that bacteria belonging to the genus Streptococcus were of particular interest. In conclusion, the findings of the current study clearly indicate that bolus-associated bacteria have the potential to play a metabolically active role in terms of ruminal colonisation and the degradation of plant material. This evidence confirms the merit of the hypothesis that the metabolically active oral bacteria present in the salivary microbiome may play a role in the ruminal degradation of plant material. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiome in Animals)
Show Figures

Figure 1

18 pages, 4857 KiB  
Article
Genome-Assisted Probiotic Characterization and Application of Lactiplantibacillus plantarum 18 as a Candidate Probiotic for Laying Hen Production
by Guoqing Zhang, Ning Yang, Zhongyuan Liu, Xinyu Chen, Mengjiao Li, Tongyu Fu, Donghong Zhang and Cuiqing Zhao
Microorganisms 2023, 11(10), 2373; https://doi.org/10.3390/microorganisms11102373 - 22 Sep 2023
Viewed by 715
Abstract
Probiotics gained significant attention for their potential to improve gut health and enhance productivity in animals, including poultry. This comprehensive study focused on the genetic analysis of Lactiplantibacillus plantarum 18 (LP18) to understand its survival and colonization characteristics in the gastrointestinal tract. LP18 [...] Read more.
Probiotics gained significant attention for their potential to improve gut health and enhance productivity in animals, including poultry. This comprehensive study focused on the genetic analysis of Lactiplantibacillus plantarum 18 (LP18) to understand its survival and colonization characteristics in the gastrointestinal tract. LP18 was supplemented in the late-stage diet of laying hens to investigate its impact on growth performance, egg quality, and lipid metabolism. The complete genome sequence of LP18 was determined, consisting of 3,275,044 base pairs with a GC content of 44.42% and two circular plasmids. Genomic analysis revealed genes associated with adaptability, adhesion, and gastrointestinal safety. LP18 supplementation significantly improved the daily laying rate (p < 0.05) during the late-production phase and showed noteworthy advancements in egg quality, including egg shape index (p < 0.05), egg albumen height (p < 0.01), Haugh unit (p < 0.01), and eggshell strength (p < 0.05), with notable improvements in eggshell ultrastructure. Additionally, LP18 supplementation resulted in a significant reduction in serum lipid content, including LDL (p < 0.01), FFA (p < 0.05), and Gly (p < 0.05). These findings provide valuable insights into the genomic characteristics of LP18 and the genes that support its survival and colonization in the gastrointestinal tract. Importantly, this study highlights the potential of LP18 as a probiotic candidate to enhance productivity, optimize egg quality, and modulate lipid metabolism in poultry production. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiome in Animals)
Show Figures

Figure 1

19 pages, 4266 KiB  
Article
Cassava Foliage Effects on Antioxidant Capacity, Growth, Immunity, and Ruminal Microbial Metabolism in Hainan Black Goats
by Mao Li, Xuejuan Zi, Renlong Lv, Lidong Zhang, Wenjun Ou, Songbi Chen, Guanyu Hou and Hanlin Zhou
Microorganisms 2023, 11(9), 2320; https://doi.org/10.3390/microorganisms11092320 - 15 Sep 2023
Viewed by 1034
Abstract
Cassava (Manihot esculenta Crantz) foliage is a byproduct of cassava production characterized by high biomass and nutrient content. In this study, we investigated the effects of cassava foliage on antioxidant capacity, growth performance, and immunity status in goats, as well as rumen [...] Read more.
Cassava (Manihot esculenta Crantz) foliage is a byproduct of cassava production characterized by high biomass and nutrient content. In this study, we investigated the effects of cassava foliage on antioxidant capacity, growth performance, and immunity status in goats, as well as rumen fermentation and microbial metabolism. Twenty-five Hainan black goats were randomly divided into five groups (n = 5 per group) and accepted five treatments: 0% (T1), 25% (T2), 50% (T3), 75% (T4), and 100% (T5) of the cassava foliage silage replaced king grass, respectively. The feeding experiment lasted for 70 d (including 10 d adaptation period and 60 d treatment period). Feeding a diet containing 50% cassava foliage resulted in beneficial effects for goat growth and health, as reflected by the higher average daily feed intake (ADFI), average daily gain (ADG) and better feed conversion rate (FCR), as well as by the reduced serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), creatinine (CRE), and triglycerides (TG). Meanwhile, cassava foliage improved antioxidant activity by increasing the level of glutathion peroxidase (GSH-Px), superoxide dismutase (SOD), and total antioxidant capacity (T-AOC) and lowering malondialdehyde (MDA). Moreover, feeding cassava foliage was also beneficial to immunity status by enhancing complement 3 (C3), complement 4 (C4), immunoglobulin A (IgA), immunoglobulin G (IgG), and immunoglobulin M (IgM). Furthermore, the addition of dietary cassava foliage also altered rumen fermentation, rumen bacterial community composition, and metabolism. The abundance of Butyrivibrio_2 and Prevotella_1 was elevated, as were the concentrations of beneficial metabolites such as butyric acid; there was a concomitant decline in metabolites that hindered nutrient metabolism and harmed host health. In summary, goats fed a diet containing 50% cassava foliage silage demonstrated a greater abundance of Butyrivibrio_2, which enhanced the production of butyric acid; these changes led to greater antioxidant capacity, growth performance, and immunity in the goats. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiome in Animals)
Show Figures

Figure 1

17 pages, 2326 KiB  
Article
Ruminal Fluid Transplantation Accelerates Rumen Microbial Remodeling and Improves Feed Efficiency in Yaks
by Yan Li, Yingkui Yang, Shatuo Chai, Kaiyue Pang, Xun Wang, Linpeng Xu, Zheng Chen, Yumin Li, Tanqin Dong, Weihua Huang, Shujie Liu and Shuxiang Wang
Microorganisms 2023, 11(8), 1964; https://doi.org/10.3390/microorganisms11081964 - 31 Jul 2023
Cited by 1 | Viewed by 785
Abstract
A relatively stable microbial ecological balance system in the rumen plays an important role in rumen environment stability and ruminant health maintenance. No studies have reported how rumen fluid transplantation (RFT) affects the composition of rumen microorganisms and yak growth performance. In this [...] Read more.
A relatively stable microbial ecological balance system in the rumen plays an important role in rumen environment stability and ruminant health maintenance. No studies have reported how rumen fluid transplantation (RFT) affects the composition of rumen microorganisms and yak growth performance. In this experiment, we transplanted fresh rumen fluid adapted to house-feeding yaks to yaks transitioned from natural pastures to house-feeding periods to investigate the effects of rumen fluid transplantation on rumen microbial community regulation and production performance. Twenty yaks were randomly divided into the control group (CON; n = 10) and the rumen fluid transplantation group (RT; n = 10). Ten yaks that had been adapted to stall fattening feed in one month were selected as the rumen fluid donor group to provide fresh rumen fluid. Ruminal fluid transplantation trials were conducted on the 1st, 3rd, and 5th. Overall, 1 L of ruminal fluid was transplanted to each yak in the RT and CON group. The formal trial then began with both groups fed the same diet. After this, growth performance was measured, rumen fluid was collected, and rumen microbial composition was compared using 16s rRNA sequencing data. The results showed that rumen fluid transplantation had no significant effect on yak total weight gain or daily weight gain (p > 0.05), and feed efficiency was higher in the RT group than in the CON group at 3 months (treatment × month: p < 0.01). Ruminal fluid transplantation significantly affected rumen alpha diversity (p < 0.05). Up to day 60, the RT group had significantly higher OTU numbers, Shannon diversity, and Simpson homogeneity than the CON group. Principal coordinate analysis showed that the rumen microbiota differed significantly on days 4 and 7 (p < 0.05). Bacteroidota, Firmicutes, Proteobacteria, and Spirochaetes were the most abundant phyla in the rumen. The relative abundances of Bacteroidota, Proteobacteria, and Spirochaetes were lower in the RT group than in the CON group, with a decrease observed in Bacteroidota in the RT group on days 7 and 28 after rumen fluid transplantation (p = 0.013), while Proteobacteria showed a decreasing trend in the CON group and an increasing trend in RT; however, this was only at day 4 (p = 0.019). The relative abundance of Firmicutes was significantly higher in the RT group than in the CON group on days 4, 7, and 28 (p = 0.001). Prevotella and Rikenellaceae_RC9_gut_group were the predominant genera. In conclusion, our findings suggest that rumen fluid transplantation improves yak growth performance and rumen microbial reshaping. The findings of this study provide new insights into yak microbial community transplantation and a reference for improving feed efficiency in the yak industry. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiome in Animals)
Show Figures

Figure 1

16 pages, 2082 KiB  
Article
Use of an Innovative Silage of Agro-Industrial Waste By-Products in Pig Nutrition: A Pilot Study of Its Effects on the Pig Gastrointestinal Microbiota
by Ioannis Skoufos, Aikaterini Nelli, Brigkita Venardou, Ilias Lagkouvardos, Ilias Giannenas, Georgios Magklaras, Christos Zacharis, Lizhi Jin, Jin Wang, Evangelia Gouva, Stylianos Skoufos, Eleftherios Bonos and Athina Tzora
Microorganisms 2023, 11(7), 1723; https://doi.org/10.3390/microorganisms11071723 - 30 Jun 2023
Viewed by 1111
Abstract
The aim of this study was to evaluate whether dietary supplementation with an innovative silage (IS) created using 60% olive mill waste, 20% grape pomace, and 20% deproteinised feta cheese waste solids can modulate the composition of the intestinal microbiota in weaned (Exp. [...] Read more.
The aim of this study was to evaluate whether dietary supplementation with an innovative silage (IS) created using 60% olive mill waste, 20% grape pomace, and 20% deproteinised feta cheese waste solids can modulate the composition of the intestinal microbiota in weaned (Exp. 1) and finishing (Exp. 2) pigs. In Exp. 1 (40 day supplementation), forty-five crossbred weaned pigs were randomly assigned to the 0% (Control), 5%, or 10% IS groups (15 replicates/experimental diet). In Exp. 2 (60 day supplementation), eighteen finishing pigs from Exp. 1 were fed the control diet for 8 weeks before being re-assigned to their original experimental groups and fed with the 0% (Control), 5%, or 10% IS diets (six replicates/experimental diet). Performance parameters were recorded. Ileal and caecal digesta and mucosa were collected at the end of each experiment for microbiota analysis using 16S rRNA gene sequencing (five pigs/experimental diet for Exp. 1 and six pigs/experimental diet for Exp. 2). No significant effects on pig growth parameters were observed in both experiments. In Exp. 1, 5% IS supplementation increased the relative abundance of the Prevotellaceae family, Coprococcus genus, and Alloprevotella rava (OTU_48) and reduced the relative abundance of Lactobacillus genus in the caecum compared to the control and/or 10% IS diets (p < 0.05). In Exp. 2, 5% IS supplementation led to compositionally more diverse and different ileal and caecal microbiota compared to the control group (p < 0.05; p = 0.066 for β-diversity in ileum). Supplementation with the 5% IS increased the relative abundance of Clostridium celatum/disporicum/saudiense (OTU_3) in the ileum and caecum and Bifidobacterium pseudolongum (OTU_17) in the caecum and reduced the relative abundance of Streptococcus gallolyticus/alactolyticus (OTU_2) in the caecum compared to the control diet (p < 0.05). Similar effects on C. celatum/disporicum/saudiense and S. gallolyticus/alactolyticus were observed with the 10% IS diet in the caecum (p < 0.05). IS has the potential to beneficially alter the composition of the gastrointestinal microbiota in pigs. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiome in Animals)
Show Figures

Figure 1

21 pages, 4052 KiB  
Article
Rumen Microbiota Predicts Feed Efficiency of Primiparous Nordic Red Dairy Cows
by Miika Tapio, Daniel Fischer, Päivi Mäntysaari and Ilma Tapio
Microorganisms 2023, 11(5), 1116; https://doi.org/10.3390/microorganisms11051116 - 25 Apr 2023
Cited by 2 | Viewed by 1845
Abstract
Efficient feed utilization in dairy cows is crucial for economic and environmental reasons. The rumen microbiota plays a significant role in feed efficiency, but studies utilizing microbial data to predict host phenotype are limited. In this study, 87 primiparous Nordic Red dairy cows [...] Read more.
Efficient feed utilization in dairy cows is crucial for economic and environmental reasons. The rumen microbiota plays a significant role in feed efficiency, but studies utilizing microbial data to predict host phenotype are limited. In this study, 87 primiparous Nordic Red dairy cows were ranked for feed efficiency during their early lactation based on residual energy intake, and the rumen liquid microbial ecosystem was subsequently evaluated using 16S rRNA amplicon and metagenome sequencing. The study used amplicon data to build an extreme gradient boosting model, demonstrating that taxonomic microbial variation can predict efficiency (rtest = 0.55). Prediction interpreters and microbial network revealed that predictions were based on microbial consortia and the efficient animals had more of the highly interacting microbes and consortia. Rumen metagenome data was used to evaluate carbohydrate-active enzymes and metabolic pathway differences between efficiency phenotypes. The study showed that an efficient rumen had a higher abundance of glycoside hydrolases, while an inefficient rumen had more glycosyl transferases. Enrichment of metabolic pathways was observed in the inefficient group, while efficient animals emphasized bacterial environmental sensing and motility over microbial growth. The results suggest that inter-kingdom interactions should be further analyzed to understand their association with the feed efficiency of animals. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiome in Animals)
Show Figures

Figure 1

Review

Jump to: Research

14 pages, 1046 KiB  
Review
The Impact of Essential Amino Acids on the Gut Microbiota of Broiler Chickens
by Thyneice Taylor-Bowden, Sarayu Bhogoju, Collins N. Khwatenge and Samuel N. Nahashon
Microorganisms 2024, 12(4), 693; https://doi.org/10.3390/microorganisms12040693 - 29 Mar 2024
Viewed by 764
Abstract
The research involving the beneficial aspects of amino acids being added to poultry feed pertaining to performance, growth, feed intake, and feed conversion ratio is extensive. Yet currently the effects of amino acids on the gut microbiota aren’t fully understood nor have there [...] Read more.
The research involving the beneficial aspects of amino acids being added to poultry feed pertaining to performance, growth, feed intake, and feed conversion ratio is extensive. Yet currently the effects of amino acids on the gut microbiota aren’t fully understood nor have there been many studies executed in poultry to explain the relationship between amino acids and the gut microbiota. The overall outcome of health has been linked to bird gut health due to the functionality of gastrointestinal tract (GIT) for digestion/absorption of nutrients as well as immune response. These essential functions of the GI are greatly driven by the resident microbiota which produce metabolites such as butyrate, propionate, and acetate, providing the microbiota a suitable and thrive driven environment. Feed, age, the use of feed additives and pathogenic infections are the main factors that have an effect on the microbial community within the GIT. Changes in these factors may have potential effects on the gut microbiota in the chicken intestine which in turn may have an influence on health essentially affecting growth, feed intake, and feed conversion ratio. This review will highlight limited research studies that investigated the possible role of amino acids in the gut microbiota composition of poultry. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiome in Animals)
Show Figures

Figure 1

Back to TopTop