Nitrogen cycling in the gut

Determination and prediction of net energy of soybean meal fed to pregnant sows by indirect calorimetry

OBJECTIVE

The study was conducted to investigate the appropriate substitution level of soybean meal (SBM) for determining its net energy (NE), and establish NE prediction equation of SBM based on the determined NE values for pregnant sows.

METHODS

In Exp. 1, eighteen pregnant sows (Landrace×Yorkshire; parity, 2 to 3) with an initial body weight (BW) of 221.2±2.6 kg at mid-gestation were blocked by BW and randomly assigned into 3 groups. Three groups fed with a corn-SBM basal diet and two test diets with 15% and 30% energy-supplying components replaced by SBM, respectively. In Exp. 2, six diets were formulated including a corn-SBM basal diet and five SBM diets (based on the substitution level determined of Exp. 1) with different soybean sources and processing methods. Moreover, 12 pregnant pigs (BW = 209.0±3.0 kg; parity, 3 to 4) at mid-gestation were arranged in a 6×3 Youden square design.

RESULTS

Increasing substitution levels of SBM linearly increased (p<0.05) fecal and urinary nitrogen excretion and the ratio of urinary energy to digestible energy (DE), while linearly decreased (p<0.05) the ratio of metabolizable energy (ME) to DE and tended to linearly decrease dietary ME (p = 0.066) and NE (p = 0.074). The coefficient of variation for the NE of SBM was lower at a 15% substitution level compared to a 30% substitution level. The nutritional compositions of SBM are influenced by the soybean sources and processing methods. As dry matter basis, NE values of SBM ranged from 11.1 to 12.7 MJ/kg and the best-fitted prediction equation for NE of SBM was: NE (MJ/kg) = -91.71+5.35×gross energy (%)-0.03×neutral detergent fiber (%; R2 = 0.96).

CONCLUSION

A substitution level of 15% was more appropriate to determine NE of SBM. Furthermore, NE values of SBM can be predicted based on their chemical compositions.

Determination of Plasma Metabolites and Basal Ileal Endogenous Amino Acid Losses in Growing Pigs Fed a Nitrogen-Free or Casein Diet

The nitrogen-free diet (NFD) method for determining basal ileal endogenous losses (BEL) of amino acids (AA) has been associated with different metabolic abnormalities that can affect the accurate determination of BEL. Consequently, the use of highly digestible proteins has been suggested. This study aimed to determine the metabolic status and BEL of AA in pigs fed either an NFD or a casein (CAS) diet. Eight cannulated, castrated male pigs (39.8 kg) were randomly assigned to a 2 × 2 crossover design. An NFD diet based on corn starch, dextrose, cellulose, oil, vitamins and minerals was used. The CAS diet was equivalent, but 18% of the corn starch was replaced with casein. Pigs were fed one of the diets for a 7-day period, and blood samples were collected at the beginning and end of each period to determine plasma metabolites. Ileal digesta samples were collected on Days 6 and 7 to estimate the BEL of the AA. Results indicated that plasma albumin was significantly higher (p < 0.05) in pigs fed the CAS diet, whereas creatinine and LDL levels were higher (p < 0.03) in pigs fed the NFD. No significant differences were observed in the levels of other plasma metabolites. The BEL of protein did not differ between diets. However, in pigs fed the CAS diet, the BEL of glutamic acid, aspartic acid, serine, glycine, histidine, threonine, alanine, tyrosine and valine significantly increased (p < 0.05), while isoleucine showed a tendency to increase (p = 0.06). In conclusion, NFD did not significantly affect energy and lipid metabolism in pigs. However, the decrease in albumin synthesis and increase in plasma creatinine levels indicate that pigs fed NFD have a negative protein balance, affecting the estimation of the BEL of AA. Therefore, it is essential to consider the metabolic state of animals when estimating the BEL of AA.

Nutrition of Escherichia coli within the intestinal microbiome

In this chapter, we update our 2004 review of "The Life of Commensal Escherichia coli in the Mammalian Intestine" (https://doi.org/10.1128/ecosalplus.8.3.1.2), with a change of title that reflects the current focus on "Nutrition of E. coli within the Intestinal Microbiome." The earlier part of the previous two decades saw incremental improvements in understanding the carbon and energy sources that E. coli and Salmonella use to support intestinal colonization. Along with these investigations of electron donors came a better understanding of the electron acceptors that support the respiration of these facultative anaerobes in the gastrointestinal tract. Hundreds of recent papers add to what was known about the nutrition of commensal and pathogenic enteric bacteria. The fact that each biotype or pathotype grows on a different subset of the available nutrients suggested a mechanism for succession of commensal colonizers and invasion by enteric pathogens. Competition for nutrients in the intestine has also come to be recognized as one basis for colonization resistance, in which colonized strain(s) prevent colonization by a challenger. In the past decade, detailed investigations of fiber- and mucin-degrading anaerobes added greatly to our understanding of how complex polysaccharides support the hundreds of intestinal microbiome species. It is now clear that facultative anaerobes, which usually cannot degrade complex polysaccharides, live in symbiosis with the anaerobic degraders. This concept led to the "restaurant hypothesis," which emphasizes that facultative bacteria, such as E. coli, colonize the intestine as members of mixed biofilms and obtain the sugars they need for growth locally through cross-feeding from polysaccharide-degrading anaerobes. Each restaurant represents an intestinal niche. Competition for those niches determines whether or not invaders are able to overcome colonization resistance and become established. Topics centered on the nutritional basis of intestinal colonization and gastrointestinal health are explored here in detail.

Microbial urea-nitrogen recycling in arctic ground squirrels: the effect of ambient temperature of hibernation

Energy conservation associated with hibernation is maximized at the intersection of low body temperature (Tb), long torpor bouts, and few interbout arousals. In the arctic ground squirrel (Urocitellus parryii), energy conservation during hibernation is best achieved at ambient temperatures (Ta) around 0 °C; however, they spend the majority of hibernation at considerably lower Ta. Because arctic ground squirrels switch to mixed fuel metabolism, including protein catabolism, at extreme low Ta of hibernation, we sought to investigate how microbial urea-nitrogen recycling is used under different thermal conditions. Injecting squirrels with isotopically labeled urea (13C/15N) during hibernation at Ta's of - 16 °C and 2 °C and while active and euthermic allowed us to assess the ureolytic activity of gut microbes and the amount of liberated nitrogen incorporated into tissues. We found greater incorporation of microbially-liberated nitrogen into tissues of hibernating squirrels. Although ureolytic activity appears higher in euthermic squirrels, liberated nitrogen likely makes up a smaller percentage of the available nitrogen pool in active, fed animals. Because non-lipid fuel is a limiting factor for torpor at lower Ta in this species, we hypothesized there would be greater incorporation of liberated nitrogen in animals hibernating at - 16 °C. However, we found higher microbial-ureolytic activity and incorporation of microbially-liberated nitrogen, particularly in the liver, in squirrels hibernating at 2 °C. Likely this is because squirrels hibernating at 2 °C had higher Tb and longer interbout arousals, a combination of factors creating more favorable conditions for gut microbes to thrive and maintain greater activity while giving the host more time to absorb microbial metabolites.

Host-diet-microbiota interplay in intestinal nutrition and health

The intestine is populated by a complex and dynamic assortment of microbes, collectively called gut microbiota, that interact with the host and contribute to its metabolism and physiology. Diet is considered a key regulator of intestinal microbiota, as ingested nutrients interact with and shape the resident microbiota composition. Furthermore, recent studies underscore the interplay of dietary and microbiota-derived nutrients, which directly impinge on intestinal stem cells regulating their turnover to ensure a healthy gut barrier. Although advanced sequencing methodologies have allowed the characterization of the human gut microbiome, mechanistic studies assessing diet-microbiota-host interactions depend on the use of genetically tractable models, such as Drosophila melanogaster. In this review, we first discuss the similarities between the human and fly intestines and then we focus on the effects of diet and microbiota on nutrient-sensing signaling cascades controlling intestinal stem cell self-renewal and differentiation, as well as disease. Finally, we underline the use of the Drosophila model in assessing the role of microbiota in gut-related pathologies and in understanding the mechanisms that mediate different whole-body manifestations of gut dysfunction.

Effects of dietary protease supplementation on in vitro soybean meal protein, dry matter digestibility, and productive performance in starter-to-finisher pigs

Background and Aim

Pig industries are currently facing a crisis in terms of protein and energy costs. Proteases were used to increase protein digestibility and metabolizable energy (ME) in diets. This study evaluated the effects of protease supplementation on in vitro protein digestibility and productive performance in starter-to-finisher pigs.

Materials and Methods

A total of 691 starter pigs were randomly allocated into three dietary treatments using a randomized complete block design. Diets were provided in three phases according to body weight (BW): Starter, grower, and finisher phases. Each phase was fed for 30, 60, and 24 days of treatment diets as T1: basal diet and T2 and T3: the basal diet supplemented with 240 ppm protease reduced by 50 kcal/kg ME plus 1% crude protein (CP) and by 100 kcal/kg ME plus 2% CP, respectively. Protease and in vitro protein digestibility were measured. BW and feed intake were recorded to calculate the average daily gain (ADG), average daily feed intake (ADFI), feed-to-gain (F:G), and gain-to-feed (G:F) ratios.

Results

There were no significant differences (p > 0.05) in the percentage of in vitro protein digestibility between the groups with and without protease supplementation. In the finisher phase, T2 had lower (p < 0.05) ADFI and F:G than T1 and T3. Overall, T3 had lower (p < 0.05) ADG, ADFI, and F:G than T1 and T2.

Conclusion

Protease supplementation significantly affects protein digestibility. Supplementing basal diets with 240 ppm protease reduced ME by 50 kcal/kg and CP by 1% without affecting ADG, ADFI, F:G, and G:F ratios for starter-to-finisher pigs.

Animal board invited review: Heritability of nitrogen use efficiency in fattening pigs: Current state and possible directions

Pork, an important component of human nutrition worldwide, contributes considerably to anthropogenic nitrogen and greenhouse gas emissions. Reducing the environmental impact of pig production is therefore essential. This can be achieved through system-level strategies, such as optimising resource use, improving manure management and recycling leftovers from human food production, and at the individual animal level by maintaining pig health and fine-tuning dietary protein levels to individual requirements. Breeding, coupled with nutritional strategies, offers a lasting solution to improve nitrogen use efficiency (NUE) - the ratio of nitrogen retained in the body to nitrogen ingested. With a heritability as high as 0.54, incorporating NUE into breeding programmes appears promising. Nitrogen use efficiency involves multiple tissues and metabolic processes, and is influenced by the environment and individual animal characteristics, including its genetic background. Heritable genetic variation in NUE may therefore occur in many different processes, including the central nervous regulation of feed intake, the endocrine system, the gastrointestinal tract where digestion and absorption take place, and the composition of the gut microbiome. An animal's postabsorptive protein metabolism might also harbour important genetic variation, especially in the maintenance requirements of tissues and organs. Precise phenotyping, although challenging and costly, is essential for successful breeding. Various measurement techniques, such as imaging techniques and mechanistic models, are being explored for their potential in genetic analysis. Despite the difficulties in phenotyping, some studies have estimated the heritability and genetic correlations of NUE. These studies suggest that direct selection for NUE is more effective than indirect methods through feed efficiency. The complexity of NUE indicates a polygenic trait architecture, which has been confirmed by genome-wide association studies that have been unable to identify significant quantitative trait loci. Building sufficiently large reference populations to train genomic prediction models is an important next step. However, this will require the development of truly high-throughput phenotyping methods. In conclusion, breeding pigs with higher NUE is both feasible and necessary but will require increased efforts in high-throughput phenotyping and improved genome annotation.

Linking serotonin homeostasis to gut function: Nutrition, gut microbiota and beyond

Serotonin (5-HT) produced by enterochromaffin (EC) cells in the digestive tract is crucial for maintaining gut function and homeostasis. Nutritional and non-nutritional stimuli in the gut lumen can modulate the ability of EC cells to produce 5-HT in a temporal- and spatial-specific manner that toning gut physiology and immune response. Of particular interest, the interactions between dietary factors and the gut microbiota exert distinct impacts on gut 5-HT homeostasis and signaling in metabolism and the gut immune response. However, the underlying mechanisms need to be unraveled. This review aims to summarize and discuss the importance of gut 5-HT homeostasis and its regulation in maintaining gut metabolism and immune function in health and disease with special emphasis on different types of nutrients, dietary supplements, processing, and gut microbiota. Cutting-edge discoveries in this area will provide the basis for the development of new nutritional and pharmaceutical strategies for the prevention and treatment of serotonin homeostasis-related gut and systematic disorders and diseases.

Nitrogen assimilation by E. coli in the mammalian intestine

Nitrogen is an essential element for all living organisms, including Escherichia coli. Potential nitrogen sources are abundant in the intestine, but knowledge of those used specifically by E. coli to colonize remains limited. Here, we sought to determine the specific nitrogen sources used by E. coli to colonize the streptomycin-treated mouse intestine. We began by investigating whether nitrogen is limiting in the intestine. The NtrBC two-component system upregulates approximately 100 genes in response to nitrogen limitation. We showed that NtrBC is crucial for E. coli colonization, although most genes of the NtrBC regulon are not induced, which indicates that nitrogen is not limiting in the intestine. RNA-seq identified upregulated genes in colonized E. coli involved in transport and catabolism of seven amino acids, dipeptides and tripeptides, purines, pyrimidines, urea, and ethanolamine. Competitive colonization experiments revealed that L-serine, N-acetylneuraminic acid, N-acetylglucosamine, and di- and tripeptides serve as nitrogen sources for E. coli in the intestine. Furthermore, the colonization defect of a L-serine deaminase mutant was rescued by excess nitrogen in the drinking water but not by an excess of carbon and energy, demonstrating that L-serine serves primarily as a nitrogen source. Similar rescue experiments showed that N-acetylneuraminic acid serves as both a carbon and nitrogen source. To a minor extent, aspartate and ammonia also serve as nitrogen sources. Overall, these findings demonstrate that E. coli utilizes multiple nitrogen sources for successful colonization of the mouse intestine, the most important of which is L-serine.

IMPORTANCE

While much is known about the carbon and energy sources that are used by E. coli to colonize the mammalian intestine, very little is known about the sources of nitrogen. Interrogation of colonized E. coli by RNA-seq revealed that nitrogen is not limiting, indicating an abundance of nitrogen sources in the intestine. Pathways for assimilation of nitrogen from several amino acids, dipeptides and tripeptides, purines, pyrimidines, urea, and ethanolamine were induced in mice. Competitive colonization assays confirmed that mutants lacking catabolic pathways for L-serine, N-acetylneuraminic acid, N-acetylglucosamine, and di- and tripeptides had colonization defects. Rescue experiments in mice showed that L-serine serves primarily as a nitrogen source, whereas N-acetylneuraminic acid provides both carbon and nitrogen. Of the many nitrogen assimilation mutants tested, the largest colonization defect was for an L-serine deaminase mutant, which demonstrates L-serine is the most important nitrogen source for colonized E. coli.

Core microbiota for nutrient digestion remained and ammonia utilization increased after continuous batch culture of rumen microbiota in vitro

Introduction

This study aimed to investigate the digestive function, urea utilization ability, and bacterial composition changes in rumen microbiota under high urea (5% urea in diet) over 23 days of continuous batch culture in vitro.

Methods

The gas production, dry matter digestibility, and bacterial counts were determined for the continuously batch-cultured rumen fluid (CRF). The changes in fermentation parameters, NH3-N utilization efficiency, and microbial taxa were analyzed in CRF and were compared with that of fresh rumen fluid (RF), frozen rumen fluid (FRF, frozen rumen fluid at -80°C for 1 month), and the mixed rumen fluid (MRF, 3/4 RF mixed with 1/4 CRF) with in vitro rumen fermentation.

Results

The results showed that the dry matter digestibility remained stable while both the microbial counts and diversity significantly decreased over the 23 days of continuous batch culture. However, the NH3-N utilization efficiency of the CRF group was significantly higher than that of RF, FRF, and MRF groups (p < 0.05), while five core genera including Succinivibrio, Prevotella, Streptococcus, F082, and Megasphaera were retained after 23 days of continuous batch culture. The NH3-N utilization efficiency was effectively improved after continuous batch culture in vitro, and Streptococcus, Succinivibrio, Clostridium_sensu_stricto_1, p.251.o5, Oxalobacter, Bacteroidales_UCG.001, and p.1088.a5_gut_group were identified to explain 75.72% of the variation in NH3-N utilization efficiency with the RandomForest model.

Conclusion

Thus, core bacterial composition and function retained under high urea (5% urea in diet) over 23 days of continuous batch culture in vitro, and bacterial biomarkers for ammonia utilization were illustrated in this study. These findings might provide potential applications in improving the efficiency and safety of non-protein nitrogen utilization in ruminants.

Beyond the Bowl: Understanding Amino Acid Requirements and Digestibility to Improve Protein Quality Metrics for Dog and Cat Foods

The determination of amino acid (AA) requirements for mammals has traditionally been done through nitrogen (N) balance studies, but this technique underestimates AA requirements in adult animals. There has been a shift toward researchers using the indicator amino acid oxidation (IAAO) technique for the determination of AA requirements in humans, and recently in dogs. However, the determination of AA requirements specific to adult dogs and cats at maintenance is lacking and the current requirements outlined by the National Research Council are based on a dearth of data and are likely underreporting the requirements of indispensable AA (IAA) for the population. To ensure the physiological requirements of our cats and dogs are met, we need methods to accurately and precisely measure digestibility. In vivo methods, such as ileal cannulation, are most commonly used, however, due to ethical considerations, we are moving away from animal models and toward in vitro methods. Harmonized static digestion models have the potential to replace in vivo methods but work needs to be done to have these methods more accurately represent the gastrointestinal tract (GIT) of cats and dogs. The Digestible IAA Score (DIAAS) is one metric that can help define protein quality for individual ingredients or mixed diets that uses AA SID estimates and ideally those can be replaced with in vitro AA digestibility estimates. Finally, we need accurate and reliable laboratory AA analyses to measure the AA present in complete diets, especially those used to quantify methionine (Met) and cysteine (Cys), both often limiting AAs in cat and dog diets. Together, this will guide accurate feed formulation for our companion animals to satisfy requirements while avoiding over-supplying protein, which inevitably contributes to excess N excretion, affecting both the environment and feed sustainability.

Use of Isotope-Labeled Body or Dietary Proteins to Determine Dietary Amino Acid Digestibility

Amino acid (AA) digestibility in humans has been determined conventionally based on oro-ileal AA disappearance. With this approach, it is necessary to account for undigested AAs of body origin (endogenous AAs) found in the ileal digesta. Determination of the endogenous AAs under physiological conditions is not straightforward, and the use of isotopes (labeled foods or body tissues) has been pivotal to advancing our understanding. The application of isotopes for determining gut endogenous AAs and AA digestibility is discussed as well as the types of digestibility coefficient generated (apparent, true, real) dependent upon methodology. Recently a new dual isotope-based method for determining ileal AA digestibility in humans has been developed that obviates the collection of ileal digesta. The dual isotope method, which awaits full validation, offers considerable promise for making noninvasive measures of AA digestibility in humans of different ages and physiological states.

Characterization of the semen, gut, and urine microbiota in patients with different semen abnormalities

Introduction

Semen quality is decreasing worldwide, leading to increased male infertility. This study analyzed the microbiota of the gut, semen, and urine in individuals with semen abnormalities to identify potential probiotics and pathogenic bacteria that affect semen parameters and help develop new methods for the diagnosis and treatment of patients with semen abnormalities.

Methods

We recruited 12 individuals with normal semen parameters (control group), 12 with asthenospermia but no semen hyperviscosity (Group_1), 6 with oligospermia (Group_2), 9 with severe oligospermia or azoospermia (Group_3), and 14 with semen hyperviscosity only (Group_4). The semen, gut, and urine microbiota were examined by analyzing the 16S ribosomal RNA gene sequence using next-generation sequencing.

Results

The gut microbes were clustered into the highest number of operational taxonomic units, followed by urine and semen. Furthermore, the α-diversity of gut microbes was highest and significantly different from that of urine and semen microbiota. The microbiota of the gut, urine, and semen were all significantly different from each other in terms of β-diversity. The gut abundance of Collinsella was significantly reduced in groups 1, 3, and 4. Furthermore, the gut abundance of Bifidobacterium and Blautia was significantly decreased in Group_1, while that of Bacteroides was significantly increased in Group_3. The abundance of Staphylococcus was significantly increased in the semen of groups 1 and 4. Finally, Lactobacillus abundance was significantly reduced in the urine of groups 2 and 4.

Discussion

This study comprehensively describes the differences in intestinal and genitourinary tract microbiota between healthy individuals and those with abnormal semen parameters. Furthermore, our study identified Collinsella, Bifidobacterium, Blautia, and Lactobacillus as potential probiotics. Finally, the study identified Bacteroides in the gut and Staphylococcus in semen as potential pathogenic bacteria. Our study lays the foundation of a new approach to the diagnosis and treatment of male infertility.

Collinsella urealyticum sp. nov., a urease-positive bacterial strain isolated from swine faeces

A novel actinobacterial strain, designated AGMB00827^T, was isolated from swine faeces. Strain AGMB00827^T was obligately anaerobic, Gram-stain-positive, non-motile, non-spore-forming and rod-shaped bacterium. Comparative analyses based on the 16S rRNA gene and whole genome sequence revealed that strain AGMB00827^T was affiliated to the genus Collinsella, and was most closely related to Collinsella vaginalis Marseille-P2666^T (= KCTC 25056^T). Biochemical analysis showed strain AGMB00827^T was negative for catalase and oxidase. Interestingly, strain AGMB00827^T possessed urease activity, which was determined by traditional methods (API test and Christensen's urea medium), unlike related strains. Furthermore, the major cellular fatty acids (> 10%) of the isolate were C_18:1 ω9c, C_16:0, C_16:0 DMA and C_18:2 ω9,12c DMA. Based on the whole genome sequence analysis, the DNA G + C content of strain AGMB00827^T was 52.3%, and the genome size and numbers of rRNA and tRNA genes were 1,945,251 bp, 3 and 46, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strain AGMB00827^T and C. vaginalis KCTC 25056 ^T were 71.0 and 23.2%, respectively. Additionally, the genome analysis revealed that strain AGMB00827^T possesses urease gene cluster including ureABC and ureDEFG while the related strains do not have those genes, which is consistent with the urease activity. On the basis of polyphasic taxonomic approach, strain AGMB00827^T represents a novel species within the genus Collinsella, for which the name Collinsella urealyticum sp. nov. is proposed. The type strain is AGMB00827^T (= KCTC 25287^T = GDMCC 1.2724^T).

Gut physiology meets microbiome science

Research on the gut microbiome has gained high popularity and almost every disease has meanwhile been linked to alterations in microbiome composition. Typically assessed via stool samples, the microbiome displays a huge diversity with a multitude of environmental parameters already identified as contributing to its character. Despite impressive scientific progress, normal microbiome diversity remains largely unexplained and it is tempting to speculate some of the yet unexplained variance is hidden in normal gut physiology. Although a few genome/phenome-wide associations studies have recently highlighted physiological parameters such as stool frequency, known as contributing to microbiome diversity, there is a large knowledge base from decades of basic research on gut functions that can be explored for possible links to stool features and microbiome characteristics. And, when extrapolating findings from faecal samples to the biology in the intestinal lumen or the mucosal microenvironment, gut anatomy and physiology features need to be considered. Similarly, differences in anatomy and physiology between rodents and humans need attention when discussing findings in animals in relation to human physiology and nutrition.

NAD precursors cycle between host tissues and the gut microbiome

Nicotinamide adenine dinucleotide (NAD) is an essential redox cofactor in mammals and microbes. Here we use isotope tracing to investigate the precursors supporting NAD synthesis in the gut microbiome of mice. We find that dietary NAD precursors are absorbed in the proximal part of the gastrointestinal tract and not available to microbes in the distal gut. Instead, circulating host nicotinamide enters the gut lumen and supports microbial NAD synthesis. The microbiome converts host-derived nicotinamide into nicotinic acid, which is used for NAD synthesis in host tissues and maintains circulating nicotinic acid levels even in the absence of dietary consumption. Moreover, the main route from oral nicotinamide riboside, a widely used nutraceutical, to host NAD is via conversion into nicotinic acid by the gut microbiome. Thus, we establish the capacity for circulating host micronutrients to feed the gut microbiome, and in turn be transformed in a manner that enhances host metabolic flexibility.

Arazyme in combination with dietary carbohydrolases influences odor emission and gut microbiome in growing-finishing pigs

This study evaluated the effects of supplementing feed with arazyme and dietary carbohydrolases derived from invertebrate gut-associated symbionts on the noxious gas emissions, gut microbiota, and host-microbiome interactions of pigs. Here, 270 and 260 growing pigs were assigned to control and treatment groups, respectively. The tested feed additives contained a mixture of arazyme (2,500,000 Unit/kg) and synergetic enzymes, xylanase (200,000 Unit/kg) and mannanase (200,000 Unit/kg), derived from insect gut-associated symbionts in a 7.5:1:1 ratio. The control group was fed a basal diet and the treatment group was fed the basal diet supplemented with 0.1 % enzyme mixture (v/v) for 2 months. Odorous gases were monitored in ventilated air from tested houses. Fecal samples were collected from steel plate under the cage at the completion of the experiment to determine chemical composition, odor emissions, and bacterial communities. There was a significant decrease in the concentration of NH₃ (22.5 vs. 11.2 ppm; P < 0.05), H₂S (7.35 vs. 3.74 ppm; P < 0.05), trimethylamine (TMA) (0.066 vs. 0.001 ppm; P < 0.05), and p-cresol (0.004 ppm vs. 0 ppm; P < 0.05) at 56 d in treatment group compared with the control group. Moreover, fecal analysis results showed that exogenous enzyme supplementation caused a reduction in VFAs and indole content with approximately >60 % and 72.7 %, respectively. The result of gas emission analysis showed that NH₃ (9.9 vs. 5.3 ppm; P < 0.05) and H₂S (5.8 vs. 4.1 ppm; P < 0.05) were significantly reduced in the treatment group compared to the control group. The gut microbiota of the treatment group differed significantly from that of the control group, and the treatment group altered predicted metabolic pathways, including sulfur and nitrogen related metabolism, urea degradation. The results demonstrated that supplementing feed with arazyme with dietary carbohydrolases effectively controls noxious gas emissions and improves health and meat quality of pigs.

Mycoplasmataceae dominate microbial community differences between gut regions in mammals with a simple gut architecture

Faunivorous mammals with simple guts are thought to rely primarily on endogenously produced enzymes to digest food, in part because they lack fermentation chambers for facilitating mutualistic interactions with microbes. However, variation in microbial community composition along the length of the gastrointestinal tract has yet to be assessed in faunivorous species with simple guts. We tested for differences in bacterial taxon abundances and community compositions between the small intestines and colons of 26 individuals representing four species of shrew in the genus Crocidura. We sampled these hosts from a single locality on Sulawesi Island, Indonesia, to control for potential geographic and temporal variation. Bacterial community composition differed significantly between the two gut regions and members of the family Mycoplasmataceae contributed substantially to these differences. Three operational taxonomic units (OTUs) of an unclassified genus in this family were more abundant in the small intestine, whereas 1 OTU of genus Ureaplasma was more abundant in the colon. Species of Ureaplasma encode an enzyme that degrades urea, a metabolic byproduct of protein catabolism. Additionally, a Hafnia–Obesumbacterium OTU, a genus known to produce chitinase in bat gastrointestinal tracts, was also more abundant in the colon compared to the small intestine. The presence of putative chitinase- and urease-producing bacteria in shrew guts suggests mutualisms with microorganisms play a role in facilitating the protein-rich, faunivorous diets of simple gut mammals.

Effects of essential oil mixtures on nitrogen metabolism and odor emission via in vitro simulated digestion and in vivo growing pig experiments

BACKGROUND

Essential oils (EOs) are extensively used in swine production because of their bioactive action in gut health. In addition, some EOs have the potential to reduce waste emission. The present study aimed to find an optimal combination of carvacrol, thymol and cinnamaldehyde to promote nitrogen utilization and reduce waste emission by a model in vitro and an animal study.

RESULTS

In the study in vitro, various dosages of essential oils (EOs) were used to evaluate the effect on nitrogen metabolism through a three-step model. Compared with other EO combinations, 2EO (10 ppm cinnamaldehyde and 20 ppm thymol), and 3EO (10 ppm cinnamaldehyde, 20 ppm thymol and 200 ppm carvacrol) displayed greater nitrogen digestibility, lesser ammonia production and lower activity of microbial enzymes. In the animal study, growing male Landrace × Yorkshire pigs (initial body weight: 31.8 ± 3.3 kg, n = 18) were randomly divided into three groups and fed the control, 2EO or 3EO diet for 4 weeks. Pigs fed 3EO exhibited the greatest nitrogen digestibility (85.4%, P < 0.05). EO supplementation decreased the emission of ammonia (130-140 vs. 223 mg g^-1 ) and total fecal nitrogen (8.0-9.9 vs. 12.4 g d^-1 ) (P < 0.05). Microbial protease and urease activities were inhibited by EO treatments (P < 0.01). Both 2EO and 3EO reduced the content of indole and 3-methylindole (P < 0.01), whereas only 2EO caused a decrease in p-cresol (P < 0.1).

CONCLUSION

2EO was suitable for reducing waste emission and odorous compounds in growing pigs, whereas 3EO was optimal for increasing nitrogen utilization and partially reducing waste odorous compounds. © 2021 Society of Chemical Industry.

Sex-Related Differences in UT-B Urea Transporter Abundance in Fallow Deer Rumen

Rumen studies have focused almost exclusively on livestock species under strictly regimented diets. This means that the ruminal condition of free-living and free-feeding wildlife remains practically unstudied. Urea nitrogen salvaging, a process by which urea is passed into the rumen, to both provide a valuable source of nitrogen for bacterial growth and to buffer the potentially harmful acidic effects of bacterial short chain fatty acids, has remained unexplored in wild ruminants, such as deer. UT-B2 transporters are the key proteins reported to facilitate the transepithelial ruminal urea transport. In this study, we investigate the expression, abundance and localisation of urea transporters in the rumen of a semi-wild fallow deer (Dama dama) population. Physical measurements confirmed that males had larger rumen than females, while adults had longer papillae than juveniles. Initial RT-PCR experiments confirmed the expression of UT-B2, while immunolocalisation studies revealed that strong UT-B staining was present in the stratum basale of deer rumen. Western blotting analysis demonstrated that a 50 kDa UT-B2 protein was significantly more abundant in adult females compared to adult males. This study confirms the presence of UT-B2 urea transporters in deer rumen and suggests that sex-related differences occur, bringing new insight into our understanding of rumen physiology.

Interference of dietary polyphenols with potentially toxic amino acid metabolites derived from the colonic microbiota

Each day, varying amounts of undigested or partially digested proteins reach the colon where they are metabolized by the microbiota, resulting in the formation of compounds such as ammonia, p-cresol, skatole, phenol, indole, and hydrogen sulfide (H₂S). In farm animals, the excessive production of these metabolites can affect the quality of meat and milk and is a source of contaminating emissions from animal manure. In humans, their accumulation is potentially harmful, and it has been proposed that they could be involved in the development of pathologies such as colorectal cancer and ulcerative colitis, among others. This review assesses the evidence supporting the use of dietary polyphenols to reduce the production of these metabolites. Most studies have used condensed (proanthocyanidins) or hydrolyzable (ellagitannins and gallotannins) tannins, and have been carried out in farm animals. Several show that the administration of tannins in pigs, chicken, and ruminants decreases the levels of ammonia, p-cresol, skatole, and/or H₂S, improving meat/milk quality and reducing manure odor. Direct application of tannins to manure also decreases ammonia emissions. Few studies were carried out in rats and humans and their results confirm, to a lesser extent, those reported in farm animals. These effects would be due to the capacity of tannins to trap ammonia and H₂S, and to modify the composition of the microbiota, reducing the bacterial populations producing metabolites. In addition, PACs prevent p-cresol and H₂S-induced alterations on intestinal cells in vitro. Tannins, therefore, appear as an interesting tool for improving the quality of animal products, human health, and the harmful emissions associated with breeding.

Gastrointestinal Interaction between Dietary Amino Acids and Gut Microbiota: With Special Emphasis on Host Nutrition

The gastrointestinal tract (GIT) of humans and animals is host to a complex community of different microorganisms whose activities significantly influence host nutrition and health through enhanced metabolic capabilities, protection against pathogens, and regulation of the gastrointestinal development and immune system. New molecular technologies and concepts have revealed distinct interactions between the gut microbiota and dietary amino acids (AAs) especially in relation to AA metabolism and utilization in resident bacteria in the digestive tract, and these interactions may play significant roles in host nutrition and health as well as the efficiency of dietary AA supplementation. After the protein is digested and AAs and peptides are absorbed in the small intestine, significant levels of endogenous and exogenous nitrogenous compounds enter the large intestine through the ileocaecal junction. Once they move in the colonic lumen, these compounds are not markedly absorbed by the large intestinal mucosa, but undergo intense proteolysis by colonic microbiota leading to the release of peptides and AAs and result in the production of numerous bacterial metabolites such as ammonia, amines, short-chain fatty acids (SCFAs), branched-chain fatty acids (BCFAs), hydrogen sulfide, organic acids, and phenols. These metabolites influence various signaling pathways in epithelial cells, regulate the mucosal immune system in the host, and modulate gene expression of bacteria which results in the synthesis of enzymes associated with AA metabolism. This review aims to summarize the current literature relating to how the interactions between dietary amino acids and gut microbiota may promote host nutrition and health.

Desulfovibrio diazotrophicus sp. nov., a sulfate-reducing bacterium from the human gut capable of nitrogen fixation

Sulfate-reducing bacteria (SRB) are widespread in human guts, yet their expansion has been linked to colonic diseases. We report the isolation, sequencing and physiological characterization of strain QI0027^T , a novel SRB species belonging to the class Desulfovibrionia. Metagenomic sequencing of stool samples from 45 Chinese individuals, and comparison with 1690 Desulfovibrionaceae metagenome-assembled genomes recovered from humans of diverse geographic locations, revealed the presence of QI0027^T in 22 further individuals. QI0027^T encoded nitrogen fixation genes and based on the acetylene reduction assay, actively fixed nitrogen. Transcriptomics revealed that QI0027^T overexpressed 42 genes in nitrogen-limiting conditions compared to cultures supplemented with ammonia, including genes encoding nitrogenases, a urea uptake system and the urease complex. Reanalyses of 835 public stool metatranscriptomes showed that nitrogenase genes from Desulfovibrio bacteria were expressed in six samples suggesting that nitrogen fixation might be active in the gut environment. Although frequently thought of as a nutrient-rich environment, nitrogen fixation can occur in the human gut. Animals are often nitrogen limited and have evolved diverse strategies to capture biologically active nitrogen, ranging from amino acid transporters to stable associations with beneficial microbes that provide fixed nitrogen. QI0027^T is the first Desulfovibrio human isolate for which nitrogen fixation has been demonstrated, suggesting that some sulfate-reducing bacteria could also play a role in the availability of nitrogen in the gut.

Effects of Infant Formula Supplemented With Prebiotics and OPO on Infancy Fecal Microbiota: A Pilot Randomized Clinical Trial

Several lines of evidence suggest that the intestinal microbiota plays crucial roles in infant development, and that it is highly influenced by extrinsic and intrinsic factors. Prebiotic-containing infant formula may increase gastrointestinal tolerance and improve commensal microbiota composition. However, it remains unknown whether supplementation of milk-formulas with prebiotics and 1,3-olein-2-palmitin (OPO) can achieve feeding outcomes similar to those of breastfeeding. In the present study, we investigated the effects of two kinds of infant formula with different additives on the overall diversity and composition of the fecal microbiota, to determine which was closer to breastfeeding. A total of 108 infants were enrolled, including breastfeeding (n=59) and formula feeding group (n=49). The formula feeding infants were prospectively randomly divided into a standard formula group (n=18), and a supplemented formula group(n=31). The fecal samples were collected at 4 months after intervention. Fecal microbiota analysis targeting the V4 region of the 16S rRNA gene was performed using MiSeq sequencing. The overall bacterial diversity and composition, key functional bacteria, and predictive functional profiles in the two different formula groups were compared with breastfeeding group. We found that the alpha diversity of the gut microbiota was not significantly different between the OPO and breastfeeding groups with Chaos 1 index (p=0.346). The relative abundances of Enhydrobacter and Akkermansia in the OPO group were more similar to those of the breastfeeding group than to those of the standard formula group. The gut microbiota metabolism function prediction analysis showed that the supplemented formula group was similar to the breastfeeding group in terms of ureolysis (p=0.297). These findings suggest that, when formula supplemented with prebiotics and OPO was given, the overall bacterial diversity and parts of the composition of the fecal microbiota would be similar to that of breastfeeding infants.

Breast milk urea as a nitrogen source for urease positive Bifidobacterium infantis

Human milk stimulates a health-promoting gut microbiome in infants. However, it is unclear how the microbiota salvages and processes its required nitrogen from breast milk. Human milk nitrogen sources such as urea could contribute to the composition of this early life microbiome. Urea is abundant in human milk, representing a large part of the non-protein nitrogen (NPN). We found that B. longum subsp. infantis (ATCC17930) can use urea as a main source of nitrogen for growth in synthetic medium and enzyme activity was induced by the presence of urea in the medium. We furthermore confirmed the expression of both urease protein subunits and accessory proteins of B. longum subsp. infantis through proteomics. To the same end, metagenome data were mined for urease-related genes. It was found that the breastfed infant's microbiome possessed more urease-related genes than formula fed infants (51.4:22.1; 2.3-fold increase). Bifidobacteria provided a total of 106 of urease subunit alpha alignments, found only in breastfed infants. These experiments show how an important gut commensal that colonizes the infant intestine can metabolize urea. The results presented herein further indicate how dietary nitrogen can determine bacterial metabolism in the neonate gut and shape the overall microbiome.

Interactions between starch source and gelatinisation degree on performance and small intestinal digestion in broiler chickens

1. A 2 × 2 factorial arrangement was used to test the hypothesis that, in pelleted diets, legume starch is digested less rapidly and to a lesser extent than cereal starch, and that increased gelatinisation through extrusion would eliminate the differences between the starch sources. In addition, the trial examined whether a lower ratio of starch to nitrogen disappearance rate (SNDR) could improve feed conversion ratio (FCR).2. At 17 d of age, male broilers were randomly distributed among four dietary treatments, consisting of either wheat or faba bean starch-rich fraction (FBS) as the sole starch source and pelleting or extrusion as processing methods. Each treatment had 10 replicate pens containing five birds each.3. Extrusion resulted in a more extensive starch gelatinisation compared to pelleting, as expected.4. No difference in weight gain at 29 d of age was observed between birds fed starch sources. However, birds fed wheat tended (P = 0.080) to have better FCR than those fed FBS, while the effect of processing methods was insignificant. Thus, there was no interaction between starch source and processing method on FCR.5. In pelleted diets, FBS had lower and slower starch digestibility compared to wheat in all intestinal segments (P < 0.05). The interaction between starch source and processing method in all intestinal segments (P < 0.001) demonstrated that FBS responded more to gelatinisation through extrusion than did wheat. Thus, differences in starch digestibility between the wheat and FBS were eliminated with extrusion.6. Feeding extruded diets significantly increased the upper jejunal expression of GLUT1, GLUT2 and SGLT1 compared to pelleted diets, which suggested that glucose absorption was less likely to be a limiting factor for starch utilisation.7. Pelleting resulted in a lower ratio (P < 0.001) of SNDR compared to extrusion (on average 1.4-fold) but did not improve FCR.

Genome Analysis and Genomic Comparison of the Novel Species Arthrobacter ipsi Reveal Its Potential Protective Role in Its Bark Beetle Host

The pine engraver beetle, Ips acuminatus Gyll, is a bark beetle that causes important damages in Scots pine (Pinus sylvestris) forests and plantations. As almost all higher organisms, Ips acuminatus harbours a microbiome, although the role of most members of its microbiome is not well understood. As part of a work in which we analysed the bacterial diversity associated to Ips acuminatus, we isolated the strain Arthrobacter sp. IA7. In order to study its potential role within the bark beetle holobiont, we sequenced and explored its genome and performed a pan-genome analysis of the genus Arthrobacter, showing specific genes of strain IA7 that might be related with its particular role in its niche. Based on these investigations, we suggest several potential roles of the bacterium within the beetle. Analysis of genes related to secondary metabolism indicated potential antifungal capability, confirmed by the inhibition of several entomopathogenic fungal strains (Metarhizium anisopliae CCF0966, Lecanicillium muscarium CCF6041, L. muscarium CCF3297, Isaria fumosorosea CCF4401, I. farinosa CCF4808, Beauveria bassiana CCF4422 and B. brongniartii CCF1547). Phylogenetic analyses of the 16S rRNA gene, six concatenated housekeeping genes (tuf-secY-rpoB-recA-fusA-atpD) and genome sequences indicated that strain IA7 is closely related to A. globiformis NBRC 12137^T but forms a new species within the genus Arthrobacter; this was confirmed by digital DNA-DNA hybridization (37.10%) and average nucleotide identity (ANIb) (88.9%). Based on phenotypic and genotypic features, we propose strain IA7^T as the novel species Arthrobacter ipsi sp. nov. (type strain IA7^T = CECT 30100^T = LMG 31782^T) and suggest its protective role for its host.

Comparison of methodologies used to define the protein quality of human foods and support regulatory claims

Protein quality (PQ) is the capacity of a protein to meet the amino acid (AA) requirements of an individual. There are several methodologies for determining the PQ of foods. The protein efficiency ratio is an animal growth bioassay. The protein-digestibility-corrected AA score considers the AA requirements of a reference population, and the true nitrogen digestibility coefficient for each ingredient. The digestible indispensable AA score is based on true ileal AA digestibility and better represents bioavailability of AAs. In vitro techniques for assessment of PQ are available but require validation against a greater range of protein sources. Isotopic methods, such as the indicator AA oxidation and dual tracer techniques measure AA relative bioavailability and digestibility, respectively, but require sophisticated equipment, and may not be cost nor time effective for the industry to adopt. The present review discusses advantages and disadvantages of methodologies for determining PQ of food for humans focused on methods that are or could be adopted by regulatory agencies. Understanding the framework and resources available for PQ determination will help in the selection of appropriate methods depending on the application. Novelty Understanding the framework and resources available for PQ determination will help in the selection of appropriate methods depending on the application.

Comparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species

Roseburia species are important denizens of the human gut microbiome that ferment complex polysaccharides to butyrate as a terminal fermentation product, which influences human physiology and serves as an energy source for colonocytes. Previous comparative genomics analyses of the genus Roseburia have examined polysaccharide degradation genes. Here, we characterize the core and pangenomes of the genus Roseburia with respect to central carbon and energy metabolism, as well as biosynthesis of amino acids and B vitamins using orthology-based methods, uncovering significant differences among species in their biosynthetic capacities. Variation in gene content among Roseburia species and strains was most significant for cofactor biosynthesis. Unlike all other species of Roseburia that we analysed, Roseburia inulinivorans strains lacked biosynthetic genes for riboflavin or pantothenate but possessed folate biosynthesis genes. Differences in gene content for B vitamin synthesis were matched with differences in putative salvage and synthesis strategies among species. For example, we observed extended biotin salvage capabilities in R. intestinalis strains, which further suggest that B vitamin acquisition strategies may impact fitness in the gut ecosystem. As differences in the functional potential to synthesize components of biomass (e.g. amino acids, vitamins) can drive interspecies interactions, variation in auxotrophies of the Roseburia spp. genomes may influence in vivo gut ecology. This study serves to advance our understanding of the potential metabolic interactions that influence the ecology of Roseburia spp. and, ultimately, may provide a basis for rational strategies to manipulate the abundances of these species.

Characterization of urea transport mechanisms in the intestinal tract of growing pigs

Pigs are capable of nitrogen salvage via urea recycling, which involves the movement of urea in the gastrointestinal tract. Aquaporins (AQP) and urea transporter B (UT-B) are involved in urea recycling in ruminants; however, their contribution to urea flux in the intestinal tract of the pig is not known. The objective of this study was to characterize the presence and relative contribution of known urea transporters to urea flux in the growing pig. Intestinal tissue samples (duodenum, jejunum, ileum, cecum, and colon) were obtained from nine barrows (50.8 ± 0.9 kg) and analyzed for mRNA abundance of UT-B and AQP-3, -7, and -10. Immediately after tissue collection, samples from the jejunum and cecum were placed in Ussing chambers for analysis of the serosal-to-mucosal urea flux (Jsm-urea) with no inhibition or when incubated in the presence of phloretin to inhibit UT-B-mediated transport, NiCl2 to inhibit AQP-mediated transport, or both inhibitors. UT-B expression was greatest (P < 0.05) in the cecum, whereas AQP-3, -7, and -10 expression was greatest (P < 0.05) in the jejunum. The Jsm-urea was greater in the cecum than the jejunum (67.8 . 42.7 ± 5.01 µmol·cm-2·h-1; P < 0.05), confirming the capacity for urea recycling in the gut in pigs; however, flux rate was not influenced (P > 0.05) by urea transporter inhibitors. The results of this study suggest that, although known urea transporters are expressed in the gastrointestinal tract of pigs, they may not play a significant functional role in transepithelial urea transport.NEW & NOTEWORTHY We characterized the location and contribution of known urea transporters to urea flux in the pig. Aquaporins are located throughout the intestinal tract, and urea transporter B is expressed only in the cecum. Urea flux occurred in both the jejunum and cecum. Transporter inhibitors had no affect on urea flux, suggesting that their contribution to urea transport in the intestinal tract is limited. Further work is required to determine which factors contribute to urea flux in swine.

Inhibition of jejunal protein synthesis and breakdown in Pseudomonas aeruginosa-induced sepsis pig model

Maintenance of gut integrity has long been recognized as crucial for survival in sepsis, but alterations in protein metabolism have not previously been documented. Therefore, in the present study, we measured in a Pseudomonas aeruginosa-induced porcine sepsis model fractional protein synthesis (FSR) and breakdown rates (FBR) in jejunal mucosa in a fasted, conscious state. FSR was measured by the incorporation rate of stable tracer amino acid (l-[ring-¹³C₆]phenylalanine) into tissue protein. FBR was determined using the relation between blood arterial enrichment and intracellular enrichment of phenylalanine in consecutive mucosal biopsies after a pulse of l-[¹⁵N]phenylalanine. Additionally, we determined the FSR in jejunum, ileum, liver, muscle, and lung tissue. We found in this sham-controlled acute sepsis pig model (control: n = 9; sepsis: n = 13) that jejunal mucosal protein turnover is reduced with both decreased FSR (control: 3.29 ± 0.22; sepsis: 2.32 ± 0.12%/h, P = 0.0008) and FBR (control: 0.72 ± 0.12; sepsis: 0.34 ± 0.04%/h, P = 0.006). We also found that FSR was unchanged in ileum and muscle, whereas it was higher in the liver (control: 0.87 ± 0.05; sepsis: 1.05 ± 0.06%/h, P = 0.041). Our data, obtained with a translational acute sepsis model, suggest that jejunal mucosal protein metabolism is diminished in acute sepsis. Comparison with other tissues indicates that the most serious acute metabolic changes in sepsis occur in the jejunum rather than the muscle. NEW & NOTEWORTHY In a highly translational acute sepsis model, presented data suggest that jejunal mucosal protein metabolism is diminished in acute sepsis, even if the origin of the sepsis is not located in the gut. Comparison with other tissues indicates that the most serious acute changes in the protein synthesis rates in sepsis occur in the gut rather than the muscle. Therefore, we hypothesize that preventing a compromised gut is critical to maintain gut function during sepsis.

Standing on giant shoulders: a personal recollection of the lives and achievements of eminent animal scientists 1965–2015

This article is a compilation of pieces that are part biographical sketches and part personal recollections of 18 scientists with whom the author was acquainted in three continents over almost 50 years. The subjects, from Australia, the United States and the United Kingdom, will be recognisable to many in the field, especially more experienced scientists. For younger scientists, the article also is intended to put a human face on a generation of famous researchers who otherwise would be familiar only as somewhat anonymous authors of classic papers and reviews.

Microbial nitrogen limitation in the mammalian large intestine

Resource limitation is a fundamental factor governing the composition and function of ecological communities. However, the role of resource supply in structuring the intestinal microbiome has not been established and represents a challenge for mammals that rely on microbial symbionts for digestion: too little supply might starve the microbiome while too much might starve the host. We present evidence that microbiota occupy a habitat that is limited in total nitrogen supply within the large intestines of 30 mammal species. Lowering dietary protein levels in mice reduced their faecal concentrations of bacteria. A gradient of stoichiometry along the length of the gut was consistent with the hypothesis that intestinal nitrogen limitation results from host absorption of dietary nutrients. Nitrogen availability is also likely to be shaped by host-microbe interactions: levels of host-secreted nitrogen were altered in germ-free mice and when bacterial loads were reduced via experimental antibiotic treatment. Single-cell spectrometry revealed that members of the phylum Bacteroidetes consumed nitrogen in the large intestine more readily than other commensal taxa did. Our findings support a model where nitrogen limitation arises from preferential host use of dietary nutrients. We speculate that this resource limitation could enable hosts to regulate microbial communities in the large intestine. Commensal microbiota may have adapted to nitrogen-limited settings, suggesting one reason why excess dietary protein has been associated with degraded gut-microbial ecosystems.

Two-carbon folate cycle of commensal Lactobacillus reuteri 6475 gives rise to immunomodulatory ethionine, a source for histone ethylation

Colonization of the gut by certain probiotic Lactobacillus reuteri strains has been associated with reduced risk of inflammatory diseases and colorectal cancer. Previous studies pointed to a functional link between immunomodulation, histamine production, and folate metabolism, the central 1-carbon pathway for the transfer of methyl groups. Using mass spectrometry and NMR spectroscopy, we analyzed folate metabolites of L. reuteri strain 6475 and discovered that the bacterium produces a 2-carbon-transporting folate in the form of 5,10-ethenyl-tetrahydrofolyl polyglutamate. Isotopic labeling permitted us to trace the source of the 2-carbon unit back to acetate of the culture medium. We show that the 2C folate cycle of L. reuteri is capable of transferring 2 carbon atoms to homocysteine to generate the unconventional amino acid ethionine, a known immunomodulator. When we treated monocytic THP-1 cells with ethionine, their transcription of TNF-α was inhibited and cell proliferation reduced. Mass spectrometry of THP-1 histones revealed incorporation of ethionine instead of methionine into proteins, a reduction of histone-methylation, and ethylation of histone lysine residues. Our findings suggest that the microbiome can expose the host to ethionine through a novel 2-carbon transporting variant of the folate cycle and modify human chromatin via ethylation.-Röth, D., Chiang, A. J., Hu, W., Gugiu, G. B., Morra, C. N., Versalovic, J., Kalkum, M. The two-carbon folate cycle of commensal Lactobacillus reuteri 6475 gives rise to immunomodulatory ethionine, a source for histone ethylation.

Drivers of Microbiome Biodiversity: A Review of General Rules, Feces, and Ignorance

The alpha diversity of ecologic communities is affected by many biotic and abiotic drivers and, in turn, affects ecosystem functioning. Yet, patterns of alpha diversity in host-associated microbial communities (microbiomes) are poorly studied and the appropriateness of general theory is untested. Expanding diversity theory to include microbiomes is essential as diversity is a frequently cited metric of their status. Here, we review and newly analyze reports of alpha diversity for animal gut microbiomes. We demonstrate that both diet and body size affect diversity in the gut but that gut physiology (fermenter versus simple) is the most important driver. We also assess the advantages of various diversity metrics. The importance of diversity in microbiomes is often assumed but has not been tested outright. Therefore, we close by discussing how to integrate microbiomes into the field of biodiversity-ecosystem functioning to more clearly understand when and why a host supports diverse microbial communities.

Butyrate presence in distinct gastrointestinal tract segments modifies differentially digestive processes and amino acid bioavailability in young broiler chickens

The hypothesis was tested that butyrate presence in the digesta of distinct gastrointestinal tract (GIT) segments of broilers leads to differential effects on digesta retention time, gut morphology, and proteolytic enzymatic activities, ultimately resulting in differences in protein digestibility. A total of 320 male day-old Ross 308 broilers were randomly assigned to 5 dietary treatments: 1) control (no butyrate), 2) unprotected butyrate (main activity in the crop and gastric regions), 3) tributyrin (main activity in the small intestine), 4) fat-coated butyrate (activity in the whole GIT) and 5) unprotected butyrate combined with tributyrin, each replicated 8 times. Rapeseed meal was used in combination with a fine dietary particle size in order to challenge the digestive capacity of young broilers. Birds were dissected at 22, 23, and 24 d of age and samples of digesta at various GIT locations as well as tissues were collected. Butyrate concentration varied significantly across GIT segments depending on treatment, indicating that the dietary contrasts were successful. The apparent ileal digestibility of methionine tended to increase when butyrate and/or propionate was present in colonic and cecal contents, possibly due to modifications of GIT development and digesta transit time. Butyrate presence in the digesta of the crop, proventriculus and gizzard, on the contrary, decreased the apparent ileal digestibility of several amino acids (AA). In addition, butyrate presence beyond the gizzard elicited anorexic effect that might be attributable to changes in intestinal enteroendocrine L-cells secretory activities. The present study demonstrates that, in broilers, effects of butyrate on digestive processes are conditioned by the GIT segment wherein the molecule is present and indicates its influence on digestive function and bioavailability of AA.

Application of kernel principal component analysis and computational machine learning to exploration of metabolites strongly associated with diet

Computer-based technological innovation provides advancements in sophisticated and diverse analytical instruments, enabling massive amounts of data collection with relative ease. This is accompanied by a fast-growing demand for technological progress in data mining methods for analysis of big data derived from chemical and biological systems. From this perspective, use of a general “linear” multivariate analysis alone limits interpretations due to “non-linear” variations in metabolic data from living organisms. Here we describe a kernel principal component analysis (KPCA)-incorporated analytical approach for extracting useful information from metabolic profiling data. To overcome the limitation of important variable (metabolite) determinations, we incorporated a random forest conditional variable importance measure into our KPCA-based analytical approach to demonstrate the relative importance of metabolites. Using a market basket analysis, hippurate, the most important variable detected in the importance measure, was associated with high levels of some vitamins and minerals present in foods eaten the previous day, suggesting a relationship between increased hippurate and intake of a wide variety of vegetables and fruits. Therefore, the KPCA-incorporated analytical approach described herein enabled us to capture input–output responses, and should be useful not only for metabolic profiling but also for profiling in other areas of biological and environmental systems.

A role for bacterial urease in gut dysbiosis and Crohn's disease

Gut dysbiosis during inflammatory bowel disease involves alterations in the gut microbiota associated with inflammation of the host gut. We used a combination of shotgun metagenomic sequencing and metabolomics to analyze fecal samples from pediatric patients with Crohn's disease and found an association between disease severity, gut dysbiosis, and bacterial production of free amino acids. Nitrogen flux studies using 15N in mice showed that activity of bacterial urease, an enzyme that releases ammonia by hydrolysis of host urea, led to the transfer of murine host-derived nitrogen to the gut microbiota where it was used for amino acid synthesis. Inoculation of a conventional murine host (pretreated with antibiotics and polyethylene glycol) with commensal Escherichia coli engineered to express urease led to dysbiosis of the gut microbiota, resulting in a predominance of Proteobacteria species. This was associated with a worsening of immune-mediated colitis in these animals. A potential role for altered urease expression and nitrogen flux in the development of gut dysbiosis suggests that bacterial urease may be a potential therapeutic target for inflammatory bowel diseases.

Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine

BACKGROUND

The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host.

METHODS

The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired-end, mate-pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) after growth on three different carbohydrate sources, and short chain fatty acids were measured via HPLC.

RESULTS

We present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed identification of the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides.

DISCUSSION

This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available.

Amino Acid Absorption in the Large Intestine of Humans and Porcine Models

Dietary protein quality has been recognized as a critical issue by international authorities because it can affect important functions of the body. To predict protein quality, the FAO introduced the Digestible Indispensable Amino Acid Score. This score depends on ileal amino acid (AA) digestibility; therefore, the assumption is made that AAs are not absorbed in nutritionally relevant amounts from the large intestine. This article reviews the evidence for this assumption by considering the role of the mammalian large intestine in dietary protein and AA digestion and absorption, with particular reference to adult humans. Although most dietary AAs and peptides are absorbed in the small intestine, substantial amounts can enter the large intestine. Nitrogen is absorbed in the large intestine, and a series of animal experiments indicate a potential small degree of AA absorption. In humans, colonocytes have the capacity for AA absorption because AA transporters are present in the large intestine. The absorption of nutritionally relevant amounts of dietary indispensable AAs and peptides in the human large intestine has not been convincingly demonstrated, however.

Clostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes

Clostridium difficile is the largest single cause of hospital-acquired infection in the United States. A major risk factor for Clostridium difficile infection (CDI) is prior exposure to antibiotics, as they disrupt the gut bacterial community which protects from C. difficile colonization. Multiple antibiotic classes have been associated with CDI susceptibility, many leading to distinct community structures stemming from variation in bacterial targets of action. These community structures present separate metabolic challenges to C. difficile. Therefore, we hypothesized that the pathogen adapts its physiology to the nutrients within different gut environments. Utilizing an in vivo CDI model, we demonstrated that C. difficile highly colonized ceca of mice pretreated with any of three antibiotics from distinct classes. Levels of C. difficile spore formation and toxin activity varied between animals based on the antibiotic pretreatment. These physiologic processes in C. difficile are partially regulated by environmental nutrient concentrations. To investigate metabolic responses of the bacterium in vivo, we performed transcriptomic analysis of C. difficile from ceca of infected mice across pretreatments. This revealed heterogeneous expression in numerous catabolic pathways for diverse growth substrates. To assess which resources C. difficile exploited, we developed a genome-scale metabolic model with a transcriptome-enabled metabolite scoring algorithm integrating network architecture. This platform identified nutrients that C. difficile used preferentially between pretreatments, which were validated through untargeted mass spectrometry of each microbiome. Our results supported the hypothesis that C. difficile inhabits alternative nutrient niches across cecal microbiomes with increased preference for nitrogen-containing carbon sources, particularly Stickland fermentation substrates and host-derived glycans. IMPORTANCE Infection by the bacterium Clostridium difficile causes an inflammatory diarrheal disease which can become life threatening and has grown to be the most prevalent nosocomial infection. Susceptibility to C. difficile infection is strongly associated with previous antibiotic treatment, which disrupts the gut microbiota and reduces its ability to prevent colonization. In this study, we demonstrated that C. difficile altered pathogenesis between hosts pretreated with antibiotics from separate classes and exploited different nutrient sources across these environments. Our metabolite score calculation also provides a platform to study nutrient requirements of pathogens during an infection. Our results suggest that C. difficile colonization resistance is mediated by multiple groups of bacteria competing for several subsets of nutrients and could explain why total reintroduction of competitors through fecal microbial transplant currently is the most effective treatment for recurrent CDI. This work could ultimately contribute to the identification of targeted, context-dependent measures that prevent or reduce C. difficile colonization, including pre- and probiotic therapies.

'Trophic' and 'source' amino acids in trophic estimation: a likely metabolic explanation

Amino acid nitrogen isotopic analysis is a relatively new method for estimating trophic position. It uses the isotopic difference between an individual's 'trophic' and 'source' amino acids to determine its trophic position. So far, there is no accepted explanation for the mechanism by which the isotopic signals in 'trophic' and 'source' amino acids arise. Yet without a metabolic understanding, the utility of nitrogen isotopic analyses as a method for probing trophic relations, at either bulk tissue or amino acid level, is limited. I draw on isotopic tracer studies of protein metabolism, together with a consideration of amino acid metabolic pathways, to suggest that the 'trophic'/'source' groupings have a fundamental metabolic origin, to do with the cycling of amino-nitrogen between amino acids. 'Trophic' amino acids are those whose amino-nitrogens are interchangeable, part of a metabolic amino-nitrogen pool, and 'source' amino acids are those whose amino-nitrogens are not interchangeable with the metabolic pool. Nitrogen isotopic values of 'trophic' amino acids will reflect an averaged isotopic signal of all such dietary amino acids, offset by the integrated effect of isotopic fractionation from nitrogen cycling, and modulated by metabolic and physiological effects. Isotopic values of 'source' amino acids will be more closely linked to those of equivalent dietary amino acids, but also modulated by metabolism and physiology. The complexity of nitrogen cycling suggests that a single identifiable value for 'trophic discrimination factors' is unlikely to exist. Greater consideration of physiology and metabolism should help in better understanding observed patterns in nitrogen isotopic values.

Isotopic ecology of coyotes from scat and road kill carcasses: A complementary approach to feeding experiments

Scat is frequently used to study animal diets because it is easy to find and collect, but one concern is that gross fecal analysis (GFA) techniques exaggerate the importance of small-bodied prey to mammalian mesopredator diets. To capitalize on the benefits of scat, we suggest the analysis of scat carbon and nitrogen isotope values (δ¹³C and δ¹⁵N). This technique offers researchers a non-invasive method to gather short-term dietary information. We conducted three interrelated studies to validate the use of isotopic values from coyote scat: 1) we determined tissue-to-tissue apparent C and N isotope enrichment factors (ε¹³* and ε¹⁵*) for coyotes from road kill animals (n = 4); 2) we derived diet-to-scat isotope discrimination factors for coyotes; and 3) we used field collected coyote scats (n = 12) to compare estimates of coyote dietary proportions from stable isotope mixing models with estimates from two GFA techniques. Scat consistently had the lowest δ¹³C and δ¹⁵N values among the tissues sampled. We derived a diet-to-scat Δ¹³C value of -1.5‰ ± 1.6‰ and Δ¹⁵N value of 2.3‰ ± 1.3‰ for coyotes. Coyote scat δ¹³C and δ¹⁵N values adjusted for discrimination consistently plot within the isotopic mixing space created by known dietary items. In comparison with GFA results, we found that mixing model estimates of coyote dietary proportions de-emphasize the importance of small-bodied prey. Coyote scat δ¹³C and δ¹⁵N values therefore offer a relatively quick and non-invasive way to gain accurate dietary information.

An assessment of the influence of macronutrients on growth performance and nutrient utilisation in broiler chickens by nutritional geometry

The right-angled triangle mixture experiment was designed to include fourteen diets with different concentrations of starch, protein and lipid. Experimental diets were offered to male Ross 308 broiler chickens from 10 to 23 d after hatching, and response curves and surfaces were generated to illustrate the influence of macronutrients on growth performance and nutrient utilisations. Despite the primary function of macronutrients, especially protein, may not be providing energy, macronutrients were expressed as energy derived from starch, protein and fat for statistical purposes in the mixture design. Energy derived from lipid had a greater impact on feed intake than energy derived from starch and protein. When we compared the influence of starch and protein on feed intake, 'equal distance rule' was observed, which means the animal consumes feed to the point on its respective nutritional rails where the shortage of starch exactly equals the surplus of consumed protein. Increasing the protein-derived energy intake increased weight gain in broiler chickens, whereas energy intake derived from starch and lipid had little impact on weight gain. Feed conversion ratio (FCR) may be reduced by either increasing protein energy intake or decreasing starch energy intake. As the slope of the contours was less than 1, the influence of starch energy intakes on FCR exceeded that of protein energy intakes. In conclusion, energy derived from protein is more important than non-protein energy in terms of weight gain, and a balance between protein and energy supplies is required for efficient muscle protein deposition.

Starch and protein digestive dynamics in low-protein diets supplemented with crystalline amino acids

Digestive dynamics of starch and protein is defined as digestion of starch and protein, absorption of glucose and amino acids from the gut lumen and their transition across enterocytes to enter the portal circulation. Digestive dynamics consider the extent, rate and site of nutrient digestion along the small intestine and the bilateral, post-enteral bioavailability of glucose and amino acids. The underlying premise is that glucose and amino acids should be made available in appropriately balanced quantities at the sites of protein synthesis for efficient protein deposition and growth performance. Previous studies have suggested that feed conversion efficiency may be enhanced by rapidly digestible protein and that crystalline amino acids could be considered sources of ‘rapid protein’. At present, crystalline lysine, methionine and threonine are routinely included in broiler diets; moreover, an increasing array of both essential and non-essential crystalline amino acids is becoming commercially available. Despite unrestricted feed access in commercial chicken-meat production systems during the period of illumination, it appears that the intermittent feed consumption patterns of broiler chickens still provide scope for asynchronies in digestion and absorption of nutrients, which affects broiler performance. A better understanding of the post-enteral, bilateral bioavailability of glucose and amino acids in low-protein diets containing high levels of synthetic amino acids is clearly desirable and this applies equally to the relationship between crystalline and protein-bound amino acids.