scholarly journals The Impact of Genetics on Gut Microbiota of Growing and Fattening Pigs under Moderate N Restriction

Animals ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 2846
Author(s):  
Laura Sarri ◽  
Sandra Costa-Roura ◽  
Joaquim Balcells ◽  
Ahmad Reza Seradj ◽  
Gabriel de la Fuente

Characterization of intestinal microbiota is of great interest due to its relevant impact on growth, feed efficiency and pig carcass quality. Microbial composition shifts along the gut, but it also depends on the host (i.e., age, genetic background), diet composition and environmental conditions. To simultaneously study the effects of producing type (PT), production phase (PP) and dietary crude protein (CP) content on microbial populations, 20 Duroc pigs and 16 crossbred pigs (F2), belonging to growing and fattening phases, were used. Half of the pigs of each PT were fed a moderate CP restriction (2%). After sacrifice, contents of ileum, cecum and distal colon were collected for sequencing procedure. Fattening pigs presented higher microbial richness than growing pigs because of higher maturity and stability of the community. The F2 pigs showed higher bacterial alpha diversity and microbial network complexity (cecum and colon), especially in the fattening phase, while Duroc pigs tended to have higher Firmicutes/Bacteroidetes ratio in cecum segment. Lactobacillus was the predominant genus, and along with Streptococcus and Clostridium, their relative abundance decreased throughout the intestine. Although low CP diet did not alter the microbial diversity, it increased interaction network complexity. These results have revealed that the moderate CP restriction had lower impact on intestinal microbiota than PP and PT of pigs.

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 180
Author(s):  
Negash Kabtimer Bereded ◽  
Getachew Beneberu Abebe ◽  
Solomon Workneh Fanta ◽  
Manuel Curto ◽  
Herwig Waidbacher ◽  
...  

The gut microbiota of fishes is known to play an essential role in diverse aspects of host biology. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. Studies of effect of environment on gut microbiota enables to have a further understanding of what comprises a healthy microbiota under different environmental conditions. However, there is insufficient understanding regarding the effects of sampling season and catching site (wild and aquaculture) on the gut microbiota of Nile tilapia. This study characterised gut microbial composition and diversity from samples collected from Lake Tana and the Bahir Dar aquaculture facility centre using 16S rDNA Illumina MiSeq platform sequencing. Firmicutes and Fusobacteria were the most dominant phyla in the Lake Tana samples, while Proteobacteria was the most dominant in the aquaculture samples. The results of differential abundance testing clearly indicated significant differences for Firmicutes, Fusobacteria, Bacteroidetes and Cyanobacteria across sampling months. However, Proteobacteria, Chloroflexi, Fusobacteria and Cyanobacteria were significantly enriched in the comparison of samples from the Lake Tana and aquaculture centre. Significant differences were observed in microbial diversity across sampling months and between wild and captive Nile tilapia. The alpha diversity clearly showed that samples from the aquaculture centre (captive) had a higher diversity than the wild Nile tilapia samples from Lake Tana. The core gut microbiota of all samples of Nile tilapia used in our study comprised Firmicutes, Proteobacteria and Fusobacteria. This study clearly showed the impact of sampling season and catching site (wild and aquaculture) on the diversity and composition of bacterial communities associated with the gut of Nile tilapia. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work is recommended to precisely explain the causes of these changes using large representative samples of Nile tilapia from different lakes and aquaculture farms.


mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Kuppan Gokulan ◽  
Matthew G. Arnold ◽  
Jake Jensen ◽  
Michelle Vanlandingham ◽  
Nathan C. Twaddle ◽  
...  

ABSTRACT Intestinal microbiota composition and gut-associated immune response can contribute to the toxicity of arsenic. We investigated the potential toxicity of short-term arsenic exposure on gut microbiome composition, intestinal immune status, microbial arsenic resistance gene, and arsenic metabolic profiles in adult and developmental stages of CD-1 mice. The potential toxicity of arsenite [As(III)] was determined for two life stages: (i) adult animals at 24 or 48 h after single gavage (0.05 mg/kg body weight [b.w.] [low dose], 0.1 mg/kg b.w. [medium dose], and 0.2 mg/kg b.w. [high dose]) and repeated exposure at 1 mg/liter for 8 days and (ii) postnatal day 10 (PND10) and PND21 after single gavage (0.05 mg/kg b.w.). Dose- and time-dependent responses in bacterial recovery/microbial composition were observed in adults after a single gavage. Repeated exposure caused a transient decrease in the recovery of intestinal bacteria, a shift in the bacterial population with abundance of arsenic resistance genes, and evidence for host metabolism of arsenite into less-reactive trivalent methylated species. Arsenic exposure in adult animals induced high levels of CC chemokines and of proinflammatory and anti-inflammatory cytokine secretion in intestine. Arsenic exposure at PND21 resulted in the development of distinct bacterial populations. Results of this study highlight significant changes in the intestinal microbiome and gut-associated immune status during a single or repeated exposure to arsenic in juvenile and adult animals. The data warrant investigation of the long-term effects of oral arsenic exposure on the microbiome and of immune system development and responses. IMPORTANCE Transformation of organic arsenic to toxic inorganic arsenic (iAs) is likely carried out by intestinal bacteria, and iAs may alter the viability of certain microbial populations. This study addressed the impact of arsenic exposure on intestinal microbiota diversity and host gut-associated immune mediators during early development or adulthood using scenarios of acute or repeated doses. During acute arsenic exposure, animals developed defense functions characterized by higher abundances of bacteria that are involved in arsenic resistance or detoxification mechanisms. Arsenite had a negative effect on the abundance of bacterial species that are involved in the conversion of protein to butyrate, which is an alternative energy source in the intestine. The intestinal mucosal immune cytokine profile reflected a mechanism of protection from arsenic toxicity.


mSystems ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Héctor Argüello ◽  
Jordi Estellé ◽  
Finola C. Leonard ◽  
Fiona Crispie ◽  
Paul D. Cotter ◽  
...  

ABSTRACT Salmonella colonization and infection in production animals such as pigs are a cause for concern from a public health perspective. Variations in susceptibility to natural infection may be influenced by the intestinal microbiota. Using 16S rRNA compositional sequencing, we characterized the fecal microbiome of 15 weaned pigs naturally infected with Salmonella at 18, 33, and 45 days postweaning. Dissimilarities in microbiota composition were analyzed in relation to Salmonella infection status (infected, not infected), serological status, and shedding pattern (nonshedders, single-point shedders, intermittent-persistent shedders). Global microbiota composition was associated with the infection outcome based on serological analysis. Greater richness within the microbiota postweaning was linked to pigs being seronegative at the end of the study at 11 weeks of age. Members of the Clostridia, such as Blautia, Roseburia, and Anaerovibrio, were more abundant and part of the core microbiome in nonshedder pigs. Cellulolytic microbiota (Ruminococcus and Prevotella) were also more abundant in noninfected pigs during the weaning and growing stages. Microbial profiling also revealed that infected pigs had a higher abundance of Lactobacillus and Oscillospira, the latter also being part of the core microbiome of intermittent-persistent shedders. These findings suggest that a lack of microbiome maturation and greater proportions of microorganisms associated with suckling increase susceptibility to infection. In addition, the persistence of Salmonella shedding may be associated with an enrichment of pathobionts such as Anaerobiospirillum. Overall, these results suggest that there may be merit in manipulating certain taxa within the porcine intestinal microbial community to increase disease resistance against Salmonella in pigs. IMPORTANCE Salmonella is a global threat for public health, and pork is one of the main sources of human salmonellosis. However, the complex epidemiology of the infection limits current control strategies aimed at reducing the prevalence of this infection in pigs. The present study analyzes for the first time the impact of the gut microbiota in Salmonella infection in pigs and its shedding pattern in naturally infected growing pigs. Microbiome (16S rRNA amplicon) analysis reveals that maturation of the gut microbiome could be a key consideration with respect to limiting the infection and shedding of Salmonella in pigs. Indeed, seronegative animals had higher richness of the gut microbiota early after weaning, and uninfected pigs had higher abundance of strict anaerobes from the class Clostridia, results which demonstrate that a fast transition from the suckling microbiota to a postweaning microbiota could be crucial with respect to protecting the animals.


2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 293-294
Author(s):  
Camila S Marcolla ◽  
Benjamin Willing

Abstract This study aimed to characterize poultry microbiota composition in commercial farms using 16S rRNA sequencing. Animals raised in sanitized environments have lower survival rates when facing pathogenic challenges compared to animals naturally exposed to commensal organisms. We hypothesized that intensive rearing practices inadvertently impair chicken exposure to microbes and the establishment of a balanced gut microbiota. We compared gut microbiota composition of broilers (n = 78) and layers (n = 20) from different systems, including commercial intensive farms with and without in-feed antibiotics, organic free-range farms, backyard-raised chickens and chickens in an experimental farm. Microbial community composition of conventionally raised broilers was significantly different from antibiotic-free broilers (P = 0.012), from broilers raised outdoors (P = 0.048) and in an experimental farm (P = 0.006) (Fig1). Significant community composition differences were observed between antibiotic-fed and antibiotic-free chickens (Fig2). Antibiotic-free chickens presented higher alpha-diversity, higher relative abundance of Deferribacteres, Fusobacteria, Bacteroidetes and Actinobacteria, and lower relative abundance of Firmicutes, Clostridiales and Enterobacteriales than antibiotic-fed chickens (P < 0.001) (Fig3). Microbial community composition significantly changed as birds aged. In experimental farm, microbial community composition was significant different for 7, 21 and 35 day old broilers (P < 0.001), and alpha diversity increased from 7 to 21d (P < 0.024), but not from 21 to 35d; whereas, in organic systems, increases in alpha-diversity were observed from 7d to 21d, and from 21d to 35d (P < 0.05). Broilers and layers raised together showed no differences in microbiota composition and alpha diversity (P > 0.8). It is concluded that production practices consistently impact microbial composition, and that antibiotics significantly reduces microbial diversity. We are now exploring the impact of differential colonization in a controlled setting, to determine the impact of the microbes associated with extensively raised chickens. This study will support future research and the development of methods to isolate and introduce beneficial microbes to commercial systems.


Nutrients ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 1199 ◽  
Author(s):  
Silke Crommen ◽  
Alma Mattes ◽  
Marie-Christine Simon

Bariatric surgery leads to sustained weight loss and the resolution of obesity-related comorbidities. Recent studies have suggested that changes in gut microbiota are associated with the weight loss induced by bariatric surgery. Several studies have observed major changes in the microbial composition following gastric bypass surgery. However, there are inconsistencies between the reported alterations in microbial compositions in different studies. Furthermore, it is well established that diet is an important factor shaping the composition and function of intestinal microbiota. However, most studies on gastric bypass have not assessed the impact of dietary intake on the microbiome composition in general, let alone the impact of restrictive diets prior to bariatric surgery, which are recommended for reducing liver fat content and size. Thus, the relative impact of bariatric surgery on weight loss and gut microbiota remains unclear. Therefore, this review aims to provide a deeper understanding of the current knowledge of the changes in intestinal microbiota induced by bariatric surgery considering pre-surgical nutritional changes.


2021 ◽  
Vol 7 (6) ◽  
pp. 447
Author(s):  
Lysiane Dunière ◽  
Damien Esparteiro ◽  
Yacine Lebbaoui ◽  
Philippe Ruiz ◽  
Mickael Bernard ◽  
...  

Background: In ruminants, physiological and nutritional changes occur peripartum. We investigated if gastro-intestinal microbiota, rumen metabolism and antioxidant status were affected around parturition and what could be the impact of a daily supplementation of a live yeast additive in late gestating ewes. Methods: Rumen, feces and blood samples were collected from 2 groups of 14 ewes one month and a few days before parturition, and 2 weeks postpartum. Results: In the control ewes close to parturition, slight changes in the ruminal microbiota were observed, with a decrease in the concentration F. succinogenes and in the relative abundance of the Fibrobacteres phylum. Moreover, a decrease in the alpha-diversity of the bacterial community and a reduced relative abundance of the Fibrobacteres phylum were observed in their feces. Control ewes were prone to oxidative stress, as shown by an increase in malondialdehyde (MDA) concentration, a lower total antioxidant status, and higher glutathione peroxidase (GPx) activity in the blood. In the yeast supplemented ewes, most of the microbial changes observed in the control group were alleviated. An increase in GPx activity, and a significant decrease in MDA concentration were measured. Conclusions: The live yeast used in this study could stabilize gastro-intestinal microbiota and reduce oxidative stress close to parturition.


2018 ◽  
Author(s):  
Craig A. Watkins ◽  
Dave J. Bartley ◽  
Burcu Gündüz Ergün ◽  
Büşra Yıldızhan ◽  
Tracy Ross-Watt ◽  
...  

ABSTRACTNematodes are one of the main impactors on health, welfare and productivity of farmed animals. Teladorsagia circumcincta is arguably one of the most globally important nematode species in sheep. Control of these nematode infections is essential and heavily reliant on chemotherapy (anthelmintics), but this has been complicated by the development of anthelmintic resistance. In mammals the composition of the intestinal microbiota has been shown to have a significant effect on overall health. The interactions between host, microbiota and pathogens are complex and influenced by numerous factors. In this study, the interactions between T. circumcincta infections and microbial composition and abundance were investigated. In a preliminary study the intra-and inter-individual diversity and composition of the microbiota of grazing sheep was assessed in two distinct regions of the ovine intestinal tract, the terminal ileum (TI) and rectal contents. Additionally, the effects of experimental infection of sheep with two strains of T. circumcincta (anthelmintic resistant or sensitive) on the microbiota were assessed with and without anthelmintic (monepantel) administration. The inter-animal variability was greater in the TI compared to the rectal samples. However, the alpha-diversity (species richness) was significantly lower in the TI samples. In the experimental study, clear differences were observed between successfully treated animals and those sheep that were left untreated and/or those carrying resistant nematodes. Differences in microbiota between the four different experimental conditions were observed and potential predictive biomarkers were identified. In particular, a restoration of potentially beneficial Bifidobacteria sp. in successfully-treated animals was observed.


2020 ◽  
Vol 7 ◽  
Author(s):  
Shrushti Shah ◽  
Paul D. S. Brown ◽  
Shyamchand Mayengbam ◽  
Michael G. Gänzle ◽  
Weilan Wang ◽  
...  

Increasing consumer interest in fermented products has driven the emergence of a number of novel foods including shelf-stable sourdough pasta. This study comprehensively examined the impact of fermentation on the microbial composition of the culture, pasta, its subsequent effects on glycemic responses and gut microbiota in overweight men and women (>25 kg/m2) compared to a conventional, non-fermented pasta. Two, randomized crossover trials were performed. Study A examined acute feeding responses to each product wherein fasted participants completed a meal tolerance test comprised of 75 g of conventional or sourdough pasta to examine glycemic responses. Results showed enhanced gastric emptying with sourdough, but no difference in overall blood glucose, insulin or satiety hormone responses between the treatments. Study B consisted of three standard oral glucose tolerance tests as well as fecal collection for sequencing at baseline and following each pasta intervention (150 g or 2 serving/d for 5 days) followed by a 2-week washout period. Results showed no differential impact of either pasta treatment on glucose tolerance. Analysis of fecal bacterial and fungal (mycobiome) microbiota showed no change at the individual species or genus levels. However, fungi were adaptive following chronic pasta consumption with decreases in alpha diversity of fungi following sourdough, but not conventional pasta. This was accompanied by reductions in total fecal short chain fatty acid concentrations. In conclusion, sourdough fermentation did not change the overall glycemic properties of the pasta, incretin responses or bacterial gut microbiota, but appears to impact microbiome fungal community structure with chronic consumption.


2020 ◽  
Vol 14 (Supplement_1) ◽  
pp. S010-S011
Author(s):  
E Brand ◽  
Y Laenen ◽  
F van Wijk ◽  
M de Zoete ◽  
B Oldenburg

Abstract Background The pathogenesis of inflammatory bowel disease (IBD) is thought to result from an interplay between microbiota, the immune system and the environment in genetically susceptible hosts. Immunoglobulin A (IgA) produced by the immune system can be specifically directed against bacteria. The IgA-coating pattern of intestinal bacteria thus reflects interactions between the immune system and specific bacteria. Studying IBD in twins, concordant and discordant for IBD, reduces the impact of genetic predisposition and childhood exposures and therefore offers the unique opportunity to focus on other factors such as intestinal microbiota composition and immune-interactions in IBD. Methods Faecal samples from twin pairs discordant for Crohn’s disease (CD) or ulcerative colitis (UC) were collected. Employing fluorescence-activated cell sorting, IgA+ and IgA− bacteria from the intestinal microbiota were sorted. Subsequently, (1) the total, (2) IgA+ and (3) IgA− microbial composition was determined by 16S rRNA sequencing (IgA-SEQ). We estimated the relative IgA coating per bacterial species by dividing the abundance of that species in the IgA+ fraction over the abundance in the IgA- fraction, representing the IgA coating index. Linear discriminant analyses were performed with LefSE. Results We included 31 twin pairs (62 individuals) discordant for IBD (CD: 15, UC: 16). 15/32 twin pairs were monozygotic, 43/62 of participants were female, the median age was 47 years (interquartile range: 34–58.5). Of 31 participants with IBD, 7 had signs of active inflammation based on endoscopy, Harvey–Bradshaw index or short clinical colitis activity index. Differences (log-linear discriminant analysis score >3) in the microbial composition of IgA-coated bacteria were observed between CD patients and their twin-siblings not affected by IBD: Dorea formicigenerans (increased in IgA coating), Parabacteroides sp., Christensenellaceae sp., Clostridium sp. and Mollicutes RF39 sp. (decreased in IgA coating). In ulcerative colitis patients, an increase in IgA-coating was observed for Ruminococcus gnavus and Dorea formicigenerans, while Turicibacter sp., Barnesiellaceae sp. and an unclassified Clostridiales sp. were decreased in IgA-coating compared with their twin-siblings not affected by IBD. Conclusion In twins affected by IBD, the pattern of IgA-coated bacteria differs between IBD and non-IBD affected individuals. These data on immune-bacteria interactions could serve as a starting point for the elucidation of the immune-responses triggered by specific bacteria in IBD.


2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Yiying Zhao ◽  
Cindy Nakatsu ◽  
Qing Jiang

Abstract Objectives Recent discoveries suggest that gut microbiota is involved in the progression of colitis-associated colorectal cancer (CAC) and natural products like polyphenols can modulate gut microbiota. Polyphenol components of grape like resveratrol have been shown to have anti-colorectal cancer effects in animal models, but the underlying mechanism is not completely understood. The objective of this study is to examine the chemo-preventive effect of a whole grape powder (GP) on tumorigenesis in a mouse CAC model and evaluated the impact of GP on gut microbiota as a potential anti-CAC mechanism. To dissect the role of polyphenols in the GP, we compared GP at 3 and 10% diet to calorie, fiber, sugar and organic acid-matched placebo. Methods We used male Balb/c mice and divided them into diseased groups treated with azoxymethane (AOM) and dextran sodium sulfate (DSS) and healthy groups, both of which had placebo control diet, GP at 3% or 10% diet. To induce tumorigenesis, we injected AOM at 9.5 mg/kg bw at 6 weeks of age, followed by 2-cycle DSS (1.5% in drinking water). During the study, we monitored animals’ body weight and food consumption weekly, and evaluated their colitis symptoms during DSS treatments. All animals were sacrificed at 16 weeks of age and 24-hr accumulative fecal samples were collected prior to sacrifice for gut microbial analysis. Results Compared to the control diet, 10% GP diet alleviated colitis symptoms including rectal bleeding and diarrhea, and reduced total tumor multiplicity by 29% (P < 0.05). GP diet increased microbial alpha-diversity and significantly shifted the gut microbial composition in both healthy and diseased groups. Under both conditions, 10% GP diet increased the abundance of various taxa belonging to Lachnospiraceae family. Canonical correspondence analysis (CCA) of gut microbiota indicated that increased GP supplementation was associated with healthier animal status. In particular, we observed that the predicted functional profile of gut microbiota from diseased mice with 10% GP diet was similar to those from healthy mice with the control diet. Conclusions 10% GP diet showed CAC chemo-preventive effects and modulated gut microbiota under both healthy and diseased conditions, and appeared to prevent CAC-associated gut microbiota changes. Funding Sources California Table Grape Commission.


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