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Animal Microbiome Jun 2022The resistome describes the array of antibiotic resistant genes (ARGs) present within a microbial community. Recent research has documented the resistome in the rumen of...
BACKGROUND
The resistome describes the array of antibiotic resistant genes (ARGs) present within a microbial community. Recent research has documented the resistome in the rumen of ruminants and revealed that the type and abundance of ARGs could be affected by diet and/or antibiotic treatment. However, most of these studies only assessed ARGs using metagenomics, and expression of the resistome and its biological function within the microbiome remains largely unexplored.
RESULTS
We characterized the pools of ARGs (resistome) and their activities in the rumen of 48 beef cattle belonging to three breeds (Angus, Charolais, Kinsella composite hybrid), using shotgun metagenomics and metatranscriptomics. Sixty (including 20 plasmid-associated) ARGs were expressed which accounted for about 30% of the total number of ARGs (187) identified in metagenomic datasets, with tetW and mefA exhibiting the highest level of expression. In addition, the bacterial hosts of 17 expressed ARGs were identified. The active resistome was less diverse in Kinsella composite hybrid than Angus, however, expression of ARGs did not differ among breeds. Although not associated with feed efficiency, the total abundance of expressed ARGs was positively correlated with metabolic pathways and 'attenuation values' (a measurement of stability) of the active rumen microbiome, suggesting that ARGs expression influences the stability and functionality of the rumen microbiome. Moreover, Ruminococcus spp., Prevotella ruminicola, Muribaculaceae spp. and Collinsella aerofaciens were all identified as hosts of expressed ARGs, possibly promoting the dominance of these carbohydrate degraders within the rumen microbiome.
CONCLUSIONS
Findings from this study provide new insight into the active rumen resistome in vivo, which may inform strategies to limit the spread of ubiquitously found ARGs from the rumen to the broader environment without negatively impacting the key functional outcomes of the rumen microbiome.
PubMed: 35659381
DOI: 10.1186/s42523-022-00189-6 -
Frontiers in Physiology 2022The integrity of the intestinal epithelium is crucial for human health and is harmed in autism spectrum disorder (ASD). An aberrant gut microbial composition resulting...
INTRODUCTION
The integrity of the intestinal epithelium is crucial for human health and is harmed in autism spectrum disorder (ASD). An aberrant gut microbial composition resulting in gut-derived metabolic toxins was found to damage the intestinal epithelium, jeopardizing tissue integrity. These toxins further reach the brain the gut-brain axis, disrupting the normal function of the brain. A mechanistic understanding of metabolic disturbances in the brain and gut is essential to design effective therapeutics and early intervention to block disease progression. Herein, we present a novel computational framework integrating constraint based tissue specific metabolic (CBM) model and whole-body physiological pharmacokinetics (PBPK) modeling for ASD. Furthermore, the role of gut microbiota, diet, and oxidative stress is analyzed in ASD.
METHODS
A representative gut model capturing host-bacteria and bacteria-bacteria interaction was developed using CBM techniques and patient data. Simultaneously, a PBPK model of toxin metabolism was assembled, incorporating multi-scale metabolic information. Furthermore, dynamic flux balance analysis was performed to integrate CBM and PBPK. The effectiveness of a probiotic and dietary intervention to improve autism symptoms was tested on the integrated model.
RESULTS
The model accurately highlighted critical metabolic pathways of the gut and brain that are associated with ASD. These include central carbon, nucleotide, and vitamin metabolism in the host gut, and mitochondrial energy and amino acid metabolisms in the brain. The proposed dietary intervention revealed that a high-fiber diet is more effective than a western diet in reducing toxins produced inside the gut. The addition of probiotic bacteria , , , and to the diet restores gut microbiota balance, thereby lowering oxidative stress in the gut and brain.
CONCLUSION
The proposed computational framework is novel in its applicability, as demonstrated by the determination of the whole-body distribution of ROS toxins and metabolic association in ASD. In addition, it emphasized the potential for developing novel therapeutic strategies to alleviate autism symptoms. Notably, the presented integrated model validates the importance of combining PBPK modeling with COBRA -specific tissue details for understanding disease pathogenesis.
PubMed: 35330929
DOI: 10.3389/fphys.2022.760753 -
Scientific Reports Dec 2021Several seaweed extracts have been reported to have potential antimethanogenic effects in ruminants. In this study, the effect of three brown seaweed species (Undaria...
Several seaweed extracts have been reported to have potential antimethanogenic effects in ruminants. In this study, the effect of three brown seaweed species (Undaria pinnatifida, UPIN; Sargassum fusiforme, SFUS; and Sargassum fulvellum, SFUL) on rumen fermentation characteristics, total gas, methane (CH), carbon dioxide (CO) production, and microbial populations were investigated using an in vitro batch culture system. Seaweed extract and its metabolites, total flavonoid and polyphenol contents were identified and compared. For the in vitro batch, 0.25 mg∙mL of each seaweed extract were used in 6, 12, 24, 36 and 48 h of incubation. Seaweed extract supplementation decreased CH yield and its proportion to total gas production after 12, 24, and 48 h of incubation, while total gas production were not significantly different. Total volatile fatty acid and molar proportion of propionate increased with SFUS and SFUL supplementation after 24 h of incubation, whereas UPIN was not affected. Additionally, SFUS increased the absolute abundance of total bacteria, ciliate protozoa, fungi, methanogenic archaea, and Fibrobacter succinogenes. The relative proportions of Butyrivibrio fibrisolvens, Butyrivibrio proteoclasticus, and Prevotella ruminicola were lower with seaweed extract supplementation, whereas Anaerovibrio lipolytica increased. Thus, seaweed extracts can decrease CH production, and alter the abundance of rumen microbial populations.
Topics: Animals; Carbon Dioxide; Fatty Acids, Volatile; Fermentation; Gases; In Vitro Techniques; Methane; Plant Extracts; Propionates; Rumen; Seaweed; Time Factors
PubMed: 34916562
DOI: 10.1038/s41598-021-03356-y -
Animals : An Open Access Journal From... Jul 2021We evaluated whether olive leaves (OLs) are effective as feed additives and supplements for ruminants and the potential methane reduction effects during in vitro...
We evaluated whether olive leaves (OLs) are effective as feed additives and supplements for ruminants and the potential methane reduction effects during in vitro fermentation. Two Hanwoo cows (460 ± 20 kg) equipped with cannula were fed Timothy hay and corn-based feed 3% of the body weight at a ratio of 6:4 (8:30 a.m. and 5:00 p.m.). Ruminal fluid from the cows was collected and mixed before morning feeding. In vitro batch fermentation was monitored after 12 and 24 h of incubation at 39 °C, and OLs were used as supplements to achieve the concentration of 5% in the basal diet. At 12 h of fermentation, methane production decreased in the 5% OLs group compared to that in the control group, but not at 24 h. The proportion of cellulose-degrading bacteria, , and , tended to increase in the 5% OLs group at 12 h. The amount of ammonia produced was the same as the polymerase chain reaction result for . At 12 h, the proportion of was significantly higher in the 5% OLs group. OLs may be used incorporated with protein byproducts or other methane-reducing agents in animal feed.
PubMed: 34359136
DOI: 10.3390/ani11072008 -
Animals : An Open Access Journal From... Jun 2021This study was conducted to evaluate the potential of hydrolysable tannin (chestnut tannin, CHT) without or with condensed tannin (quebracho tannin, QT) for modulating...
Effects of Hydrolysable Tannin with or without Condensed Tannin on Alfalfa Silage Fermentation Characteristics and In Vitro Ruminal Methane Production, Fermentation Patterns, and Microbiota.
This study was conducted to evaluate the potential of hydrolysable tannin (chestnut tannin, CHT) without or with condensed tannin (quebracho tannin, QT) for modulating alfalfa silage fermentation characteristics and in vitro ruminal methane (CH) production, fermentation profile, and microbiota. Alfalfa (235 g/kg fresh weight) was ensiled with no tannins (control), 2% CHT (CHT2), 5% CHT (CHT5), the combination of CHT and QT at 1% each (CHQ2), and CHT and QT at 2.5% each (CHQ5) of forage dry matter (DM). The CHQ2 treatment was more effective in reducing DM losses, pH, and ammonia-nitrogen to total nitrogen ratios of alfalfa silage than CHT2 and CHT5 treatments. All tannin treatments decreased ruminal CH production, and the magnitude of the decrease was greater for the combinations than the individual ones. Total volatile fatty acid (VFA) concentrations and DM degradation decreased by tannin treatments, but microbial protein (MCP) synthesis increased. The total VFA concentrations and DM degradation were lower with CHQ2 treatment than with CHT5 and CHQ5 treatments, but the MCP concentrations were comparable among these treatments. Tannin inclusion decreased the abundance of the anaerobic fungi and , but enhanced . The combination of CHT and QT alleviated the inhibition of CHT supply alone in , , and as well as protease. The results revealed that a combination of HT from CHT and CT from QT at a low level can reduce proteolysis and CH production of alfalfa silage without impairing ruminal fermentation and microbiota.
PubMed: 34209256
DOI: 10.3390/ani11071967 -
Journal of Animal Science and Technology Nov 2020The main objective of this study was to evaluate red ginseng byproduct (RGP) as a protein resource and its effects on rumen fermentation characteristics, microflora,...
The main objective of this study was to evaluate red ginseng byproduct (RGP) as a protein resource and its effects on rumen fermentation characteristics, microflora, CO, and CH production in ruminants. Four treatments for fermentation using buffered rumen fluid over a 48 h incubation period were used: 1, RGP; 2, corn gluten feed (CGF); 3, wheat gluten (WG); and 4, corn germ meal. dry matter digestibility (IVDMD), neutral detergent fiber digestibility (IVNDFD), crude protein digestibility (IVCPD), volatile fatty acids, pH, and ammonia nitrogen (NH-N) were estimated after 48 h incubation. Gas production was investigated after 3, 6, 12, 24, 36 and 48 h. The CO and CH were evaluated after 12, 24, 36, and 48 h. A significant difference in total gas production and CO emissions was observed ( < 0.01) at all incubation times. CH production in RGP were higher ( < 0.05) than that in other treatments but a higher CH portion in the total gas production was observed in WG ( < 0.05) at 48 h incubation. The IVDMD, IVNDFD, and IVCPD of RGP was lower than those of other conventional ingredients ( < 0.01). The RGP had the lowest NH-N value among the treatments ( < 0.01). The RGP also had the lowest total VFA concentration ( < 0.01), but presented the highest acetate proportion and acetate to propionate ratio among the treatments (both, < 0.01). The abundance of was higher in RGP than in WG ( < 0.01), whereas RGP has lower methanogenic archaea ( < 0.01). In conclusion, based on the nutritive value, IVDMD, low NH-N, and decreased methanogenic archaea, RGP inclusion as a protein source in ruminant diets can be an option in replacing conventional feed sources.
PubMed: 33987561
DOI: 10.5187/jast.2020.62.6.801 -
Frontiers in Microbiology 2021Previous studies have focused on the rumen microbiome and enteric methane (CH) emissions in dairy cows, yet little is known about steers, especially steers of dairy...
Previous studies have focused on the rumen microbiome and enteric methane (CH) emissions in dairy cows, yet little is known about steers, especially steers of dairy breeds. In the present study, we comparatively examined the rumen microbiota, fermentation characteristics, and CH emissions from six non-cannulated Holstein (710.33 ± 43.02 kg) and six Jersey (559.67 ± 32.72 kg) steers. The steers were fed the same total mixed ration (TMR) for 30 days. After 25 days of adaptation to the diet, CH emissions were measured using GreenFeed for three consecutive days, and rumen fluid samples were collected on last day using stomach tubing before feeding (0 h) and 6 h after feeding. CH production (g/d/animal), CH yield (g/kg DMI), and CH intensity (g/kg BW) were higher in the Jersey steers than in the Holstein steers. The lowest pH value was recorded at 6 h after feeding. The Jersey steers had lower rumen pH and a higher concentration of ammonia-nitrogen (NH-N). The Jersey steers had a numerically higher molar proportion of acetate than the Holstein steers, but the opposite was true for that of propionate. Metataxonomic analysis of the rumen microbiota showed that the two breeds had similar species richness, Shannon, and inverse Simpson diversity indexes. Principal coordinates analysis showed that the overall rumen microbiota was different between the two breeds. Both breeds were dominated by , and its highest relative abundance was observed 6 h after feeding. The genera , , and the species , and were more abundant in Holstein steers while the genera , , and the species , and in the Jersey steers. The Jersey steers were dominated by while the Holstein steers by . The overall results suggest that sampling hour has little influence on the rumen microbiota; however, breeds of steers can affect the assemblage of the rumen microbiota and different mitigation strategies may be needed to effectively manipulate the rumen microbiota and mitigate enteric CH emissions from these steers.
PubMed: 33868186
DOI: 10.3389/fmicb.2021.601061 -
Toxics Mar 2021Gossypol is a key anti-nutritional factor which limits the feeding application of cottonseed by-products in animal production. A 2 × 4 factorial in vitro experiment was...
Gossypol is a key anti-nutritional factor which limits the feeding application of cottonseed by-products in animal production. A 2 × 4 factorial in vitro experiment was conducted to determine the effect of gossypol addition levels of 0, 0.25, 0.5, and 0.75 mg/g on ruminal fermentation of a high-forage feed (HF, Chinese wildrye hay/corn meal = 3:2) in comparison with a low-forage feed (LF, Chinese wildrye hay/corn meal = 2:3). After 48 h of incubation, in vitro dry matter disappearance was greater in the LF than the HF group, while the cumulative gas production and asymptotic gas production were greater in the HF than the LF group ( < 0.05). Regardless of whatever ration type was incubated, the increasing gossypol addition did not alter in vitro dry matter disappearance. The asymptotic gas production, cumulative gas production, molar percentage of CO and H in fermentation gases, and microbial protein in cultural fluids decreased with the increase in the gossypol addition. Conversely, the gossypol addition increased the molar percentage of CH, ammonia N, and total volatile fatty acid production. More than 95% of the gossypol addition disappeared after 48 h of in vitro incubation. Regardless of whatever ration type was incubated, the real-time PCR analysis showed that the gossypol addition decreased the populations of , , , , , and fungi but increased , protozoa, and total bacteria in culture fluids in comparison with the control ( < 0.01). Additionally, the tendency of a smaller population was observed for , , and fungi with greater inclusion of gossypol, but a greater population was observed for , , , protozoa, and total bacteria. In summary, the present results suggest that rumen microorganisms indeed presented a high ability to degrade gossypol, but there was an obvious detrimental effect of the gossypol addition on rumen fermentation by decreasing microbial activity when the gossypol inclusion exceeded 0.5 mg/g, and such inhibitory effect was more pronounced in the low-forage than the high-forage group.
PubMed: 33800444
DOI: 10.3390/toxics9030051 -
Frontiers in Microbiology 2021This study was conducted to examine the influences of replacing soybean meal (SBM) with fermented soybean meal (FSBM) in the diet of lactating Holstein cattle on rumen...
This study was conducted to examine the influences of replacing soybean meal (SBM) with fermented soybean meal (FSBM) in the diet of lactating Holstein cattle on rumen fermentation and ruminal bacterial microbiome. Twenty-four lactating Chinese Holstein dairy cattle were assigned to each of the two treatments in a completely randomized design: the SBM group [the basal total mixed ration (TMR) diet containing 5.77% SBM] and the FSBM group (the experimental TMR diet containing 5.55% FSBM). This trial lasted for 54 days (14 days for adjustment and 40 days for data and sample collection), and samples of rumen liquid were collected on 34 d and 54 d, respectively. The results showed that replacing SBM with FSBM significantly increased the molar percentages of propionate ( < 0.01) and valerate ( < 0.05), but reduced the total volatile fatty acid (TVFA) concentration ( < 0.05), butyrate molar proportion ( < 0.05), and the acetate to propionate ratio ( < 0.01). The copy numbers of total bacteria ( < 0.05), ( < 0.01), ( < 0.01), and spp. ( < 0.05) in the FSBM group were greater, while the density of ( < 0.05) was lower than those in the SBM treatment. Additionally, and were significantly enriched ( < 0.05) in the rumen fluid of FSBM-fed cows, despite the fact that there was no remarkable difference in the Alpha diversity indexes, structure and KEGG pathway abundances of the bacterial community across the two treatments. It could hence be concluded that the substitution of FSBM for SBM modulated rumen fermentation and rumen bacterial microbiota in lactating Holstein dairy cows. Further research is required to elucidate the relevant mechanisms of FSBM, and provide more insights into the application of FSBM in dairy cattle.
PubMed: 33584627
DOI: 10.3389/fmicb.2021.625857 -
Applied and Environmental Microbiology Apr 2021As a water-soluble polymer, the widely used polyvinyl alcohol (PVA) is produced from hydrolysis of polyvinyl acetate. Microbial PVA carbon backbone cleavage via a...
As a water-soluble polymer, the widely used polyvinyl alcohol (PVA) is produced from hydrolysis of polyvinyl acetate. Microbial PVA carbon backbone cleavage via a two-step reaction of dehydrogenation and hydrolysis has been well studied. Content of acetyl group is a pivotal factor affecting performance of PVA derivatives in industrial application, and deacetylation is a non-negligible part in PVA degradation. However, the genetic and biochemical studies of its deacetylation remain largely elusive. Here, sp. strain NyZ500 was isolated for its capability of growing on acetylated PVA from activated sludge. A spontaneous PVA-utilization deficient mutant strain NyZ501 was obtained when strain NyZ500 was cultured in rich media. Comparative analysis between the genomes of these two strains revealed a fragment (containing a putative hydrolase gene ) deletion in NyZ501 and complemented strain NyZ501 restored the ability to grow on PVA. DacA which shares 21% identity with xylan esterase AxeA1 from 23, is a unique deacetylase catalyzing the conversion of acetylated PVA and its derivatives to deacetylated counterparts. This indicates that strain NyZ500 utilizes acetylated PVA via acetate as a carbon source to grow. DacA also possessed the deacetylation ability for acetylated xylan and the antibiotic intermediate 7-aminocephalosporanic acid (7ACA) but the enzymes for the above two compounds had no activities against PVA derivatives. This study enhanced our understanding of the diversity of microbial degradation of PVA and DacA characterized here is also a potential biocatalyst for the eco-friendly biotransformation of PVA derivatives and other acetylated compounds. Water-soluble PVA, which possesses a very robust ability to accumulate in the environment, has a very grave environmental impact due to its widespread use in industrial and household applications. On the other hand, chemical transformation of PVA derivatives is currently being carried out at high energy consumption and high pollution conditions using hazardous chemicals (such as NaOH, methanol) under high temperatures. The DacA reported here performs PVA deacetylation under mild conditions, then it has a great potential to be developed into an eco-friendly biocatalyst for biotransformation of PVA derivatives. DacA also has deacetylation activity for compounds other than PVA derivatives, which facilitates its development into a broad-spectrum deacetylation biocatalyst for production of certain desired compounds.
PubMed: 33547060
DOI: 10.1128/AEM.03016-20