How to Feed the Mammalian Gut Microbiota: Bacterial and Metabolic Modulation by Dietary Fibers

Deciphering the interplay between pectin structural variability, intestinal bioavailability and gut microbiota metabolism: A review

Pectins are parts of fruits, vegetables and other plant-based foods in the human daily diet. They are resilient to gastric digestion but undergo fermentation primarily in the large intestine, peaking in the cecum. The depolymerization of the pectins induced by the gut microbiota generally facilitates the subsequent fermentation of sugar monomers, during which SCFAs are primarily generated to exert multiple beneficial functions. Given structural heterogeneity of pectins and intricate process of microbial metabolism, it is crucial to elucidate how the multi-scale structure of pectins impacts their gut fermentation behavior. This review delves into distinct structural domains and fine structural characteristics of pectins, describes their degradation mechanism and bioavailability in the gastrointestinal tract, and provides an overview of the associated pectinolytic enzymes, gut microbiota community, and microbial metabolites. Moreover, recent advances are summarized in the relationships between gut fermentability and various structural parameters of pectins, including molecular size, esterification degree, monosaccharides composition and molecular conformation. Furthermore, how the structural complexity of pectins influences the interplay between saccharolytic metabolism and proteolytic metabolism during microbial fermentation is proposed. This work would help to unravel the "pectin structure - gut microbiota - host health" interactions, thereby guiding the design of functional foods targeting specific microorganisms in future personalized diets.

Effect of Dietary Concentrate-to-Forage Ratios During the Cold Season on Slaughter Performance, Meat Quality, Rumen Fermentation and Gut Microbiota of Tibetan Sheep

This study aimed to investigate the effects of different dietary concentrate-to-forage ratios on slaughter performance, meat quality, rumen fermentation, rumen microbiota and fecal microbiota in Tibetan sheep. A total of sixty male Tibetan sheep were equally allocated into three dietary groups based on concentrate-to-forage ratios, i.e., 30:70 (C30), 50:50 (C50), and 70:30 (C70). Compared with the C30 group, sheep fed the C70 diet resulted in a higher (p < 0.05) slaughter live weight (SLW), hot carcass weight (HCW), dressing percentage (DP), eye muscle area, average daily gain (ADG), and ruminal total volatile fatty acids concentration and propionate molar proportion and lower (p < 0.05) shear force and cooking loss of meat, and ruminal acetate molar proportion and acetate:propionate ratio. Sheep in the C50 group exhibited a higher (p < 0.05) SLW, HCW, ADG, and ruminal propionate molar proportion and lower (p < 0.05) shear force and cooking loss of meat, and ruminal acetate molar proportion and acetate: propionate ratio compared with the C30 group. In rumen fluid, the relative abundance of Butyrivibrio was lower (p = 0.031) in the C30 group, and that of Ruminococcus was higher (p = 0.003) in the C70 group compared with the C50 group. In feces, genus Monoglobus and UCG_002 were the most abundant in the C30 group (p < 0.05), and the relative abundance of Prevotella was significantly higher in the C70 group than in other groups (p = 0.013). Correlation analysis revealed possible links between slaughter performance and meat quality and altered microbiota composition in the rumen and feces of Tibetan sheep. Overall, feeding a C70 diet resulted in superior carcass characteristics and meat quality in Tibetan sheep, thus laying a theoretical basis for the application of short-term remote feeding during the cold season.

From microbes to medicine: harnessing the power of the microbiome in esophageal cancer

Esophageal cancer (EC) is a malignancy with a high incidence and poor prognosis, significantly influenced by dysbiosis in the esophageal, oral, and gut microbiota. This review provides an overview of the roles of microbiota dysbiosis in EC pathogenesis, emphasizing their impact on tumor progression, drug efficacy, biomarker discovery, and therapeutic interventions. Lifestyle factors like smoking, alcohol consumption, and betel nut use are major contributors to dysbiosis and EC development. Recent studies utilizing advanced sequencing have revealed complex interactions between microbiota dysbiosis and EC, with oral pathogens such as Porphyromonas gingivalis and Fusobacterium nucleatum promoting inflammation and suppressing immune responses, thereby driving carcinogenesis. Altered esophageal microbiota, characterized by reduced beneficial bacteria and increased pathogenic species, further exacerbate local inflammation and tumor growth. Gut microbiota dysbiosis also affects systemic immunity, influencing chemotherapy and immunotherapy efficacy, with certain bacteria enhancing or inhibiting treatment responses. Microbiota composition shows potential as a non-invasive biomarker for early detection, prognosis, and personalized therapy. Novel therapeutic strategies targeting the microbiota-such as probiotics, dietary modifications, and fecal microbiota transplantation-offer promising avenues to restore balance and improve treatment efficacy, potentially enhancing patient outcomes. Integrating microbiome-focused strategies into current therapeutic frameworks could improve EC management, reduce adverse effects, and enhance patient survival. These findings highlight the need for further research into microbiota-tumor interactions and microbial interventions to transform EC treatment and prevention, particularly in cases of late-stage diagnosis and poor treatment response.

A Comparison of Growth Performance, Blood Parameters, Rumen Fermentation, and Bacterial Community of Tibetan Sheep When Fattened by Pasture Grazing versus Stall Feeding

Traditionally, Tibetan sheep only graze pastures without any supplementary feed. However, in recent years, feedlots are being used for fattening Tibetan sheep. The present study compared the growth rates, blood parameters, rumen fermentation, and bacterial communities in Tibetan sheep fattened by pasture grazing (PG) versus those fattened by stall feeding (SF). Twenty 18-month-old Tibetan sheep wethers (42.6 ± 2.11 kg) were divided randomly into PG (n = 10) and SF (n = 10) groups. The PG sheep grazed the grasslands without any supplementary feed, while the SF sheep were offered a commercial total mixed ration (TMR) at a crude protein content of 16.2% DM and an ME of 10.59 MJ/kg. The sheep were on their treatments for 70 days, which included 10 days for adaptation and 60 days for measurements. The average daily gain, white blood cell and lymphocyte counts were greater (p < 0.05), while the platelet count was lower (p < 0.05) in the SF group than in the PG group. The serum glutathione peroxidase activity, and concentrations of total proteins and albumin were greater (p < 0.05), while glucose was lower (p < 0.01) in the PG group compared to the SF group. The concentrations of ruminal ammonia-N and total volatile fatty acids (VFAs) were greater (p < 0.05), while the pH was lower (p < 0.05) in the SF group compared to the PG group. The molar proportion of acetate and the ratio of acetate to propionate were greater (p < 0.01) in the PG sheep than in the SF sheep, but the molar proportion of propionate and iso-VFAs did not differ (p > 0.05) between the groups. Based on the PCoA, the ruminal bacterial communities were distinct between groups, and the alpha diversity was greater (p < 0.001) in the PG sheep than in the SF sheep. The dominant phyla of the rumen bacteria were Firmicutes and Bacteroidetes, while the Firmicutes to Bacteroidetes ratio was greater (p < 0.001) in the SF group than in the PG group. At the genus level, the relative abundance of Ruminococcus was greater (p < 0.05) in the SF group, while the abundances of Prevotella, the Rikenellaceae_RC9_gut_group, Butyrivibrio, and unclassified_f_Lachnospiraceae were greater (p < 0.05) in the PG group. It was concluded that the Tibetan sheep adopted a short-term intensive fattening strategy when stall fed which altered the rumen bacterial community and blood parameters, enhanced rumen fermentation, and, ultimately, improved their average daily gain.

Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation

The human gut microbiota is a dynamic community of microorganisms that undergo variable changes over the entire life span. To thoroughly investigate the possible fluctuations of the microbiota throughout human life, we performed a pooled analysis of healthy fecal samples across different age groups covering the entire human life span. Our study integrated data from 79 publicly available studies and new stool samples from an Italian cohort, i.e., the Parma Microbiota project, resulting in 6,653 samples processed through the shotgun metagenomic approach. This approach has allowed species-level taxonomic reconstruction of the gut microbiota and investigation of its metabolic potential across the human life span. From a taxonomic point of view, our findings confirmed and detailed at species-level accuracy that the microbial richness of the gut microbiota gradually increases in the first stage of life, becoming relatively stable during adolescence. Moreover, the analysis identified the potential core microbiota representative of distinct age groups, revealing age-related bacterial patterns and the continuous rearrangement of the microbiota in terms of relative abundances across the life span rather than the acquisition and loss of taxa. Furthermore, the shotgun approach provided insights into the functional contribution of the human gut microbiome. The metagenomic analysis revealed functional age-related differences, particularly in carbohydrate and fiber metabolism, suggesting a co-evolution of the microbiome assembly with diet. Additionally, we identified correlations between vitamin synthesis, such as thiamine and niacin, and early life, suggesting a potential role of the microbiome in human physiology, in particular in the functions of the host's nervous and immune systems.

IMPORTANCE

In this study, we provided comprehensive insights into the dynamic nature of the human gut microbiota across the human life span. In detail, we analyzed a large data set based on a shotgun metagenomic approach, combining public data sets and new samples from the Parma Microbiota project and obtaining a detailed overview of the possible relationship between gut microbiota development and aging. Our findings confirmed the main stages in microbial richness development and revealed specific core microbiota associated with different age stages. Moreover, the shotgun metagenomic approach allowed the disentangling of the functional changes in the microbiome across the human life span, particularly in diet-related metabolism, which is probably correlated to bacterial co-evolution with dietary habits. Notably, our study also uncovered positive correlations with vitamin synthesis in early life, suggesting a possible impact of the microbiota on human physiology.

Preliminary Results on the Effects of Soybean Isoflavones on Growth Performance and Ruminal Microbiota in Fattening Goats

Soybean isoflavones (SIFs), a group of secondary metabolites, have antioxidant, anti-inflammatory, and hormone-like activities. Supplementation with SIFs in the diet was reported to promote lactation performance in ruminants. The present study was performed to further decipher the effect of various concentrations of SIFs on growth and slaughter performance, serum parameters, meat quality, and ruminal microbiota in fattening goats. After a two-week acclimation, a total of 27 5-month-old Guanzhong male goats (18.29 ± 0.44 kg) were randomly assigned to control (NC), 100 mg/d SIF (SIF1), or 200 mg/d SIF (SIF2) groups. The experimental period lasted 56 days. The weight of the large intestine was greater (p < 0.05) in the SIF1 and SIF2 groups compared with the NC group. Meat quality parameters indicated that SIF1 supplementation led to lower (p < 0.05) cooking loss and shear force (0.05 < p < 0.10). The 16S rRNA sequencing analysis demonstrated that SIF1 supplementation led to lower (p < 0.05) proportions of Papillibacter and Prevotellaceae_UCG-004 but greater (p < 0.05) CAG-352 abundance in the rumen; these responses might have contributed to the improvement in production performance. In conclusion, meat quality and ruminal microbiome could be manipulated in a positive way by oral supplementation with 100 mg/d of SIFs in fattening goats. Thus, this study provides new insights and practical evidence for the introduction of SIFs as a novel additive in goat husbandry.

Concentrate supplementation improves cold-season environmental fitness of grazing yaks: responsive changes in the rumen microbiota and metabolome

Yak (Bos grunniens) is an important economic animal species on the Qinghai-Tibet Plateau. Yaks grazed in the cold season often suffer from nutritional stress, resulting in low production performance. This situation can be improved by properly feeding the grazing yaks in the cold season; however, there is still little information about the effect of different feeding levels on the intestinal microflora and metabolites of yaks. Therefore, this study aimed to explore the effect of feeding different doses of concentrate supplements on rumen bacterial communities and metabolites in grazing yaks during the cold season. Feed concentrate supplementation significantly improved the production performance and rumen fermentation status of grazing yaks during the cold season, and switched the type of ruminal fermentation from acetic acid fermentation to propionic acid fermentation. Ruminal fermentation parameters and ruminal bacterial abundance correlated strongly. At the phylum level, the abundance of Firmicutes increased with increasing concentrate supplementation, while the opposite was true for Bacteroidota. At the genus level, the abundance of Christensenellaceae_R-7_group, NK4A214_group, Ruminococcus, norank_f__Eubacterium_coprostanoligenes_group, norank_f__norank_o__ Clostridia_UCG-014, Lachnospiraceae_NK3A20_group, Acetitomaculum, and Family_XIII_AD3011_group increased with increasing concentrate supplementation, while the abundance of Rikenellaceae_RC9_gut_ group decreased. Dietary concentrate supplementation altered the concentration and metabolic mode of metabolites in the rumen, significantly affecting the concentration of metabolites involved in amino acid and derivative metabolism (e.g., L-aspartic acid, L-glutamate, and L-histidine), purine metabolism (e.g., guanine, guanosine, and hypoxanthine), and glycerophospholipid metabolism (e.g., phosphatidate, phosphatidylcholine, and phosphocholine), and other metabolic pathways. The strong correlation between yak rumen microorganisms and metabolites provided a more comprehensive understanding of microbial community composition and function. This study showed significant changes in the composition and abundance of bacteria and metabolites in the rumen of cool season grazing yaks fed with concentrate supplements. Changes in ruminal fermentation parameters and metabolite concentration also showed a strong correlation with ruminal bacterial communities. These findings will be helpful to formulate supplementary feeding strategies for grazing yaks in the cold season from the perspective of intestinal microorganisms.

The Role of Carbohydrate Intake on the Gut Microbiome: A Weight of Evidence Systematic Review

(1) Background: Carbohydrates are the most important source of nutritional energy for the human body. Carbohydrate digestion, metabolism, and their role in the gut microbiota modulation are the focus of multiple studies. The objective of this weight of evidence systematic review is to investigate the potential relationship between ingested carbohydrates and the gut microbiota composition at different taxonomic levels. (2) Methods: Weight of evidence and information value techniques were used to evaluate the relationship between dietary carbohydrates and the relative abundance of different bacterial taxa in the gut microbiota. (3) Results: The obtained results show that the types of carbohydrates that have a high information value are: soluble fiber with Bacteroides increase, insoluble fiber with Bacteroides and Actinobacteria increase, and Firmicutes decrease. Oligosaccharides with Lactobacillus increase and Enterococcus decrease. Gelatinized starches with Prevotella increase. Starches and resistant starches with Blautia decrease and Firmicutes increase. (4) Conclusions: This work provides, for the first time, an integrative review of the subject by using statistical techniques that have not been previously employed in microbiota reviews.

Comparative analysis of the gut microbiota of wild adult rats from nine district areas in Hainan, China

BACKGROUND

Wild rats have the potential to hold zoonotic infectious agents that can spread to humans and cause disease.

AIM

To better understand the composition of gut bacterial communities in rats is essential for preventing and treating such diseases. As a tropical island located in the south of China, Hainan province has abundant rat species. Here, we examined the gut bacterial composition in wild adult rats from Hainan province.

METHODS

Fresh fecal samples were collected from 162 wild adult rats, including three species (Rattus norvegicus, Leopoldamys edwardsi, and Rattus losea), from nine regions of Hainan province between 2017-2018.

RESULTS

We analyzed the composition of gut microbiota using the 16S rRNA gene amplicon sequencing. We identified 4903 bacterial operational taxonomic units (30 phyla, 175 families, and 498 genera), which vary between samples of different rat species in various habitats at various times of the year. In general, Firmicutes were the most abundant phyla, followed by Bacteroidetes (15.55%), Proteobacteria (6.13%), and Actinobacteria (4.02%). The genus Lactobacillus (20.08%), unidentified_Clostridiales (5.16%), Romboutsia (4.33%), unidentified_Ruminococcaceae (3.83%), Bacteroides (3.66%), Helicobacter (2.40%) and Streptococcus (2.37%) were dominant.

CONCLUSION

The composition and abundance of the gut microbial communities varied between rat species and locations. This work provides fundamental information to identify microbial communities useful for disease control in Hainan province.

Dietary fiber during gestation improves lactational feed intake of sows by modulating gut microbiota

BACKGROUND

The feed intake of sows during lactation is often lower than their needs. High-fiber feed is usually used during gestation to increase the voluntary feed intake of sows during lactation. However, the mechanism underlying the effect of bulky diets on the appetites of sows during lactation have not been fully clarified. The current study was conducted to determine whether a high-fiber diet during gestation improves lactational feed intake (LFI) of sows by modulating gut microbiota.

METHODS

We selected an appropriate high-fiber diet during gestation and utilized the fecal microbial transplantation (FMT) method to conduct research on the role of the gut microbiota in feed intake regulation of sows during lactation, as follows: high-fiber (HF) diet during gestation (n = 23), low-fiber (LF) diet during gestation (n = 23), and low-fiber diet + HF-FMT (LFM) during gestation (n = 23).

RESULTS

Compared with the LF, sows in the HF and LFM groups had a higher LFI, while the sows also had higher peptide tyrosine tyrosine and glucagon-like peptide 1 on d 110 of gestation (G110 d). The litter weight gain of piglets during lactation and weaning weight of piglets from LFM group were higher than LF group. Sows given a HF diet had lower Proteobacteria, especially Escherichia-Shigella, on G110 d and higher Lactobacillus, especially Lactobacillus_mucosae_LM1 and Lactobacillus_amylovorus, on d 7 of lactation (L7 d). The abundance of Escherichia-Shigella was reduced by HF-FMT in numerically compared with the LF. In addition, HF and HF-FMT both decreased the perinatal concentrations of proinflammatory factors, such as endotoxin (ET), lipocalin-2 (LCN-2), tumor necrosis factor-α (TNF-α), and interleukin-1β (IL-1β). The concentration of ET and LCN-2 and the abundance of Proteobacteria and Escherichia-Shigella were negatively correlated with the LFI of sows.

CONCLUSION

The high abundance of Proteobacteria, especially Escherichia-Shigella of LF sows in late gestation, led to increased endotoxin levels, which result in inflammatory responses and adverse effects on the LFI of sows. Adding HF during gestation reverses this process by increasing the abundance of Lactobacillus, especially Lactobacillus_mucosae_LM1 and Lactobacillus_amylovorus.

Different Approaches to Ergogenic, Pre-, and Probiotic Supplementation in Sports with Different Metabolism Characteristics: A Mini Review

Sport disciplines with different metabolic characteristics require different dietary approaches. Bodybuilders or sprinters ("anaerobic" athletes) need a high-protein diet (HPD) in order to activate muscle protein synthesis after exercise-induced muscle damage and use nitric oxide enhancers (such as citrulline and nitrates) to increase vasodilatation, whereas endurance athletes, such as runners or cyclists ("aerobic" athletes), prefer a high-carbohydrate diet (HCHD), which aims to restore the intramuscular glycogen, and supplements containing buffering agents (such as sodium bicarbonate and beta-alanine). In both cases, nutrient absorption, neurotransmitter and immune cell production and muscle recovery depend on gut bacteria and their metabolites. However, there is still insufficient data on the impact of an HPD or HCHD in addition to supplements on "anaerobic" and "aerobic" athletes' gut microbiota and how this impact could be affected by nutritional interventions such as pre- and probiotic therapy. Additionally, little is known about the role of probiotics in the ergogenic effects of supplements. Based on the results of our previous research on an HPD in amateur bodybuilders and an HCHD in amateur cyclists, we reviewed human and animal studies on the effects of popular supplements on gut homeostasis and sport performance.

High-energy diet modify rumen microbial composition and microbial energy metabolism pattern in fattening sheep

Higher dietary energy is often used to achieve better animal performance in mutton sheep production. Notably, changing the diet formula affects rumen fermentation and the microbiota of ruminants. In this study, we investigated the effect of dietary energy on rumen fermentation and ruminal microbiota in fattening sheep. Fifteen 2-month-old white-headed Suffolk sheep (♂) × Hu sheep (♀) crossbred lambs were randomly divided into three treatments based on the dietary energy of the feeds fed: 8.67 MJ/kg (Low energy (LE); n = 5), 10.38 MJ/kg (standard energy (CON); n = 5), and 12.31 MJ/kg (high energy (HE); n = 5) groups. After 70 days of feeding, sheep were slaughtered and the ruminal fluids were collected and analyzed to determine fermentation parameters. Microbiota was determined using metagenomics sequencing. Notably, the microbial cell protein (MCP) and butyric acid concentrations were significantly high in the HE group. Metagenomic sequencing revealed that ACE and Chao indexes of the HE group were significantly decreased. Four genera among the major classified taxa across all the kingdoms differed in relative abundance in the three dietary energy levels. The relative abundances of Prevotella_brevis, Succiniclasticum_ruminis, Prevotellace-ae_bacterium, and Lachnospiraceae_bacterium were significantly correlated with rumen fermentation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis further revealed that a high-energy diet increased lipid metabolism of microbiota. The Carbohydrate Active enzymes (CAZy) gene, which participates in energy metabolism, was upregulated, while genes regulating plant cell wall degradation were downregulated in the HE group. These results suggest that a high-energy diet had minimal influence on the rumen fermentation pattern but altered the composition of the rumen microbiota, enhancing microbial lipid metabolism and limiting crude fiber metabolism. The findings of this study provide scientific evidence of the effect of dietary energy on ruminant fermentation and fattening sheep production.

First evidence for multimodal animal seed dispersal in orchids

Identifying the mechanisms for seed dispersal and persistence of species is a central aim of ecology. Seed dispersal by animals is an essential form of dissemination in many plant communities, including seeds of over 66% of neotropical canopy tree species.^1,2 Besides physical dispersal, animals influence seed germination probabilities through scarification, breaking dormancy, and preventing rotting, so plants often invest important resources in attracting them. Orchids are predominantly adapted to wind dispersal, having dust-like seeds that are easily uplifted. Exceptions include bird-,^3,4 cricket-,^5,6 and mammal-dispersed⁷ species, featuring fleshy fruits with hard seeds that germinate after passing the animal's digestive system. Given the similarity in fruit and seed morphology, zoochory has also been suggested in Vanilla,^{8,9,10,11,12,13,14,15} a pantropical genus of 118 species with vine-like growth.^16,17,18 We test this prediction through in situ and ex situ experimentation using fruits of Vanilla planifolia, and wild relatives, from which vanillin-a widely used natural aroma and flavoring-is obtained. Seeds from dehiscent fruits are removed by male Euglossini collecting fragrances, a unique case in plants, and female Meliponini bees gathering nest-building materials, a first among monocots. By contrast, mammals, mostly rodents, consume the nutritious indehiscent fruits, passing the seeds up to 18 h after consumption. Protocorm formation in digested and undigested seeds proves that scarification in the gut is not strictly required for germination. Multimodal seed dispersal mechanisms are proven for the first time in Orchidaceae, with ectozoochory and endozoochory playing crucial roles in the unusually broad distribution of Vanilla.

The improvement of parturition duration by high intake of dietary fibre in late gestation is associated with gut microbiota and metabolome in sows

Prolonged parturition duration has been widely demonstrated to be a risk factor for incidence of stillbirth. This study evaluated the supply of dietary fibre on the parturition duration, gut microbiota and metabolome using sows as a model. A total of 40 Yorkshire sows were randomly given diet containing normal level of dietary fibre (NDF, 17·5 % dietary fibre) or high level of dietary fibre (HDF, 33·5 % dietary fibre). Faecal microbiota profiled with 16S rRNA amplicon sequencing, SCFA and metabolome in the faeces and plasma around parturition were compared between the dietary groups. Correlation analysis was conducted to further explore the potential associations between specific bacterial taxa and metabolites. Results showed that HDF diet significantly improved the parturition process as presented by the shorter parturition duration. HDF diet increased the abundance of the phyla Bacteroidetes and Synergistetes and multiple genera. Except for butyrate, SCFA levels in the faeces and plasma of sows at parturition were elevated in HDF group. The abundances of fifteen and twelve metabolites in the faeces and plasma, respectively, markedly differ between HDF and NDF sows. These metabolites are involved in energy metabolism and bacterial metabolism. Correlation analysis also showed associations between specific bacteria taxa and metabolites. Collectively, our study indicates that the improvement of parturition duration by high fibre intake in late gestation is associated with gut microbiota, production of SCFA and other metabolites, potentially serving for energy metabolism.

Influence of Dietary Inulin on Fecal Microbiota, Cardiometabolic Risk Factors, Eicosanoids, and Oxidative Stress in Rats Fed a High-Fat Diet

The present study examined the influence of inulin on fecal microbiota, cardiometabolic risk factors, eicosanoids, and oxidative stress in rats on a high-fat (HF) diet. Thirty-six male Wistar-Kyoto rats were divided into three dietary groups: standard diet, HF diet, and HF diet + Inulin diet. After 10 weeks, the HF + Inulin diet promoted high dominance of a few bacterial genera including Blautia and Olsenella in feces while reducing richness, diversity, and rarity compared to the HF diet. These changes in fecal microbiota were accompanied by an increased amount of propionic acid in feces. The HF + Inulin diet decreased cardiometabolic risk factors, decreased the amount of the eicosanoids 11(12)-EET and 15-HETrE in the liver, and decreased oxidative stress in blood compared to the HF diet. In conclusion, increasing consumption of inulin may be a useful nutritional strategy to protect against the onset of obesity and its associated metabolic abnormalities by means of modulation of gut microbiota.

Dietary fiber chemical structure determined gut microbiota dynamics

Precision modulation of gut microbiota requires elucidation of the relation between dietary fiber intake and gut microbe dynamics. However, current studies on this aspect are few due to many technical limitations. Here, we used Caenorhabditis elegans to minimize the complicated host-microbial factors and to find the relation between dietary fiber chemical structures and gut microbiota dynamics. The Allium schoenoprasum polysaccharide (AssP) structure was elucidated and used as the complex dietary fiber against the simple fiber inulin. In vitro bacterial growth and genome analysis indicated that AssP supports bacterial growth better than inulin, while in vivo gut microbiota analysis of C. elegans fed with AssP showed that microbiota richness increased significantly compared with those fed with inulin. It is concluded that the more complex the dietary fiber chemical structure, the more gut bacteria growth it supports. Together with the community bacterial interactions that alter their abundances in vivo, these factors regulate gut microbiota synergistically.

Time-course effects of different fiber-rich ingredients on energy values, microbiota composition and SCFA profile in growing pigs

This study was to investigate time-course effects of different types of dietary fiber on the energy values, fecal microbiota and short-chain fatty acid (SCFA) concentration in growing pigs. A total of 24 barrows (initial body weight, 19.8 ± 0.5 kg) were assigned to 4 dietary treatments based on body weight (BW) in a completely randomized design, including a basal diet (CON) and 3 fiber-rich diets replacing corn, soybean meal and soybean oil in the CON diet with 20% sugar beet pulp (SBP), defatted rice bran (DFRB) or soybean hull (SBH), respectively. Fresh feces were sampled on d 7, 14 and 21, followed by 5 d total feces and urine collections. The results showed that there were no differences in DE and ME between any of the fiber ingredients on d 7, 14 or 21. However, fiber inclusion decreased the DE and ME of the diet (P < 0.05) regardless of the time effect. Principal coordinate analysis (PCoA) revealed distinctly different microbial communities on the DFRB diet and SBH diet across different times (P < 0.05) and the fecal microbiota of the 4 diet groups demonstrated notably distinct clusters at each time point (P < 0.05). With adaptation time increased from 7 to 21 d, cellulose-degrading bacteria and SCFA-producing bacteria (e.g., Ruminococcaceae _UCG-014, Rikenellaceae _RC9_gut_group and Bifidobacterium) increased in the fiber inclusion diets, and pathogenic genera (e.g., Streptococcus and Selenomonas) were increased in the basal diet (P < 0.05). Furthermore, the gut microbiota of growing pigs adapted more easily and quickly to the SBP diet compared to the DFRB diet, as reflected by the concentration of propionate, butyrate, isovalerate and total SCFA which increased with time for growing pigs fed the DFRB diet (P < 0.05). Collectively, our results indicated at least 7 d adaptation was required to evaluate the energy values of fiber-rich ingredients, as the hindgut microbiota of growing pigs may need more time to adapt to a high fiber diet, especially for insoluble dietary fiber.

Insoluble dietary fibers: structure, metabolism, interactions with human microbiome, and role in gut homeostasis

Consumption of food rich in dietary fibers (DFs) has been long recognized to exert an overall beneficial effect on human health. This review aims to provide a holistic overview on how IDFs impact human gut health either directly, or through modulation of the gut microbiome. Several databases were searched for collecting papers such as PubMed, Google Scholar, Web of Science, Scopus and Reaxys from 2000 till 2022. Firstly, an overview of the chemical structure of the various IDFs and the pathways employed by gut microbiota for their degradation is provided. The impact of IDFs on microbial community structure and pathogens colonization inside the human gut was discussed. Finally, the impact of IDFs on gut homeostasis and systemic effects at the cellular level, as well as the overall immunological benefits of IDFs consumption were analyzed. IDFs viz., cellulose, hemicellulose, resistant starch, and lignin found enriched in food are discussed for these effects. IDFs were found to induce gut immunity, improve intestinal integrity and mucosal proliferation, and favor adhesion of probiotics and hence improve human health. Also, IDFs were concluded to improve the bioavailability of plant polyphenols and improve their health-related functional roles. Ultimately, dietary fibers processing by modification shows potential to enhance fibers-based functional food production, in addition to increase the economic value and usage of food-rich fibers and their by-products.

Dietary Concentrate-to-Forage Ratio Affects Rumen Bacterial Community Composition and Metabolome of Yaks

Changes in dietary composition affect the rumen microbiota in ruminants. However, information on the effects of dietary concentrate-to-forage ratio changes on yak rumen bacteria and metabolites is limited. This study characterized the effect of three different dietary concentrate-to-forage ratios (50:50, C50 group; 65:35, C65 group; 80:20, C80 group) on yak rumen fluid microbiota and metabolites using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS) analyses. Rumen fermentation parameters and the abundance of rumen bacteria were affected by changes in the dietary concentrate-to-forage ratio, and there was a strong correlation between them. At the genus level, higher relative abundances of norank_f__F082, NK4A214_group, Lachnospiraceae_NK3A20_group, Acetitomaculum, and norank_f__norank_o__Clostridia_UCG-014 were observed with a high dietary concentrate-to-forage ratio (P < 0.05). Combined metabolomic and enrichment analyses showed that changes in the dietary concentrate-to-forage ratio significantly affected rumen metabolites related to amino acid metabolism, protein digestion and absorption, carbohydrate metabolism, lipid metabolism, and purine metabolism. Compared with the C50 group, 3-methylindole, pantothenic acid, D-pantothenic acid, and 20-hydroxy-leukotriene E4 were downregulated in the C65 group, while spermine and ribose 1-phosphate were upregulated. Compared to the C50 group, Xanthurenic acid, tyramine, ascorbic acid, D-glucuronic acid, 6-keto-prostaglandin F1a, lipoxin B4, and deoxyadenosine monophosphate were upregulated in the C80 group, while 3-methylindole and 20-hydroxy-leukotriene E4 were downregulated. All metabolites (Xanthurenic acid, L-Valine, N-Acetyl-L-glutamate 5-semialdehyde, N-Acetyl-L-glutamic acid, Tyramine, 6-Keto-prostaglandin F1a, Lipoxin B4, Xanthosine, Thymine, Deoxyinosine, and Uric acid) were upregulated in the C80 group compared with the C65 group. Correlation analysis of microorganisms and metabolites provided new insights into the function of rumen bacteria, as well as a theoretical basis for formulating more scientifically appropriate feeding strategies for yak.

Effects of active, inactive, and derivatives of Akkermansia muciniphila on the expression of the endocannabinoid system and PPARs genes

This study aimed to investigate the effects of active and heat-inactivated forms of Akkermansia muciniphila, bacterium-derived outer membrane vesicles (OMVs), and cell-free supernatant on the transcription of endocannabinoid system (ECS) members, including cannabinoid receptors 1 and 2 (CB1 and CB2), fatty acid amide hydrolase (FAAH), and peroxisome proliferator-activated receptors (PPARs) genes (i.e., α, β/δ, and δ) in Caco-2 and HepG-2 cell lines. After the inoculation of A. muciniphila in brain heart infusion enriched medium, OMVs and cell-free supernatant were extracted. For the investigation of the effects of bacteria and its derivatives on the expression of ECS and PPARs genes, the aforementioned cells were treated by active and heat-inactivated bacteria, OMVs, and cell-free supernatant. Quantitative real-time polymerase chain reaction analysis revealed that both forms of the bacterium, bacterial-derived OMVs, and cell-free supernatant could affect the expression of CB1, CB2, FAAH, and PPARs genes (i.e., α, β/δ, and δ) significantly (P < 0.05). Considering the engagement of the aforementioned genes in metabolic pathways, it might be suggested that both forms of the bacterium, OMVs, and cell-free supernatant might have the potential to serve as a probiotic, paraprobiotic, and postbiotic candidate to prevent obesity, metabolic disorders, and liver diseases.

Exploring the Ecological Effects of Naturally Antibiotic-Insensitive Bifidobacteria in the Recovery of the Resilience of the Gut Microbiota during and after Antibiotic Treatment

Amoxicillin-clavulanic acid (AMC) is the most widely used antibiotic, being frequently prescribed to infants. Particular members of the genus Bifidobacterium are among the first microbial colonizers of the infant gut, and it has been demonstrated that they exhibit various activities beneficial for their human host, including promotion/maintenance of the human gut microbiota homeostasis. It has been shown that natural resistance of bifidobacteria to AMC is limited to a small number of strains. In the current study, we investigated the mitigation effects of AMC-resistant bifidobacteria in diversity preservation of the gut microbiota during AMC treatment. To this end, an in vitro coculture experiment based on infant fecal samples and an in vivo study employing a rodent model were performed. The results confirmed the ability of AMC-resistant bifidobacterial strains to bolster gut microbiota resilience, while specific covariance analysis revealed strain-specific and variable impacts on the microbiota composition by individual bifidobacterial taxa. IMPORTANCE The first microbial colonizers of the infant gut are members of the genus Bifidobacterium, which exhibit different activities beneficial to their host. Amoxicillin-clavulanic acid (AMC) is the most frequently prescribed antibiotic during infancy, and few strains of bifidobacteria are known to show a natural resistance to this antibiotic. In the present work, we evaluated the possible positive effects of AMC-resistant bifidobacterial strains in maintaining gut microbiota diversity during AMC exposure, performing an in vitro and in vivo experiment based on an infant gut model and a rodent model, respectively. Our results suggested the ability of AMC-resistant bifidobacterial strains to support gut microbiota restoration.

The Methanol Extract of Polygonatum odoratum Ameliorates Colitis by Improving Intestinal Short-Chain Fatty Acids and Gas Production to Regulate Microbiota Dysbiosis in Mice

The potential impacts of methanol extract from Polygonatum odoratum on (YZM) colonic histopathology, gut gas production, short-chain fatty acids (SCFAs), and intestinal microbiota composition were evaluated with dextran sulfate sodium (DSS)-induced colitis mice in this study. These results indicated that YZM increased colon length and ameliorated colonic histopathology in DSS-induced colitis mice. Moreover, YZM administration reversed intestinal microbiota compositions leading to the inhibition of H₂S-related bacteria (e.g., Desulfovibrionaceae) and the lower level of H₂S and higher contents of SCFA-related bacteria (e.g., Muribaculaceae). Taken together, the effects of methanol extract from Polygonatum odoratum are studied to provide new enlightenment and clues for its application as a functional food and clinical drug. Our study first revealed the relationship between intestinal gas production and key bacteria in ulcerative colitis.

Changes in the Profile of Fecal Microbiota and Metabolites as Well as Serum Metabolites and Proteome After Dietary Inulin Supplementation in Dairy Cows With Subclinical Mastitis

The occurrence and development of mastitis is linked to dysbiostic gastrointestinal microbiota. Inulin is a dietary prebiotic that improves the profile of intestinal flora. Our previous study showed that inulin supplementation could improve the ruminal microbes of subclinical mastitis (SCM) cows. The current study attempted to further investigate the response of hindgut (fecal) microbiome and metabolites, serum metabolism, and protein expression to inulin in the in SCM cows. Different levels of inulin (0, 100, 200, 300, and 400 g/day per cow) were supplemented in SCM cows. Compared with control group, Bacteroides and Bifidobacteria were increased, and Paeniclostridium, Ruminococcaceae, Coprococcus, and Clostridia were decreased in the feces of inulin groups, and accompanied with elevated propionate and butyrate concentrations, while secondary bile acid (SBA) metabolites were increased and proinflammatory lipid oxidation products were dropped in both feces and serum. In serum, inulin intake suppressed the levels of triglyceride (TG) and low-density lipoprotein (LDL). Serum proteome analysis found that CD44 antigen, phosphatidylinositol-glycan-specific phospholipase D, apolipoprotein A-II, and superoxide dismutase [Cu-Zn] were upregulated, while cathelicidin-1, haptoglobin, serpin A3, inter-alpha-trypsin inhibitor heavy chain H4 were downregulated in inulin groups. These findings suggested further evidence for inulin supplementation in amelioration of inflammatory symptoms in SCM cows, which might provide alternative treatment for mastitis.

Exploring the relationship between bacterial genera and lipid metabolism in bovine rumen

The rumen is characterised by a complex microbial ecosystem, which is particularly active in lipid metabolism. Several studies demonstrated a role of diet and breed on bacterial community profile, with the effect on metabolic pathways. Despite the knowledge achieved on metabolism and the bacterial profile, little is known about the relationship between individual bacteria and metabolic pathways. Therefore, a multivariate approach was used to search for possible relationships between bacteria and products of several pathways. The correlation between rumen bacterial community composition and rumen lipid metabolism was assessed in 40 beef steers (20 Maremmana and 20 Aubrac) reared with the same system and fed the same diet. A canonical discriminant analysis combined with a canonical correlation analysis (CCA) was performed to explore this correlation. The variables showing a Pearson correlation higher than 0.6 as absolute value and significant were retained for CCA considering the relationship of bacterial composition with several metabolic pathways. The results indicated that some bacterial genera could have significant impacts on the presence of several fatty acids. However, the relationship between genera and fatty acid changes according to the breed, demonstrating that the metabolic pathways change according to the host genetic background, related to breed evolution, although there is also an intra-breed genetic background which should not be ignored. In Maremmana, Succiniclasticum and Rikenellaceae_RC9_gut_group showed a high positive correlation with dimethylacetals (DMAs) DMA_C13:0, DMA_C14:0, DMA_C14:0iso, DMA_C15:0, DMA_C15:0iso, and DMA_C18:0. Prevotellaceae_UCG-003 correlates with C18:3c9c12c15 and C18:1t11, while Fibrobacter and Succiniclasticum correlate with C18:2c9t11 and Lachnospiraceae_NK3A20_group correlates with C18:1c12. Prevotellaceae_UCG-003, Ruminococcaceae_UCG-010, and Oribacterium showed a positive correlation with C13:0iso, and C17:0. Conversely, in Aubrac, Treponema_2 and Rikenellaceae_RC9_gut_group correlated with DMA_C14:0iso, DMA_C16:0iso, DMA_C17:0iso, while Ruminococcaceae_UCG-010, Christensenellaceae_R-7_group and Ruminococcaceae_NK4A214_group correlated with DMA_C18:1t11, DMA_C14:0, DMA_C18:1c12. Acetitomaculum correlated with C18:2c9c12, C18:1c12, C18:1c13, C18:1t12 and Lachnospiraceae_NK3A20_group with C18:1t6-8 and C18:1t9. Saccharofermentas, Ruminococcaceae_UCG-010 and Rikenellaceae_RC9_gut_group correlated with C18:2c9t11 while, Prevotellaceae_UCG-001 and Ruminococcus_1 correlated with C14:0iso, C15:0, C15:0iso, C17:0. Saccharofermentans, Rikenellaceae_RC9_gut_group, Ruminococcaceae_NK4A214_group, and Ruminococcaceae_UCG-010 correlated with C13:1c12 and C16:0iso. These results lead to hypothesise a possible association between several metabolic pathways and one or a few bacterial genera. If these associations are confirmed by further investigations that verify the causality of a bacterial genus with a particular metabolic process, it will be possible to deepen the knowledge on the activity of the rumen population in lipid metabolism. This approach appears to be a promising tool for uncovering the correlation between bacterial genera and products of rumen lipid metabolism.

Association between gut microbiota and prediabetes in people living with HIV

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Gut microbiota are known to be associated with various metabolic syndromes.

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Diversity of gut microbiota decreases in PLWH with prediabetes.

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Streptococcus and Anaerostignum are more abundant in the prediabetes group.

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Further study of alteration in gut microbiota on glucose metabolism is warranted.

The prevalence of prediabetes is rapidly increasing in general population and in people living with HIV (PLWH). Gut microbiota play an important role in human health, and dysbiosis is associated with metabolic disorders and HIV infection. Here, we aimed to evaluate the association between gut microbiota and prediabetes in PLWH. A cross-sectional study enrolled 40 PLWH who were receiving antiretroviral therapy and had an undetectable plasma viral load. Twenty participants had prediabetes, and 20 were normoglycemic. Fecal samples were collected from all participants. The gut microbiome profiles were analyzed using 16S rRNA sequencing. Alpha-diversity was significantly lower in PLWH with prediabetes than in those with normoglycemia (p<0.05). A significant difference in beta-diversity was observed between PLWH with prediabetes and PLWH with normoglycemia (p<0.05). Relative abundances of two genera in Firmicutes (Streptococcus and Anaerostignum) were significantly higher in the prediabetes group. In contrast, relative abundances of 13 genera (e.g., Akkermansia spp., Christensenellaceae R7 group) were significantly higher in the normoglycemic group. In conclusion, the diversity of gut microbiota composition decreased in PLWH with prediabetes. The abundances of 15 bacterial taxa in the genus level differed between PLWH with prediabetes and those with normoglycemia. Further studies on the effect of these taxa on glucose metabolism are warranted.

Directional Changes in the Intestinal Bacterial Community in Black Soldier Fly (Hermetia illucens) Larvae

Black soldier fly (BSF) larvae, Hermetia illucens (Diptera: Stratiomyidae) have emerged as an efficient system for the bioconversion of organic waste. Intestinal microorganisms are involved in several insect functions, including the development, nutrition, and physiology of the host. In order to transform the intestinal bacterial community of BSF directionally, six different potential functional strains (Lysinibacillus sphaericus, Proteus mirabilis, Citrobacter freundii, Pseudocitrobacter faecalis, Pseudocitrobacter anthropi, and Enterococcus faecalis) were added to aseptic food waste, and aseptic food waste was used without inoculants as a blank control to evaluate the changes in the intestinal microbiota of BSF under artificial intervention conditions. These six strains (which were isolated from the larval intestinal tract in selective media and then identified and screened) may be considered responsible for the functional characteristics of larvae. The results imply that the increase in the abundance of Lysinibacillus in the experimental group that was exposed to Lysinibacillus sphaericus was significantly different to the other groups (p < 0.05). The results revealed that it is feasible to transform the intestinal microbiota of BSF directionally; there are differences in the proliferation of different strains in the intestine of BSF.

Implications of Gut Microbiota in Complex Human Diseases

Humans, throughout the life cycle, from birth to death, are accompanied by the presence of gut microbes. Environmental factors, lifestyle, age and other factors can affect the balance of intestinal microbiota and their impact on human health. A large amount of data show that dietary, prebiotics, antibiotics can regulate various diseases through gut microbes. In this review, we focus on the role of gut microbes in the development of metabolic, gastrointestinal, neurological, immune diseases and, cancer. We also discuss the interaction between gut microbes and the host with respect to their beneficial and harmful effects, including their metabolites, microbial enzymes, small molecules and inflammatory molecules. More specifically, we evaluate the potential ability of gut microbes to cure diseases through Fecal Microbial Transplantation (FMT), which is expected to become a new type of clinical strategy for the treatment of various diseases.

Pediatric intestinal failure and the microbiome

Neonatal intestinal failure is a complex medical condition that is associated with the need for long term parenteral nutrition and its associated complications. The microbiome in this diseased state is different from what is now understood to be a healthy microbiome. The effect of this dysbiotic microbiome on the complications of intestinal failure are only starting to be understood. The ability to modulate the microbiome with enteral/parenteral nutrients, as well probiotics to a healthier state, is an exciting opportunity that holds promise.

Ruminiclostridium 5, Parabacteroides distasonis, and bile acid profile are modulated by prebiotic diet and associate with facilitated sleep/clock realignment after chronic disruption of rhythms

Chronic disruption of rhythms (CDR) impacts sleep and can result in circadian misalignment of physiological systems which, in turn, is associated with increased disease risk. Exposure to repeated or severe stressors also disturbs sleep and diurnal rhythms. Prebiotic nutrients produce favorable changes in gut microbial ecology, the gut metabolome, and reduce several negative impacts of acute severe stressor exposure, including disturbed sleep, core body temperature rhythmicity, and gut microbial dysbiosis. In light of previous compelling evidence that prebiotic diet broadly reduces negative impacts of acute, severe stressors, we hypothesize that prebiotic diet will also effectively mitigate the negative impacts of chronic disruption of circadian rhythms on physiology and sleep/wake behavior. Male, Sprague Dawley rats were fed diets enriched in prebiotic substrates or calorically matched control chow. After 5 weeks on diet, rats were exposed to CDR (12 h light/dark reversal, weekly for 8 weeks) or remained on undisturbed normal light/dark cycles (NLD). Sleep EEG, core body temperature, and locomotor activity were recorded via biotelemetry in freely moving rats. Fecal samples were collected on experimental days -33, 0 (day of onset of CDR), and 42. Taxonomic identification and relative abundances of gut microbes were measured in fecal samples using 16S rRNA gene sequencing and shotgun metagenomics. Fecal primary, bacterially modified secondary, and conjugated bile acids were measured using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Prebiotic diet produced rapid and stable increases in the relative abundances of Parabacteroides distasonis and Ruminiclostridium 5. Shotgun metagenomics analyses confirmed reliable increases in relative abundances of Parabacteroides distasonis and Clostridium leptum, a member of the Ruminiclostridium genus. Prebiotic diet also modified fecal bile acid profiles; and based on correlational and step-wise regression analyses, Parabacteroides distasonis and Ruminiclostridium 5 were positively associated with each other and negatively associated with secondary and conjugated bile acids. Prebiotic diet, but not CDR, impacted beta diversity. Measures of alpha diversity evenness were decreased by CDR and prebiotic diet prevented that effect. Rats exposed to CDR while eating prebiotic, compared to control diet, more quickly realigned NREM sleep and core body temperature (ClockLab) diurnal rhythms to the altered light/dark cycle. Finally, both cholic acid and Ruminiclostridium 5 prior to CDR were associated with time to realign CBT rhythms to the new light/dark cycle after CDR; whereas both Ruminiclostridium 5 and taurocholic acid prior to CDR were associated with NREM sleep recovery after CDR. These results support our hypothesis and suggest that ingestion of prebiotic substrates is an effective strategy to increase the relative abundance of health promoting microbes, alter the fecal bile acid profile, and facilitate the recovery and realignment of sleep and diurnal rhythms after circadian disruption.

Short-Chain Inulin Modulates the Cecal Microbiota Structure of Leptin Knockout Mice in High-Fat Diet

The aim of this study was to explore the effect of short-chain inulin on cecal microbiota of high-fat diet-fed leptin knockout mice and the different influences of cecal microbiota on wild-type and leptin knockout mice. A total of 18 specific pathogen-free male C57BL/6J wild-type mice and 18 C57BL/6J leptin knockout mice (OB/OB mice) were selected. Mice were divided into six groups according to their genotype: wild-type mice have three groups, including the normal diet group (CT), 60% high-fat diet group (CH), and 60% high fat with 10% short-chain inulin group (CHI); OB/OB mice were also divided into three groups, including the normal diet group (OT), 60% high-fat diet group (OH), and 60% high fat with 10% short-inulin group (OHI). The mice were fed for 8 weeks to analyze the diversity of cecal microbiota. The results show that compared with CH and OH, the variety of cecal microbiota was significantly reduced in CH and OH and further reduced in CHI and OHI. Bifidobacterium and Lactobacillus are the biomarkers in genus level. Dietary short-chain inulin significantly enhanced Bifidobacterium in OHI compared with OH (p < 0.01) and significantly reduced in CHI and compared with CH (p < 0.01). Lactobacillus was significantly enhanced in CHI and OHI compared with CH and OH, respectively (p < 0.01). Blautia was significantly enhanced in CH and OH compared with other groups (p < 0.01). Both Escherichia-Shigella and Enterococcus were significantly reduced in CHI and OHI, compared with CH and OH, respectively (p < 0.05). Escherichia-Shigella was even lower than CT and OT in CHI and OHI. Functional prediction of microbial communities showed that the abundance of amino acid sugar and nucleotide sugar metabolism pathways were significantly enhanced (p < 0.05) in CH and OH, and OH was significantly higher than CH (p < 0.05). Among the leptin knockout groups, PICRUSt2 function prediction showed that the fatty acid metabolism pathway significantly reduced (p < 0.05) in OHI and OT compared with OH. In conclusion, short-chain inulin modulated the dysbiosis induced by high-fat diet, improved probiotics growth and inhibited conditioned pathogenic bacteria, and the influences were significantly different in wild-type and leptin knockout mice.

Variations on gut health and energy metabolism in pigs and humans by intake of different dietary fibers

Many studies have reported that dietary fibers play a crucial role in promoting intestinal health of the host, since it strengthens functions of epithelial barrier and meanwhile maintains intestinal homeostasis of the host by modulating gut microbiota and short-chain fatty acid (SCFA) production. Pig is a good animal model to study effects of dietary fiber on gut health and microbial community. This review has summarized the relevant knowledge available based on roles of various dietary fibers in gut health and energy metabolism of pigs and humans. Evidences summarized in our review indicated that modulating intestinal microbial composition and SCFA production by consuming specific dietary fibers properly could be conducive to health improvement and disease prevention of the host. However, types of dietary fiber from edible foods exert divergent impacts on gut health, energy metabolism, microbial composition, and SCFA production. Therefore, more attention should be focused on different responses of various dietary fibers intake on host metabolism and health.

Newly Obtained Apple Pectin as an Adjunct to Irinotecan Therapy of Colorectal Cancer Reducing E. coli Adherence and β-Glucuronidase Activity

Colorectal cancer (CRC) is the second cause of cancer death worldwide. The composition and enzymatic activity of colonic microbiota can significantly affect the effectiveness of CRC chemotherapy. Irinotecan is a drug widely used to treat colon cancer. However, the transformation of a drug-glucuronide (SN-38G) back to its active form (SN-38) by bacterial β-glucuronidase (GUS) constitutes the primary reason for the observed intestinal toxicity of irinotecan. It was demonstrated that novel enzymatically extracted apple pectin (PC) might be a promising candidate for an adjunct to irinotecan therapy. PC itself reduced the viability of HCT 116 and Caco-2 colorectal cancer cells, induced apoptosis, and increased intracellular reactive oxygen species production. Moreover, PC enhanced the cytotoxic and proapoptotic effect of irinotecan (at concentrations below its IC₅₀), i.e., synergistic effect was recorded. Additionally, PC exhibited potent anti-inflammatory properties and prevented adhesion of prototype adherent-invasive E. coli (AIEC) LF82 strain and laboratory K-12_C600 strain to colon cancer cells. PC was also identified to be an effective inhibitor of bacterial GUS activity. Altogether, novel apple pectin was identified as a promising candidate for a supplement to irinotecan therapy that might alleviate its side-effects via inhibition of bacterial GUS and thus increasing its therapeutic efficacy.

Parasites, Drugs and Captivity: Blastocystis-Microbiome Associations in Captive Water Voles

(1) Background: Blastocystis is a microbial eukaryote inhabiting the gastrointestinal tract of a broad range of animals including humans. Several studies have shown that the organism is associated with specific microbial profiles and bacterial taxa that have been deemed beneficial to intestinal and overall health. Nonetheless, these studies are focused almost exclusively on humans, while there is no similar information on other animals. (2) Methods: Using a combination of conventional PCR, cloning and sequencing, we investigated presence of Blastocystis along with Giardia and Cryptosporidium in 16 captive water voles sampled twice from a wildlife park. We also characterised their bacterial gut communities. (3) Results: Overall, alpha and beta diversities between water voles with and without Blastocystis did not differ significantly. Differences were noted only on individual taxa with Treponema and Kineothrix being significantly reduced in Blastocystis positive water voles. Grouping according to antiprotozoal treatment and presence of other protists did not reveal any differences in the bacterial community composition either. (4) Conclusion: Unlike human investigations, Blastocystis does not seem to be associated with specific gut microbial profiles in water voles.

Antimicrobial peptides as an alternative to relieve antimicrobial growth promoters in poultry

1. This review describes different classes of antimicrobial peptides (AMP) found in the gastrointestinal (GI) tract of avian species, and their antimicrobial and immunomodulatory activities. The potential benefits of synthetic AMP in poultry production are examined, in the context of the use of AMP as alternatives to antimicrobial growth promoters (AGP).2. Since the mid-1950s, antibiotic growth promoters (AGP) have been used in feed at low prophylactic doses to modulate the homoeostasis of intestinal microbiota, decreasing the risk of intestinal dysbacteriosis and the growth of pathogens within the avian gut. Over the last three decades, AGP have faced major regulatory restrictions due to concerns of generating antimicrobial resistance (AMR). It is now well documented that the rate of infectious disease outbreaks is higher in flocks that are not fed prophylactic antibiotics, resulting in a compensatory increase in antimicrobial use for therapeutic purposes.3. Endogenous natural AMP production is associated with the presence of microbiota and their interaction with the intestinal epithelial and lamina propria lymphoid cells. Their antimicrobial activity shapes the beneficial microbiota population and controls intestinal pathogens such Clostridium and Salmonella spp., and stimulates the development and maturation of the local immune system.4. Similar to AGP, AMP can establish a well-balanced gut beneficial microbiota for adequate immune-competence, animal health and high growth performance parameters such as feed intake, daily weight, feed conversion and accumulated mortality.5. Antimicrobial proteins and peptides constitute an essential part of the innate immune system of all organisms and protect the host from invading pathogenic bacteria, viruses, fungi, and parasites by interacting with the negatively charged pathogen membranes.

Antibiotic Therapy and the Gut Microbiome: Investigating the Effect of Delivery Route on Gut Pathogens

The contribution of the gut microbiome to human health has long been established, with normal gut microbiota conferring protection against invasive pathogens. Antibiotics can disrupt the microbial balance of the gut, resulting in disease and the development of antimicrobial resistance. The effect of antibiotic administration route on gut dysbiosis remains under-studied to date, with conflicting evidence on the differential effects of oral and parenteral delivery. We have profiled the rat gut microbiome following treatment with commonly prescribed antibiotics (amoxicillin and levofloxacin), via either oral or intravenous administration. Fecal pellets were collected over a 13-day period and bacterial populations were analyzed by 16S rRNA gene sequencing. Significant dysbiosis was observed in all treatment groups, regardless of administration route. More profound dysbiotic effects were observed following amoxicillin treatment than those with levofloxacin, with population richness and diversity significantly reduced, regardless of delivery route. The effect on specific taxonomic groups was assessed, revealing significant disruption following treatment with both antibiotics. Enrichment of a number of groups containing known gut pathogens was observed, in particular, with amoxicillin, such as the family Enterobacteriaceae. Depletion of other commensal groups was also observed. The degree of dysbiosis was significantly reduced toward the end of the sampling period, as bacterial populations began to return to pretreatment composition. Richness and diversity levels appeared to return to pretreatment levels more quickly in intravenous groups, suggesting convenient parenteral delivery systems may have a role to play in reducing longer term gut dysbiosis in the treatment of infection.

Enterolignan Production in a Flaxseed Intervention Study in Postmenopausal US Women of African Ancestry and European Ancestry

Lignans are phytochemicals studied extensively as dietary factors in chronic disease etiology. Our goal was to examine associations between the gut microbiota and lignan metabolism and whether these associations differ by ethnicity. We conducted a flaxseed (FS) dietary intervention in 252 healthy, postmenopausal women of African ancestry (AA) and European ancestry (EA). Participants consumed ~10 g/d ground flaxseed for 6 weeks and provided overnight urine collections and fecal samples before and after intervention. The gut microbiota was characterized using 16S rRNA gene sequencing and differences in microbial community composition compared by ethnicity and intervention status. We observed a significant difference in the composition of the microbiota measured as beta diversity (p < 0.05) between AA and EA at baseline that was attenuated with FS consumption. Genera that were significantly associated with ENL production (e.g., Klebsiella, Lactobacillus, Slackia, Senegalimassilia) were unique to each group. Bacteria (e.g., Fusobacteria, Pyramidobacter and Odoribacter) previously associated with colorectal cancer and cardiovascular disease, both diet-related chronic diseases, were unique to either AA or EA and were significantly reduced in the FS intervention. This study suggests that ethnic variation in ENL metabolism may be linked to gut microbiota composition, and its impact on disease risk deserves future investigation.

Unraveling the Gut Microbiome of the Invasive Small Indian Mongoose (Urva auropunctata) in the Caribbean

Small Indian mongooses (Urva auropunctata) are among the most pervasive predators to disrupt the native ecology on Caribbean islands and are strongly entrenched in their areas of introduction. Few studies, however, have considered the microbial ecology of such biological invasions. In this study, we investigated the gut microbiota of invasive small Indian mongooses in terms of taxonomic diversity and functional potential. To this end, we collected fecal samples from 60 free-roaming mongooses trapped in different vegetation zones on the island Saint Kitts. The core gut microbiome, assessed by 16S rRNA amplicon gene sequencing on the Ion S5^TM XL platform, reflects a carnivore-like signature with a dominant abundance of Firmicutes (54.96%), followed by Proteobacteria (13.98%) and Fusobacteria (12.39%), and a relatively minor contribution of Actinobacteria (10.4%) and Bacteroidetes (6.40%). Mongooses trapped at coastal sites exhibited a higher relative abundance of Fusobacterium spp. whereas those trapped in scrubland areas were enriched in Bacteroidetes, but there was no site-specific difference in predicted metabolic properties. Between males and females, beta-diversity was not significantly different and no sex-specific strategies for energy production were observed. However, the relative abundance of Gammaproteobacteria, and more specifically, Enterobacteriaceae, was significantly higher in males. This first description of the microbial profile of small Indian mongooses provides new insights into their bioecology and can serve as a springboard to further elucidating this invasive predator’s impact throughout the Caribbean.

Comparison of Fecal Microbiota of Horses Suffering from Atypical Myopathy and Healthy Co-Grazers

Equine atypical myopathy (AM) is caused by hypoglycin A (HGA) and methylenecyclopropylglycine (MCPG) intoxication resulting from the ingestion of seeds or seedlings of some Acer tree species. Interestingly, not all horses pasturing in the same toxic environment develop signs of the disease. In other species, it has been shown that the intestinal microbiota has an impact on digestion, metabolism, immune stimulation and protection from disease. The objective of this study was to characterize and compare fecal microbiota of horses suffering from AM and healthy co-grazers. Furthermore, potential differences in fecal microbiota regarding the outcome of diseased animals were assessed. This prospective observational study included 59 horses with AM (29 survivors and 30 non-survivors) referred to three Belgian equine hospitals and 26 clinically healthy co-grazers simultaneously sharing contaminated pastures during spring and autumn outbreak periods. Fresh fecal samples (rectal or within 30 min of defecation) were obtained from all horses and bacterial taxonomy profiling obtained by 16S amplicon sequencing was used to identify differentially distributed bacterial taxa between AM-affected horses and healthy co-grazers. Fecal microbial diversity and evenness were significantly (p < 0.001) higher in AM-affected horses as compared with their non-affected co-grazers. The relative abundance of families Ruminococcaceae, Christensenellaceae and Akkermansiaceae were higher (p ≤ 0.001) whereas those of the Lachnospiraceae (p = 0.0053), Bacteroidales (p < 0.0001) and Clostridiales (p = 0.0402) were lower in horses with AM, especially in those with a poor prognosis. While significant shifts were observed, it is still unclear whether they result from the disease or might be involved in the onset of disease pathogenesis.

Exploring the Gut Microbiome Alteration of the European Hare (Lepus europaeus) after Short-Term Diet Modifications

Simple Summary

The composition of gut microbial communities can be altered by host diet shift. In this study, we investigated the microbiome composition of European hares and the potential changes in their gut communities after 4 days from the introduction in the diet of new nourishment. The control group was fed with standard fodder; the diet of the experimental group was integrated with apples and carrots. DNA was extracted from fresh faecal pellets and the V3-V4 hypervariable regions were amplified and sequenced using the Illumina MiSeq^® platform. The amplicon sequence variants were classified into 735 bacterial genera belonging to 285 families and 36 phyla; the most abundant phyla represented by Bacteroidetes and Firmicutes. Experimental and control hares did not show statistically significant differences in their microbial communities suggesting the exposition time to a new diet should be extended to define the time frame necessary to affect microbiome composition.

Abstract

This study aimed to characterise the gut microbiome composition of European hares (Lepus europaeus) and its potential changes after a short-term diet modification. The high sensitivity of European hare to habitat changes makes this species a good model to analyse possible alterations in gut microbiome after the introduction of additional nourishment into the diet. In total, 20 pairs were chosen for the experiments; 10 pairs formed the control group and were fed with standard fodder. The other 10 pairs represented the experimental group, whose diet was integrated with apples and carrots. The DNA from fresh faecal pellets collected after 4 days from the start of the experiment was extracted and the V3-V4 hypervariable regions were amplified and sequenced using the Illumina MiSeq^® platform. The obtained amplicon sequence variants were classified into 735 bacterial genera belonging to 285 families and 36 phyla. The control and the experimental groups appeared to have a homogenous dispersion for the two taxonomic levels analysed with the most abundant phyla represented by Bacteroidetes and Firmicutes. No difference between control and experimental samples was detected, suggesting that the short-term variation in food availability did not alter the hares’ gut microbiome. Further research is needed to estimate significant time threshold.

The intervention of unique plant polysaccharides - Dietary fiber on depression from the gut-brain axis

As an invisible organ of human body, the gut microbiota plays an important role in human life and has become a hot spot in the field of life science in recent years. Due to the increasing pressure of work and life, people are prone to depression. The in-depth mechanism studies indicated that the gut microbiota could improve the depression symptom through the gut-brain axis (GBA). As unique plant polysaccharides, dietary fiber can effectively modulate the intestinal flora disorders and its crucial role in orchestrating host-microbiota crosstalk has been confirmed. This review highlights the mechanisms that the gut microbiota affects the development of depression through GBA and focuses on dietary fiber intervention on the improvement of intestinal microbiota imbalance, which may provide new ideas for the prevention and treatment of depression.

Effects of Maternal Fiber Intake on Intestinal Morphology, Bacterial Profile and Proteome of Newborns Using Pig as Model

Dietary fiber intake during pregnancy may improve offspring intestinal development. The aim of this study was to evaluate the effect of maternal high fiber intake during late gestation on intestinal morphology, microbiota, and intestinal proteome of newborn piglets. Sixteen sows were randomly allocated into two groups receiving the control diet (CD) and high-fiber diet (HFD) from day 90 of gestation to farrowing. Newborn piglets were selected from each litter, named as CON and Fiber group, respectively. Maternal high fiber intake did not markedly improve the birth weight, but increased the body length, the ileal crypt depth and colonic acetate level. In addition, maternal high fiber intake increased the -diversity indices (Observed species, Simpson, and ACE), and the abundance of Acidobacteria and Bacteroidetes at phylum level, significantly increased the abundance of Bradyrhizobium and Phyllobacterium at genus level in the colon of newborn piglets. Moreover, maternal high fiber intake markedly altered the ileal proteome, increasing the abundances of proteins associated with oxidative status, energy metabolism, and immune and inflammatory responses, and decreasing abundances of proteins related to cellular apoptosis, cell structure, and motility. These findings indicated that maternal high fiber intake could alter intestinal morphology, along with the altered intestinal microbiota composition and proteome of offspring.

Anti-Obesity Effect of Dictyophora indusiata Mushroom Polysaccharide (DIP) in High Fat Diet-Induced Obesity via Regulating Inflammatory Cascades and Intestinal Microbiome

Obesity is a multifactorial metabolic disorder characterized by low-grade chronic inflammation, hyper-permeability of the gut epithelium, and perturbation of the intestinal microbiome. Despite the numerous therapeutic efficacies of Dictyophora indusiata mushroom, its biological activity in alleviating obesity through regulation of the gut microbiota and inflammatory cascades remain obscure. Henceforth, we determined the modulatory impact of D. indusiata polysaccharide (DIP) in the high-fat diet (HFD)-induced obesity mice model. The experimental subjects (BALB/C mice) were supplemented with chow diet (Control group), high-fat diet (HFD group), or HFD along with DIP at a low dose [HFD + DIP(L)] and high dose [HFD + DIP(H)]. Obesity-related parameters, including body weight gain, epididymal adipocyte size, fat accumulation, adipogenic markers, lipogenic markers, inflammatory associated markers, intestinal integrity, and intestinal microbiome, were elucidated. Our findings demonstrated that the oral administration of DIP at low dose partially and at high dose significantly reversed HFD-induced obesity parameters. Furthermore, the body weight, fat accumulation, adipocyte size, adipogenic and liver associated markers, glucose levels, inflammatory cytokines, and endotoxin (Lipopolysaccharide, LPS) levels were reduced considerably. Moreover, the study revealed that DIP treatment reversed the dynamic alterations of the gut microbiome community by decreasing the Firmicutes to Bacteroidetes ratio. These findings led us to infer the therapeutic potential of DIP in alleviating HFD-induced obesity via regulating inflammatory cascades, modulating intestinal integrity and intestinal microbiome community.

Behaviour of citrus pectin and modified citrus pectin in an azoxymethane/dextran sodium sulfate (AOM/DSS)-induced rat colorectal carcinogenesis model

Large intestine cancer is one of the most relevant chronic diseases taking place at present. Despite therapies have evolved very positively, this pathology is still under deep investigation. One of the recent approaches is the prevention by natural compounds such as pectin. In this paper, we have assessed the impact of citrus pectin and modified citrus pectin on colorectal cancer in rats (Rattus norvegicus F344) to which azoxymethane and DSS were supplied. The lowest intake of food and body weight were detected in animals fed with citrus pectin, together with an increase in the caecum weight, probably due to the viscosity, water retention capacity and bulking properties of pectin. The most striking feature was that, neither citrus pectin nor modified citrus pectin gave rise to a tumorigenesis prevention. Moreover, in both, more than 50% of rats with cancer died, probably ascribed to a severe dysbiosis state in the gut, as shown by the metabolism and metagenomics studies carried out. This was related to a decrease of pH in caecum lumen and increase in acetate and lactic acid levels together with the absence of propionic and butyric acids. A relevant increase in Proteobacteria (Enterobacteriaceae) were thought to be one of the reasons for enteric infection that could have provoked the death of rats and the lack of cancer prevention. However, a reduction of blood glucose and triacylglycerides level and an increase of Bifidobacterium and Lactobacillaceae were found in animals that intake pectin, as compared to universal and modified citrus pectin feeding.

Modulation of gut microbiota in healthy rats after exposure to nutritional supplements

INTRODUCTION

Rats are experimental animals, frequently used as model organisms in the biomedical studies, and increasingly used to study the gut microbiota. Specifically, the aim of latter studies is either the elucidation of relationship between intestinal dysbiosis and diseases or the determination of nutrients or pharmaceutical agents which can cause the modulation in the presence or abundance of gut microbiota.

AIM

Herein, the research studies conducted on the gut microbiota of healthy rats are presented in a summarized and concise overview. The focus is on studies aimed to reveal the shifts in microbial composition and functional changes after exposure to various types of nutritional supplements.

METHODS

We performed the search of PubMed database using the term "rat gut microbiome microbiota" and examined studies aimed to assess the composition of gut microbiota in physiological homeostasis as well as the effect of various nutritional supplements on the gut microbiota of healthy rats.

Gut dysbacteriosis and intestinal disease: mechanism and treatment

The gut microbiome functions like an endocrine organ, generating bioactive metabolites, enzymes or small molecules that can impact host physiology. Gut dysbacteriosis is associated with many intestinal diseases including (but not limited to) inflammatory bowel disease, primary sclerosing cholangitis-IBD, irritable bowel syndrome, chronic constipation, osmotic diarrhoea and colorectal cancer. The potential pathogenic mechanism of gut dysbacteriosis associated with intestinal diseases includes the alteration of composition of gut microbiota as well as the gut microbiota-derived signalling molecules. The many correlations between the latter and the susceptibility for intestinal diseases has placed a spotlight on the gut microbiome as a potential novel target for therapeutics. Currently, faecal microbial transplantation, dietary interventions, use of probiotics, prebiotics and drugs are the major therapeutic tools utilized to impact dysbacteriosis and associated intestinal diseases. In this review, we systematically summarized the role of intestinal microbiome in the occurrence and development of intestinal diseases. The potential mechanism of the complex interplay between gut dysbacteriosis and intestinal diseases, and the treatment methods are also highlighted.

Dietary Lipids Influence Bioaccessibility of Polyphenols from Black Carrots and Affect Microbial Diversity under Simulated Gastrointestinal Digestion

The bioaccessibility and activity of polyphenols is dependent on their structure and entrapment in the food matrix. While dietary lipids are known to transit into the colon, the impact of different lipids on the microbiome, and their interactions with dietary polyphenols are largely unknown. Here, we investigated the effect of dietary lipids on the bioaccessibility of polyphenols from purple/black carrots and adaptation of the gut microbiome in a simulated in vitro digestion-fermentation. Coconut oil, sunflower oil, and beef tallow were selected to represent common dietary sources of medium-chain fatty acids (MCFAs), long-chain polyunsaturated fatty acids (PUFAs), and long-chain polysaturated fatty acids (SFAs), respectively. All lipids promoted the bioaccessibility of both anthocyanins and phenolic acids during intestinal digestion with coconut oil exhibiting the greatest protection of anthocyanins. Similar trends were shown in antioxidant assays (2,2-Diphenyl-1-pricrylhydrazyl (DPPH), ferric reducing ability (FRAP), and total phenolic content (TPC)) with higher phytochemical bioactivities observed with the addition of dietary lipids. Most bioactive polyphenols were decomposed during colonic fermentation. Black carrot modulated diversity and composition of a simulated gut microbiome. Dramatic shifts in gut microbiome were caused by coconut oil. Inclusion of sunflower oil improved the production of butyrate, potentially due to the presence of PUFAs. The results show that the impact of polyphenols in the digestive tract should be considered in the context of other components of the diet, particularly lipids.

Effects of Dietary Energy Levels on Rumen Fermentation, Microbial Diversity, and Feed Efficiency of Yaks (Bos grunniens)

The microbial community of the yak (Bos grunniens) rumen plays an important role in surviving the harsh Tibetan environment where seasonal dynamic changes in pasture cause nutrient supply imbalances, resulting in weight loss in yaks during the cold season. A better understanding of rumen microbiota under different feeding regimes is critical for exploiting the microbiota to enhance feed efficiency and growth performance. This study explored the impact of different dietary energy levels on feed efficiency, rumen fermentation, bacterial community, and abundance of volatile fatty acid (VFA) transporter transcripts in the rumen epithelium of yaks. Fifteen healthy castrated male yaks were divided into three groups and fed with low (YL), medium (YM), and high energy (YH) levels diet having different NEg of 5.5, 6.2, and 6.9 MJ/kg, respectively. The increase in feed efficiency was recorded with an increase in dietary energy levels. The increase in dietary energy levels decreased the pH and increased the concentrations of acetate, propionate, butyrate, and valerate in yak rumens. The increase in the mRNA abundance of VFA transporter genes (MCT1, DRA, PAT1, and AE2) in the rumen epithelium of yaks was recorded as dietary energy level increased. High relative abundances of Firmicutes and Bacteroidetes were recorded with the increase in dietary energy levels. Significant population shifts at the genus level were recorded among the three treatments. This study provides new insights into the dietary energy-derived variations in rumen microbial community.