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Microorganisms Dec 2022Ruminants are foregut fermenters that have the remarkable ability of converting plant polymers that are indigestible to humans into assimilable comestibles like meat and... (Review)
Review
Ruminants are foregut fermenters that have the remarkable ability of converting plant polymers that are indigestible to humans into assimilable comestibles like meat and milk, which are cornerstones of human nutrition. Ruminants establish a symbiotic relationship with their microbiome, and the latter is the workhorse of carbohydrate fermentation. On the other hand, during carbohydrate fermentation, synthesis of propionate sequesters H, thus reducing its availability for the ultimate production of methane (CH4) by methanogenic archaea. Biochemically, methane is the simplest alkane and represents a downturn in energetic efficiency in ruminants; environmentally, it constitutes a potent greenhouse gas that negatively affects climate change. is a very versatile microbe capable of processing a wide range of proteins and polysaccharides, and one of its fermentation products is propionate, a trait that appears conspicuous in strain 23. Since propionate, but not acetate or butyrate, constitutes an H sink, propionate-producing microbes have the potential to reduce methane production. Accordingly, numerous studies suggest that members of the genus have the ability to divert the hydrogen flow in glycolysis away from methanogenesis and in favor of propionic acid production. Intended for a broad audience in microbiology, our review summarizes the biochemistry of carbohydrate fermentation and subsequently discusses the evidence supporting the essential role of in lignocellulose processing and its association with reduced methane emissions. We hope this article will serve as an introduction to novice researchers and as an update to others more conversant with the topic.
PubMed: 36677293
DOI: 10.3390/microorganisms11010001 -
Oncogene Feb 2023Appendectomy impacts the homeostasis of gut microbiome in patients. We aimed to study the role of appendectomy in colorectal cancer (CRC) risk through causing gut...
Appendectomy impacts the homeostasis of gut microbiome in patients. We aimed to study the role of appendectomy in colorectal cancer (CRC) risk through causing gut microbial dysbiosis. Population-based longitudinal study (cohort 1, n = 129,155) showed a 73.0% increase in CRC risk among appendectomy cases throughout 20 years follow-up (Adjusted sub-distribution hazard ratio (SHR) 1.73, 95% CI 1.49-2.01, P < 0.001). Shotgun metagenomic sequencing was performed on fecal samples from cohort 2 (n = 314). Gut microbial dysbiosis in appendectomy subjects was observed with significant enrichment of 7 CRC-promoting bacteria (Bacteroides vulgatus, Bacteroides fragilis, Veillonella dispar, Prevotella ruminicola, Prevotella fucsa, Prevotella dentalis, Prevotella denticola) and depletion of 5 beneficial commensals (Blautia sp YL58, Enterococcus hirae, Lachnospiraceae bacterium Choco86, Collinsella aerofaciens, Blautia sp SC05B48). Microbial network analysis showed increased correlation strengths among enriched bacteria and their enriched oncogenic pathways in appendectomy subjects compared to controls. Of which, B. fragilis was the centrality in the network of the enriched bacteria. We further confirmed that appendectomy promoted colorectal tumorigenesis in mice by causing gut microbial dysbiosis and impaired intestinal barrier function. Collectively, this study revealed appendectomy-induced microbial dysbiosis characterized by enriched CRC-promoting bacteria and depleted beneficial commensals, signifying that the gut microbiome may play a crucial role in CRC development induced by appendectomy.
Topics: Animals; Mice; Gastrointestinal Microbiome; Dysbiosis; Appendectomy; Longitudinal Studies; Colorectal Neoplasms
PubMed: 36539569
DOI: 10.1038/s41388-022-02569-3 -
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 -
Nutrients Jul 2022Precision dietary interventions (e.g., altering proportions of dietary protein fractions) has significant implications for the efficiency of nutrient use in ruminants,...
Precision dietary interventions (e.g., altering proportions of dietary protein fractions) has significant implications for the efficiency of nutrient use in ruminants, as well as lowering their environmental footprint, specifically nitrogen (N) emissions. Soluble protein (SP) is defined as the protein fraction that is rapidly degraded in the rumen (e.g., non-protein N and true protein), and our previous study found that regulating SP levels could improve N efficiency in Hu sheep. Thus, the present study was conducted to explore in vitro how protein fractions with different SP levels modulate the rumen microbial community and its association with N metabolism. Four dietary treatments with different SP proportions and similar crude protein (CP) content (~14%) were formulated (% of CP): 20 (S20), 30 (S30), 40 (S40) and 50 (S50). Results showed that NH3-N content increased with increasing SP levels at 4, 12 and 24 h; TVFA, acetate, propionate and valerate were higher in S30 and S40 (p < 0.05) and had quadratic effects (p < 0.05). Moreover, dry matter digestibility (DMD) and N digestibility (ND) were all decreased with S20 and S50 (p < 0.05). The S30 and S40 treatments increased the abundance of Bacteroidetes and Prevotella (Prevotella_ruminicola) but decreased the abundance of Firmicutes and Proteobacteria (p < 0.05). Bacterial pathways related to amino acid and fatty acid metabolism also were enriched with S30 and S40. The abundance of Entodinium was increased with S30 and S40 and had a positive correlation with Prevotella, and these two genera also played an important role in N metabolism and VFA synthesis of this study. In conclusion, bacterial and protozoal communities were altered by the level of SP (% of CP), with higher SP levels (~50% of CP) increasing the microbial diversity but being detrimental to rumen N metabolism.
Topics: Animal Feed; Animals; Bacteria; Diet; Dietary Proteins; Digestion; Fermentation; Nitrogen; Rumen; Sheep; Solubility
PubMed: 35889928
DOI: 10.3390/nu14142972 -
Journal of Animal Science Nov 2022The rumen is a vital organ containing vast amounts of microbes that play a key role in the digestion of nutrients and affect the production performance of ruminants....
The rumen is a vital organ containing vast amounts of microbes that play a key role in the digestion of nutrients and affect the production performance of ruminants. However, few studies have focused on the characterization of the ruminal microbiota composition and function in cows with long-term difference milk protein concentrations, and the relationship between milk protein concentration and ruminal microbiota remains elusive. In this study, we collected the data of milk protein concentrations of 1,025 Holstein cows for 10 mo on a commercial farm. Based on the milk protein concentrations, 30 cows were selected and divided into three groups (n = 10 per group): low milk protein group (LMP, milk protein concentration < 3.1%), medium milk protein group (MMP, 3.1% ≤ milk protein concentration < 3.4%), and high milk protein group (HMP, milk protein concentration ≥ 3.4%). The ruminal microbiome, metabolome, VFA concentrations and proportions, and amino acid profiles of the three groups were analyzed. The data showed that free amino acid (FAA) levels were lower in the rumen and higher in the plasma of HMP cows (P < 0.05). In addition, lower NH3 concentrations were observed in the rumen, plasma, and milk of the HMP cows (P < 0.05). Protease activity and isobutyric acid molar proportion in the rumen were lower in the HMP group (P < 0.05). Microbiome analysis showed that HMP cows had lower microbial diversity (represented as Shannon and Simpson indices) than LMP cows. At the genus level, lower relative abundances of Prevotella_1 and Ruminococcaceae_UCG_005 were observed in the HMP group (P < 0.05). At the operational taxonomic unit (OTU) level, a lower relative abundance of OTU3 (Prevotella ruminicola) was observed in the HMP group (P < 0.05). We found that the relative abundances of ruminal Prevotella_1 and OTU3 (Prevotella ruminicola) were negatively correlated with milk protein concentration (P < 0.05). These findings suggested that the cows with long-term high milk protein concentrations had lower microbial diversity and weaker protein degradation ability in the rumen. Furthermore, our observations identified a correlation between the milk protein concentration and ruminal microbiota.
Topics: Female; Cattle; Animals; Milk Proteins; Rumen; Lactation; Fatty Acids, Volatile; Fermentation; Diet; Microbiota; Prevotella; Metabolome; Amino Acids; Animal Feed
PubMed: 35938984
DOI: 10.1093/jas/skac253 -
Frontiers in Microbiology 2022It was acknowledged long ago that microorganisms have played critical roles in animal evolution. Tibetan wild asses (TWA, ) are the only wild perissodactyls on the...
It was acknowledged long ago that microorganisms have played critical roles in animal evolution. Tibetan wild asses (TWA, ) are the only wild perissodactyls on the Qinghai-Tibet Plateau (QTP) and the first national protected animals; however, knowledge about the relationships between their gut microbiota and the host's adaptability remains poorly understood. Herein, 16S rRNA and meta-genomic sequencing approaches were employed to investigate the gut microbiota-host associations in TWA and were compared against those of the co-resident livestock of yak () and Tibetan sheep (). Results revealed that the gut microbiota of yak and Tibetan sheep underwent convergent evolution. By contrast, the intestinal microflora of TWA diverged in a direction enabling the host to subsist on sparse and low-quality forage. Meanwhile, high microbial diversity (Shannon and Chao1 indices), cellulolytic activity, and abundant indicator species such as Spirochaetes, Bacteroidetes, , and supported forage digestion and short-chain fatty acid production in the gut of TWA. Meanwhile, the enterotype identification analysis showed that TWA shifted their enterotype in response to low-quality forage for a better utilization of forage nitrogen and short-chain fatty acid production. Metagenomic analysis revealed that plant biomass degrading microbial consortia, genes, and enzymes like the cellulolytic strains (, and ), as well as carbohydrate metabolism genes (GH43, GH3, GH31, GH5, and GH10) and enzymes (β-glucosidase, xylanase, and β-xylosidase, etc.) had a significantly higher enrichment in TWA. Our results indicate that gut microbiota can improve the adaptability of TWA through plant biomass degradation and energy maintenance by the functions of gut microbiota in the face of nutritional deficiencies and also provide a strong rationale for understanding the roles of gut microbiota in the adaptation of QTP wildlife when facing harsh feeding environments.
PubMed: 35923394
DOI: 10.3389/fmicb.2022.949002 -
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 -
Animal Nutrition (Zhongguo Xu Mu Shou... Mar 2020Rumen fermentation parameters and microbiota were evaluated in 3 in vitro rumen fermentation experiments after addition of chestnut tannins (CWT) or an extract from...
Rumen fermentation parameters and microbiota were evaluated in 3 in vitro rumen fermentation experiments after addition of chestnut tannins (CWT) or an extract from Bertoni (SB) to substrates. A control (CTR) substrate was fermented alone or added with 1.5% of CWT or SB extracts in a batch culture system (Exp. 1, fermentation in 500 mL for 24 h) and in a subsequent continuous culture system (Exp. 2, fermentation in 2 L bottles for 9 d). Experiment 3 used the fermentation system of Exp. 1 and tested 7 doses of each extract added to CTR (additions of 0.2%, 0.4%, 0.6%, 0.8%, 1.0%, 1.2% and 1.4% for 48 h). The addition of CWT lowered ( < 0.01) the in vitro rumen ammonia concentration in all experiments and reduced the protozoa counts in Exp. 1 ( < 0.05). In contrast, the SB extract did not modify the ammonia concentrations, but significantly lowered the protozoa counts in all 3 experiments (reduction of 47% and 20% in Exp. 1 and 2, < 0.05; and a quadratic reduction in Exp. 3, = 0.63, < 0.01). Neither extract affected the fermentation in terms of gas production (Exp. 1 and 3) nor volatile fatty acids (VFA) yield (Exp. 1 and 2), if we exclude a reduction at the highest CWT concentration in Exp. 3. Changes in VFA profile were induced by CWT and were limited to reductions in the iso-valerate ( < 0.01, in Exp. 2) and iso-butyrate levels ( < 0.01, Exp. 2). The CWT increased the abundance of and and decreased that of ( < 0.01, < 0.05 and < 0.05, respectively). The SB extract increased the relative abundance of ( < 0.05). Both of the studied substances had an impact on rumen metabolism, with SB reducing protozoa counts and CWT lowering the rumen ammonia concentration. The effects of both extracts on the rumen were appreciable at low dietary doses, and the negative impacts on fermentation were limited to the reduction in protein degradation with the addition of CWT.
PubMed: 32211529
DOI: 10.1016/j.aninu.2019.11.009 -
Frontiers in Cellular and Infection... 2020Gut dysbiosis has been associated with several disease outcomes including diabetes in human populations. Currently, there are no studies of the gut microbiome...
Gut dysbiosis has been associated with several disease outcomes including diabetes in human populations. Currently, there are no studies of the gut microbiome composition in relation to type 2 diabetes (T2D) in Africans. Here, we describe the profile of the gut microbiome in non-diabetic adults (controls) and investigate the association between gut microbiota and T2D in urban West Africans. Gut microbiota composition was determined in 291 Nigerians (98 cases, 193 controls) using fecal 16S V4 rRNA gene sequencing done on the Illumina MiSeq platform. Data analysis of operational taxonomic units (OTU) was conducted to describe microbiome composition and identify differences between T2D and controls. The most abundant phyla were , and . , and were significantly lower in cases than controls ( < 0.001). Feature selection analysis identified a panel of 18 OTUs enriched in cases that included . A panel of 17 OTUs that was enriched in the controls included , and . OTUs with strain-level annotation showing the largest fold-change included (logFC = -3.1; = 4.2 × 10), (logFC = -2.5; = 0.005), (logFC = -1.76; = 0.01), all lower in cases. These findings are notable because supplementation with and has been shown to improve hyperglycemia and reduce insulin resistance in murine models. This first investigation of gut microbiome and diabetes in urban Africans shows that T2D is associated with compositional changes in gut microbiota highlighting the possibility of developing strategies to improve glucose control by modifying bacterial composition in the gut.
Topics: Actinobacteria; Bacteroidetes; Black People; Case-Control Studies; Diabetes Mellitus, Type 2; Dysbiosis; Female; Firmicutes; Gastrointestinal Microbiome; Humans; Hypoglycemic Agents; Male; Metformin; Middle Aged; Nigeria; Urban Health
PubMed: 32158702
DOI: 10.3389/fcimb.2020.00063 -
Animal Bioscience May 2024This study investigated the impact of Aspergillus niger lysing polysaccharide monooxygenase (AnLPMO) on in vitro rumen microbial fermentation of rice straw.
OBJECTIVE
This study investigated the impact of Aspergillus niger lysing polysaccharide monooxygenase (AnLPMO) on in vitro rumen microbial fermentation of rice straw.
METHODS
AnLPMO was heterologously expressed in Escherichia coli. Fourier transform infrared spectrometry and X-ray photoelectron spectroscopy analyzed the surface structure of rice straw after AnLPMO treatment. Two in vitro experiments, coupled with 16S high-throughput sequencing and qRT-PCR techniques, assessed the influence of AnLPMO on rumen microbial fermentation of rice straw.
RESULTS
AnLPMO exhibited peak activity at 40 °C and pH 6.5, with a preference for rice straw xylan hydrolysis, followed by Avicel. AnLPMO application led to the fractional removal of cellulose and hemicelluloses and a notable reduction in the levels of carbon elements and C-C groups present on the surface of rice straw. Compared to the control (no AnLPMO), supplementing AnLPMO at 1.1 U-2.0 U significantly enhanced in vitro digestibility of dry matter (IVDMD, P < 0.01), total gas production (P < 0.01), and concentrations of total volatile fatty acids (VFA, P < 0.01), acetate (P < 0.01), and ammonia-N (P < 0.01). Particularly, the 1.4 U AnLPMO group showed a 14.8% increase in IVDMD. In the second experiment, compared to deactivated AnLPMO (1.4 U), supplementing bioactive AnLPMO at 1.4 U increased IVDMD (P = 0.01), total gas production (P = 0.04), and concentrations of total VFA (P < 0.01), propionate (P < 0.01), and ammonia-N (P < 0.01), with a limited 9.6% increase in IVDMD. Supplementing AnLPMO stimulated the growth of ruminal bacterial taxa facilitating fiber degradation, including Proteobacteria, Spirochaetes, Succinivibrio, Rikenellaceae_RC9_Gut_Group, Prevotelaceae_UCG-003, Desulfovibrio, Fibrobacter succinogenes, Ruminococcus albus, R. flavefaciens, Prevotella bryantii, P. ruminicola, and Treponema bryantii.
CONCLUSION
These findings highlight AnLPMO's potential as a feed additive for improving rice straw utilization in ruminant production.
PubMed: 38754847
DOI: 10.5713/ab.24.0026