Determination of Resistant Starch Assimilating Bacteria in Fecal Samples of Mice by In vitro RNA-Based Stable Isotope Probing

Proteomic stable isotope probing with an upgraded Sipros algorithm for improved identification and quantification of isotopically labeled proteins

BACKGROUND

Proteomic stable isotope probing (SIP) is used in microbial ecology to trace a non-radioactive isotope from a labeled substrate into de novo synthesized proteins in specific populations that are actively assimilating and metabolizing the substrate in a complex microbial community. The Sipros algorithm is used in proteomic SIP to identify variably labeled proteins and quantify their isotopic enrichment levels (atom%) by performing enrichment-resolved database searching.

RESULTS

In this study, Sipros was upgraded to improve the labeled protein identification, isotopic enrichment quantification, and database searching speed. The new Sipros 4 was compared with the existing Sipros 3, Calisp, and MetaProSIP in terms of the number of identifications and the accuracy and precision of atom% quantification on both the peptide and protein levels using standard E. coli cultures with 1.07 atom%, 2 atom%, 5 atom%, 25 atom%, 50 atom%, and 99 atom% 13C enrichment. Sipros 4 outperformed Calisp and MetaProSIP across all samples, especially in samples with ≥ 5 atom% 13C labeling. The computational speed on Sipros 4 was > 20 times higher than Sipros 3 and was on par with the overall speed of Calisp- and MetaProSIP-based pipelines. Sipros 4 also demonstrated higher sensitivity for the detection of labeled proteins in two 13C-SIP experiments on a real-world soil community. The labeled proteins were used to trace 13C from 13C-methanol and 13C-labeled plant exudates to the consuming soil microorganisms and their newly synthesized proteins.

CONCLUSION

Overall, Sipros 4 improved the quality of the proteomic SIP results and reduced the computational cost of SIP database searching, which will make proteomic SIP more useful and accessible to the border community. Video Abstract.

Effects of Long-Term Cold Stress on Growth Performance, Behavior, Physiological Parameters, and Energy Metabolism in Growing Beef Cattle

This study aimed to evaluate the effects of a long-term cold environment on growth performance, physiological behavior, biochemical blood indexes, and hormone levels in Simmental cattle. Thirty Simmental crossbred bulls (weight = 350 ± 17 kg, 13-14 months old) were selected for two trials at autumn suitable temperatures (A-ST) and winter cold temperatures (W-CT) (15 cattle per season). The results showed that compared with the A-ST group, dry matter intake (p < 0.05) and feed:gain (p < 0.01) of the W-CT group increased, while body weight (p < 0.01) and average daily gain (p < 0.01) significantly decreased. Long-term cold stress also increased lying time (p < 0.01), feeding time (p < 0.05), and pulse rate (p < 0.01) in the W-CT group, while the rumen volatile fatty acids content (p < 0.01) and apparent digestibility of nutrients (p < 0.05) were significantly decreased. In terms of blood indicators, long-term cold stress increased the concentrations of glucose, glucose metabolic enzymes, glucocorticoids, triiodothyronine, and tetraiodothyronine in the plasma of the W-CT group (p < 0.05), but the levels of triglycerides, β-hydroxybutyrate, propionate, insulin, and growth hormone were decreased (p < 0.01). In summary, long-term cold stress may inhibit the digestive function of Simmental cattle and enhance the body's energy metabolism and stress hormone imbalance, ultimately damaging the normal growth and development of the body.

Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting

The composition and metabolism of the human gut microbiota are strongly influenced by dietary complex glycans, which cause downstream effects on the physiology and health of hosts. Despite recent advances in our understanding of glycan metabolism by human gut bacteria, we still need methods to link glycans to their consuming bacteria. Here, we use a functional assay to identify and isolate gut bacteria from healthy human volunteers that take up different glycans. The method combines metabolic labeling using fluorescent oligosaccharides with fluorescence-activated cell sorting (FACS), followed by amplicon sequencing or culturomics. Our results demonstrate metabolic labeling in various taxa, such as Prevotella copri, Collinsella aerofaciens and Blautia wexlerae. In vitro validation confirms the ability of most, but not all, labeled species to consume the glycan of interest for growth. In parallel, we show that glycan consumers spanning three major phyla can be isolated from cultures of sorted labeled cells. By linking bacteria to the glycans they consume, this approach increases our basic understanding of glycan metabolism by gut bacteria. Going forward, it could be used to provide insight into the mechanism of prebiotic approaches, where glycans are used to manipulate the gut microbiota composition.

Effect of resistant starch types as a prebiotic

Since the role of intestinal microbiota in metabolism was understood, the importance of dietary components such as fibres and prebiotics, which affect the modulation of microbiota, has been increasing day by day. While all prebiotic components are considered dietary fibre, not every dietary fibre is considered a prebiotic. While fructooligosaccharides, galactooligosaccharides, inulin, and galactans are considered prebiotics, other fermentable carbohydrates are considered candidate prebiotic components based on in vitro and preclinical studies. Resistant starch, one of such carbohydrates, is considered a potential prebiotic component when it is made resistant to digestion naturally or chemically. In this review, both in vitro and in vivo studies in which the prebiotic capacity of type II, type III, and type IV resistant starch isolated from food and produced commercially was assessed were analyzed. According to the results of current studies, certain types of resistant starch are thought to have a high prebiotic capacity, and they may be candidate prebiotic components although positive results have not been achieved in all studies. KEY POINTS: • Resistant starch is undigested in the small intestine and is fermented in the large intestine. • Resistant starch fermentation positively affects the growth of Bifidobacterium and Lactobacillus. • Resistant starch can be considered a prebiotic ingredient.

Sesamolin Attenuates Kidney Injury, Intestinal Barrier Dysfunction, and Gut Microbiota Imbalance in High-Fat and High-Fructose Diet-Fed Mice

This study investigated the effects of sesamolin on kidney injury, intestinal barrier dysfunction, and gut microbiota imbalance in high-fat and high-fructose (HF-HF) diet-fed mice and explored the underlying correlations among them. The results indicated that sesamolin suppressed metabolic disorders and increased renal function parameters. Histological evaluation showed that sesamolin mitigated renal epithelial cell degeneration and brush border damage. Meanwhile, sesamolin inhibited the endotoxin-mediated induction of the Toll-like receptor 4-related IKKα/NF-κB p65 pathway activation. Additionally, sesamolin mitigated intestinal barrier dysfunction and improved the composition of gut microbiota. The correlation results further indicated that changes in the dominant phyla, including Firmicutes, Deferribacterota, Desulfobacterota, and Bacteroidota, were more highly correlated with a reduction in endotoxemia and metabolic disorders, as well as decreases in intestinal proinflammatory response and related renal risk biomarkers. The results of this study suggest that sesamolin attenuates kidney injuries, which might be associated with its effects on the reduction of endotoxemia and related metabolic disorders through the restoration of the intestinal barrier and the modulation of gut microbiota. Thus, sesamolin may be a potential dietary supplement for protection against obesity-associated kidney injury.

Expression Analysis and the Roles of the Sec1 Gene in Regulating the Composition of Mouse Gut Microbiota

The Sec1 gene encodes galactose 2-L-fucosyltransferase, whereas expression during development of the Sec1 gene mouse and its effect on the composition of the gut microbiota have rarely been reported. In this study, we examined Sec1 gene expression during mouse development, constructed Sec1 knockout mice, and sequenced their gut microbial composition. It was found that Sec1 was expressed at different stages of mouse development. Sec1 knockout mice have significantly higher intraperitoneal fat accumulation and body weight than wild-type mice. Analysis of gut microbial composition in Sec1 knockout mice revealed that at the phylum level, Bacteroidetes accounted for 68.8%and 68.3% of gut microbial composition in the Sec1-/- and Sec1+/+ groups, respectively, and Firmicutes accounted for 27.1% and 19.7%, respectively; while Firmicutes/Bacteroidetes were significantly higher in Sec1-/- mice than in Sec1+/+ mice (39.4% vs. 28.8%). In verucomicrobia, it was significantly higher in Sec1-/- mice than in Sec1+/+ group mice. At the family level, the dominant bacteria Prevotellaceae, Akkermansiaceae, Bacteroidaceae, and Lacilltobacaceae were found to be significantly reduced in the gut of Sec1-/- mice among Sec1+/+ gut microbes, while Lachnospiraceae, Ruminococcaceae, Rikenellaceae, Helicobacteraceae, and Tannerellaceae were significantly increased. Indicator prediction also revealed the dominant bacteria Akkermansiaceae and Lactobacillaceae in Sec1+/+ gut microorganisms, while the dominant bacteria Rikenellaceae, Marinifilaceae, ClostridialesvadinBB60aceae, Erysipelotrichaceae, Saccharimonadaceae, Clostridiaceae1, and Christensenellaceae in Sec1-/- group. This study revealed that the Sec1 gene was expressed in different tissues at different time periods in mice, and Sec1 knockout mice had significant weight gain, significant abdominal fat accumulation, and significant changes in gut microbial flora abundance and metabolic function, providing a theoretical basis and data support for the study of Sec1 gene function and effects on gut microbiota-related diseases.

Octenyl Succinic Anhydride-Modified Starch Attenuates Body Weight Gain and Changes Intestinal Environment of High-Fat Diet-Fed Mice

Effects of octenylsuccinate (OS) starch on body composition and intestinal environment in high-fat diet-fed mice were investigated. C57BL/6J mice were treated with a regular-fat (RF) diet, a high-fat (HF) diet, or a high-fat diet supplemented with OS starch (HFOSS). Fecal short-chain fatty acids (SCFAs) were quantified using gas chromatography, and the fecal microbiota profile was analyzed by 16S rDNA sequencing. One-way ANOVA and metastats analysis were performed for statistical analysis. After 22 weeks of feeding, mice in the HFOSS group had significantly lower body weight, body fat, liver weight, and cumulative food intake than those in the HF group but higher than that of the RF group. Fecal total SCFA, acetic, propionic, and butyric acid concentrations were significantly higher in the HFOSS group than that in the HF and RF groups. OS starch intervention increased the relative abundance of Parabacteroides, Alistipes, and Ruminiclostridium_5 and decreased that of Tyzzerella, Oscillibacter, Desulfovibrio, and Anaerotruncus compared with the RF and HF groups. The relative abundance of Lachnospiraceae_UCG-006 in the HFOSS group was lower than that in the HF group but higher than that in the RF group. In conclusion, OS starch prevents fat accumulation in high-fat diet-fed mice and might provide potential health benefits due to its fermentability in the gut and its ability to regulate gut microbial community structure.

Compromised Hindgut Microbial Digestion, Rather Than Chemical Digestion in the Foregut, Leads to Decreased Nutrient Digestibility in Pigs Fed Low-Protein Diets

Background: Reduced nutrient digestibility due to low-protein (LP) diets occurring in the foregut or hindgut of pigs remains unclear. Methods: Growing barrows (21.7 ± 1.7 kg) were allotted into LP and high-protein (HP) diet treatments. Ileal digesta and feces were collected for in vitro cross-fermentation and microbial sequencing, and cross-feeding assessed nutrient digestibility. Results: No difference in foregut digesta flora and nutrient digestibility between treatments was observed. LP diet caused decreased total tract digestibility of dry matter (DM), organic matter (OM), gross energy (GE), neutral detergent fiber (NDF), and acid detergent fiber (ADF) compared with the HP diet (p < 0.05). The fermentation broth from LP diet-fed pigs induced less full fermentation digestion of DM, OM, crude protein, and GE than HP broth (p < 0.05). Additionally, LP broth fermentation presented lower fermentation gas and short-chain fatty acids (SCFAs) generation than HP group (p < 0.05). This situation above may be related to decreased abundances of Lachnospiraceae, Eubacterium_eligens_group, Roseburia, and Ruminococcaceae_UCG-009, which can efficiently ferment nutrients to produce SCFA. Conclusions: Change in the flora caused compromise in hindgut microbial fermentation digestion leads to decreased total tract nutrient digestibility in pigs fed an LP diet.

RNA-based stable isotope probing provides no indication for rapid α-synuclein assimilation by murine gut bacteria

In Parkinson’s disease (PD), α-synuclein is a key protein in the process of neurodegeneration. Besides motor symptoms, most PD patients additionally suffer from gastrointestinal tract (GIT) dysfunctions, even several years before the onset of motor disabilities. Studies have reported a dysbiosis of gut bacteria in PD patients compared to healthy controls and have suggested that the enteric nervous system (ENS) can be involved in the development of the disease. As α-synuclein was found to be secreted by neurons of the ENS, we used RNA-based stable isotope probing (RNA-SIP) to identify gut bacteria that might be able to assimilate this protein. The gut contents of 24 mice were pooled and incubated with isotopically labelled (¹³C) and unlabelled (¹²C) α-synuclein. After incubation for 0, 4 and 24 h, RNA was extracted from the incubations and separated by density gradient centrifugation. However, RNA quantification of density-resolved fractions revealed no incorporation of the ¹³C isotope into the extracted RNA, suggesting that α-synuclein was not assimilated by the murine gut bacteria. Potential reasons and consequences for follow-up-studies are discussed.

A polysaccharide from Rosa roxburghii Tratt fruit attenuates high-fat diet-induced intestinal barrier dysfunction and inflammation in mice by modulating the gut microbiota

Obesity-induced colonic inflammation-stimulated colitis is one of the main causes of colorectal cancer. Dietary polysaccharides are considered an effective agent for relieving obesity-induced inflammatory diseases such as diabetes and colitis. In this work, the protective effects of a polysaccharide (RTFP) extracted from Rosa roxburghii Tratt fruit on barrier dysfunction and inflammation were investigated using obesity-induced colitis model mice. RTFP treatment repaired intestinal barrier dysfunction by increasing the expression of tight junction proteins (ZO-1, claudin-1, and occludin) and reducing the levels of inflammatory cytokines, intestinal permeability, and colonic oxidative stress in mice fed a high-fat diet. Most significantly, RTFP decreased gut inflammation and ameliorated the metabolic dysbiosis of intestinal microflora by decreasing the Firmicutes/Bacteroidetes ratio, reducing the levels of serum D-lactic acid and lipopolysaccharides, and inhibiting the TLR4/NF-κB signaling pathway. Furthermore, RTFP significantly increased the abundance of beneficial bacteria (Ruminococcaceae, Muribaculaceae, Akkermansiaceae, etc.) but decreased the abundance of pathogenic bacteria. These findings indicate that RTFP can be used as a natural anti-inflammatory agent to reduce chronic obesity-induced colitis.

Effect of AMY1 copy number variation and various doses of starch intake on glucose homeostasis: data from a cross-sectional observational study and a crossover meal study

Background

Copy number (CN) variation (CNV) of the salivary amylase gene (AMY1) influences the ability to digest starch and may influence glucose homeostasis, obesity and gut microbiota composition. Hence, the aim was to examine the association of AMY1 CNV with fasting glucose, BMI, and gut microbiota composition considering habitual starch intake and to investigate the effect of AMY1 CNV on the postprandial response after two different starch doses.

Methods

The Malmö Offspring Study (n = 1764, 18–71 years) was used to assess interaction effects between AMY1 CNV (genotyped by digital droplet polymerase chain reaction) and starch intake (assessed by 4-day food records) on fasting glucose, BMI, and 64 gut bacteria (16S rRNA sequencing). Participants with low (≤ 4 copies, n = 9) and high (≥ 10 copies, n = 10) AMY1 CN were recruited for a crossover meal study to compare postprandial glycemic and insulinemic responses to 40 g and 80 g starch from white wheat bread.

Results

In the observational study, no overall associations were found between AMY1 CNV and fasting glucose, BMI, or gut microbiota composition. However, interaction effects between AMY1 CNV and habitual starch intake on fasting glucose (P = 0.03) and BMI (P = 0.05) were observed, suggesting inverse associations between AMY1 CNV and fasting glucose and BMI at high starch intake levels and positive association at low starch intake levels. No associations with the gut microbiota were observed. In the meal study, increased postprandial glucose (P = 0.02) and insulin (P = 0.05) were observed in those with high AMY1 CN after consuming 40 g starch. This difference was smaller and nonsignificant after consuming 80 g starch.

Conclusions

Starch intake modified the observed association between AMY1 CNV and fasting glucose and BMI. Furthermore, depending on the starch dose, a higher postprandial glucose and insulin response was observed in individuals with high AMY1 CN than in those with low AMY1 CN.

Trial registration

ClinicalTrials.gov, NCT03974126. Registered 4 June 2019—retrospectively registered.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12263-021-00701-8.

Side-by-side and exo-pitting degradation mechanism revealed from in vitro human fecal fermentation of granular starches

The in vitro fecal fermentation characteristics and microbiota responses to A- and B-type polymorphic starches as model (whole) foods enriched with resistant starch was investigated. Marked difference in fermentation rate as well as microbial genera was observed during fermentation, the degradation pattern as well as structural evolution during fermentation was almost similar. The final butyrate concentrations of both HAMS and PS (ca. 38 mM) were significantly higher than that of WMS (23 mM) and NMS (33 mM), which was associated with the increase of the relative abundance of Roseburia, Blautia, and Lachnospiraceae. A-type polymorphic starches, on the other hand had remarkably faster fermentation rate and promoted Megamonas. X-ray diffraction and size-exclusion chromatography of residual starch during the fermentation course demonstrated the "side-by-side" fermentation pattern. Based on the structural changes observed, we conclude that in vitro fecal fermentation of starch granules predominantly controlled by the surface features rather than the molecular and supra-molecular structure.

RS5 Produced More Butyric Acid through Regulating the Microbial Community of Human Gut Microbiota

The objective of this research was to compare the in vitro fermentability of three resistant starches (RS2, RS3, and RS5). Structural analyses showed that there were small changes in the long- and short-range ordered structure of three RSs after fermentation by human gut microbiota. The fermentation of RSs by gut microbiota produced large amounts of short-chain fatty acids, with RS5 producing more butyric acid and RS3 producing more lactic acid. RS3 and RS5 decreased the pH of the fermentation culture to a greater extent compared with RS2. Moreover, RS5 increased significantly the relative abundance of Bifidobacterium, Dialister, Collinsella, Romboutsia, and Megamonas. The results suggested that the form of RS was the main factor affecting the physiological function of RS and that RS5, as a recently recognized form of resistant starch, could be a better functional ingredient to improve health compared with RS2 and RS3.

Changes in Rumen Microbiota Affect Metabolites, Immune Responses and Antioxidant Enzyme Activities of Sheep under Cold Stimulation

Simple Summary

Under a cold environment, the animal’s weight is reduced and even health is affected. As we all know, microbiota is beneficial to animal health. It can produce metabolites to improve animal immunity and avoid damage. Therefore, we aimed to understand the self-protection mechanisms of sheep under cold stress. To investigate this mechanism, we designed two experiments to explore the effects of low temperature and wind speed on sheep phenotypes, rumen microbes, immune cytokines and oxidative stress. Our results identified that the sheep remained healthy in a cold environment. This may be due to the enrichment of Lachnospiraceae in the rumen. A large amount of propionate may enter into the gluconeogenesis reaction, resulting in a decrease in the content of propionate in the rumen, thereby reducing animal’s immunity. In summary, the increase of Lachnospiraceae and propionate in the rumen may help sheep live in a cold environment. Our experiments provide some direction for the healthy feeding of animals in cold environments.

Abstract

Low-temperature environments can strongly affect the normal growth and health of livestock. In winter, cold weather can be accompanied by strong winds that aggravate the effects of cold on livestock. In this study, two experiments were conducted to investigate the effect of low temperature and/or wind speed on physiological indices, rumen microbiota, immune responses and oxidative stress in sheep. When sheep were exposed to cold temperature and/or stronger wind speeds, the average daily gain (ADG) decreased (p < 0.05), and the abundance of Lachnospiraceae was significantly higher (p < 0.05). The acetate and propionate contents and the proportion of propionate in the rumen also significantly reduced (p < 0.05). The immunoglobulin G (IgG) and TH1-related cytokines in the blood were significantly lower (p < 0.05). However, antioxidant enzyme contents were significantly increased and the concentration of malondialdehyde (MDA) was reduced (p < 0.05). In a cold environment, the abundance of Lachnospiraceae in the rumen of sheep was highly enriched, and the decreasing of propionate might be one of the factors affecting the immunity of the animals, the sheep did not suffer from oxidative damage during the experiment.

Towards safer stable isotope probing - effect of formamide on the separation of isotope-labeled and unlabeled Escherichia coli RNA by isopycnic density ultracentrifugation

RNA-based stable isotope probing (RNA-SIP) is used in molecular microbial ecology to link the identity of microorganisms in a complex community with the assimilation of a distinct substrate. The technique is highly dependent on a reliable separation of isotopic-labeled RNA from unlabeled RNA by isopycnic density gradient ultracentrifugation. Here we show that ¹³C-labeled and unlabeled Escherichia coli RNA can be sufficiently separated by isopycnic ultracentrifugation even in the absence of formamide. However, a slightly lower starting density is needed to obtain a distribution pattern similar to that obtained when formamide was used. Hence, the commonly used addition of formamide to the centrifugation solution might not be needed to separate ¹³C-labeled RNA from unlabeled RNA, but this must be verified for more complex environmental mixtures of RNA. Clearly, an omission of formamide would increase the safety of RNA-SIP analyses.

Conserved and variable responses of the gut microbiome to resistant starch type 2

Resistant starch type 2 (RS2), a dietary fiber comprised solely of glucose, has been extensively studied in clinical trials and animal models for its capacity to improve metabolic and systemic health. Because the health modulatory effects of RS2 and other dietary fibers are thought to occur through modification of the gut microbiome, those studies frequently include assessments of RS2-mediated changes to intestinal microbial composition and function. In this review, we identify the conserved responses of the gut microbiome among 13 human and 35 animal RS2 intervention studies. Consistent outcomes of RS2 interventions include reductions in bacterial α-diversity; increased production of lumenal short-chain fatty acids; and enrichment of Ruminococcus bromii, Bifidobacterium adolescentis, and other gut taxa. Different taxa are usually responsive in animal models, and many RS2-mediated changes to the gut microbiome vary within and between studies. The root causes for this variation are examined with regard to methodological and analytical differences, host genetics and age, species differences (eg, human, animal), health status, intervention dose and duration, and baseline microbial composition. The significant variation found for this single dietary compound highlights the challenges in targeting the gut microbiome to improve health with dietary interventions. This knowledge on RS2 also provides opportunities to improve the design of nutrition studies targeting the gut microbiome and to ultimately identify the precise mechanisms via which dietary fiber benefits human health.

Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes

Host genetic variation influences microbiome composition. While studies have focused on associations between the gut microbiome and specific alleles, gene copy number (CN) also varies. We relate microbiome diversity to CN variation of the AMY1 locus, which encodes salivary amylase, facilitating starch digestion. After imputing AMY1-CN for ∼1,000 subjects, we identified taxa differentiating fecal microbiomes of high and low AMY1-CN hosts. In a month-long diet intervention study, we show that diet standardization drove gut microbiome convergence, and AMY1-CN correlated with oral and gut microbiome composition and function. The microbiomes of low-AMY1-CN subjects had enhanced capacity to break down complex carbohydrates. High-AMY1-CN subjects had higher levels of salivary Porphyromonas; their gut microbiota had increased abundance of resistant starch-degrading microbes, produced higher levels of short-chain fatty acids, and drove higher adiposity when transferred to germ-free mice. This study establishes AMY1-CN as a genetic factor associated with microbiome composition and function.

Biocatalytic Fabrication of α-Glucan-Coated Porous Starch Granules by Amylolytic and Glucan-Synthesizing Enzymes as a Target-Specific Delivery Carrier

In this study, we created biocatalytically coated porous starch granules (PSGs) using amylosucrase from Neisseria polysaccharea to apply them as an encapsulant for target-specific delivery. Field-emission scanning electron and confocal laser scanning microscopic images showed that the PSGs were completely concealed by the α-glucan coating layer. This carbohydrate-based encapsulant displayed higher amount of resistant glucan contents due to the elongated chains of the glucan coating, resulting in lower digestibility of these PSGs in simulated digestive fluid systems. Among the various PSGs evaluated, the highest loading efficiency for the bioactive molecule crocin was observed with the β-amylase-induced PSGs (β-PSGs) that had the smallest nanosize pores. Furthermore, α-glucan-coated β-PSGs showed the highest capacity to preserve the loaded crocin when incubated in simulated digestive fluids. This suggests that the α-glucan-coated β-PSGs can potentially be used for the delayed release of the core material in the upper region of the gastrointestinal tract. Therefore, this system can be potentially utilized as an effective carrier for colon-specific delivery, and the release of the bioactive compound can be triggered by beneficial intestinal microbiota.

Analysis of microbial community in a continuous flow process at gene and transcription level to enhance biological nutrients removal from municipal wastewater

In biological municipal wastewater treatment, gene level analysis of community structure could not determine functional genes that actually played a role and expression of viable microorganism. In this study, reverse transcriptional PCR (RT-PCR), cDNA high throughput sequencing and transcriptional activity analysis were conducted to investigate active microbial community with nitrogen and phosphorus removal from municipal wastewater. RT-PCR and correlation heatmap analysis suggested that transcriptional activities of bacteria had strong correlation with performance of nitrogen and phosphorus removal, they might be therefore regarded as an indicator for wastewater treatment monitoring. When DO concentration were raised from 0.6 mg/L to 2 mg/L and C/N ratio from 3-4 to 5, the increase of population abundance and transcriptional activities of denitrifying genes improved the removal efficiencies of COD and TN. The species with relatively high abundance at gene level were not really active species at transcription level, and vice versa.

Modulation of the Caecal Gut Microbiota of Mice by Dietary Supplement Containing Resistant Starch: Impact Is Donor-Dependent

Alterations in the gut microbiota have been associated with a wide range of pathologies and conditions. Maintaining a well-balanced microbiota is a key factor in sustaining good health. Our aim was to investigate the impact of a resistant starch-containing dietary supplement (SymbioIntest^®) on the composition of the human gut microbiota and on intestinal short chain fatty acid (SCFA) concentration. Human microbiota-associated mice were used. Ex-germ-free mice were inoculated with fecal suspensions from four different donors. Three weeks later, the mice were orally gavaged for 1 month with either a daily dose of 10 mg of SymbioIntest^® or the vehicle (water) for the negative control group. The composition of the microbiota and SCFA levels were analyzed by 16S rRNA gene sequencing and gas chromatography, respectively. In three groups of mice, SymbioIntest^® supplementation increased the concentration of caecal butyrate. This was in conjunction with a remodeling of the gut microbiota. OTUs belonging to the Bacteroidaceae, Porphyromonadaceae, Lachnospiraceae and Ruminococcaceae families were affected. In two groups of mice the greatest changes in OTUs were seen in the Faecalibacterium genus. The supplementation’s highest impact was observed in mice inoculated with gut microbiota containing a lower number of Ruminococcaceae and Faecalibacterium and a higher number of Prevotellaceae. SymbioIntest^® supplementation elicited a beneficial effect on the healthy adult gut microbiota by increasing caecal butyrate production and health-promoting taxa. We highlight the fact that screening the gut microbiota may be used for predicting individualized responses to dietary interventions and thus developing personalized nutritional strategies.

Stepwise Development of an in vitro Continuous Fermentation Model for the Murine Caecal Microbiota

Murine models are valuable tools to study the role of gut microbiota in health or disease. However, murine and human microbiota differ in species composition, so further investigation of the murine gut microbiota is important to gain a better mechanistic understanding. Continuous in vitro fermentation models are powerful tools to investigate microbe-microbe interactions while circumventing animal testing and host confounding factors, but are lacking for murine gut microbiota. We therefore developed a novel continuous fermentation model based on the PolyFermS platform adapted to the murine caecum and inoculated with immobilized caecal microbiota. We followed a stepwise model development approach by adjusting parameters [pH, retention time (RT), growth medium] to reach fermentation metabolite profiles and marker bacterial levels similar to the inoculum. The final model had a stable and inoculum-alike fermentation profile during continuous operation. A lower pH during startup and continuous operation stimulated bacterial fermentation (115 mM short-chain fatty acids at pH 7 to 159 mM at pH 6.5). Adjustments to nutritive medium, a decreased pH and increased RT helped control the in vitro Enterobacteriaceae levels, which often bloom in fermentation models, to 6.6 log gene copies/mL in final model. In parallel, the Lactobacillus, Lachnospiraceae, and Ruminococcaceae levels were better maintained in vitro with concentrations of 8.5 log gene copies/mL, 8.8 log gene copies/mL and 7.5 log gene copies/mL, respectively, in the final model. An independent repetition with final model parameters showed reproducible results in maintaining the inoculum fermentation metabolite profile and its marker bacterial levels. Microbiota community analysis of the final model showed a decreased bacterial diversity and compositional differences compared to caecal inoculum microbiota. Most of the caecal bacterial families were represented in vitro, but taxa of the Muribaculaceae family were not maintained. Functional metagenomics prediction showed conserved metabolic and functional KEGG pathways between in vitro and caecal inoculum microbiota. To conclude, we showed that a rational and stepwise approach allowed us to model in vitro the murine caecal microbiota and functions. Our model is a first step to develop murine microbiota model systems and offers the potential to study microbiota functionality and structure ex vivo.

Generation of 13C-Labeled MUC5AC Mucin Oligosaccharides for Stable Isotope Probing of Host-Associated Microbial Communities

Stable isotope probing (SIP) has emerged as a powerful tool to address key questions about microbiota structure and function. To date, diverse isotopically labeled substrates have been used to characterize in situ growth activity of specific bacterial taxa and have revealed the flux of bioavailable substrates through microbial communities associated with health and disease. A major limitation to the growth of the field is the dearth of biologically relevant "heavy" labeled substrates. Mucin glycoproteins, for example, comprise an abundant source of carbon in the gut, oral cavity, respiratory tract, and other mucosal surfaces but are not commercially available. Here, we describe a method to incorporate a ¹³C-labeled monosaccharide into MUC5AC, a predominant mucin in both gastrointestinal and airway environments. Using the lung adenocarcinoma cell line, Calu-3, polarized cell cultures grown in ¹³C-labeled d-glucose resulted in liberal mucin production on the apical surface. Mucins were isolated by size-exclusion chromatography, and O-linked glycans were released by β-elimination, permethylated, and analyzed by electrospray ionization tandem mass spectrometry (ESI-MS/MS) and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) techniques. We demonstrate a 98.7% incorporation of ¹³C in the heterogeneous O-linked oligosaccharides that make up >80% of mucin dry weight. These "heavy" labeled glycoproteins represent a valuable tool for probing in vivo activity of host-associated bacterial communities and their interactions with the mucosal barrier. The continued expansion of labeled substrates for use in SIP will eventually allow bacterial taxa that degrade host compounds to be identified, with long-term potential for improved health and disease management.

Infant Complementary Feeding of Prebiotics for theMicrobiome and Immunity

Complementary feeding transitions infants from a milk-based diet to solid foods, providing essential nutrients to the infant and the developing gut microbiome while influencing immune development. Some of the earliest microbial colonisers readily ferment select oligosaccharides, influencing the ongoing establishment of the microbiome. Non-digestible oligosaccharides in prebiotic-supplemented formula and human milk oligosaccharides promote commensal immune-modulating bacteria such as Bifidobacterium, which decrease in abundance during weaning. Incorporating complex, bifidogenic, non-digestible carbohydrates during the transition to solid foods may present an opportunity to feed commensal bacteria and promote balanced concentrations of beneficial short chain fatty acid concentrations and vitamins that support gut barrier maturation and immunity throughout the complementary feeding window.

Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats

BACKGROUND

Resistant starch is a prebiotic metabolized by the gut bacteria. It has been shown to attenuate chronic kidney disease (CKD) progression in rats. Previous studies employed taxonomic analysis using 16S rRNA sequencing and untargeted metabolomics profiling. Here we expand these studies by metaproteomics, gaining new insight into the host-microbiome interaction.

METHODS

Differences between cecum contents in CKD rats fed a diet containing resistant starch with those fed a diet containing digestible starch were examined by comparative metaproteomics analysis. Taxonomic information was obtained using unique protein sequences. Our methodology results in quantitative data covering both host and bacterial proteins.

RESULTS

5,834 proteins were quantified, with 947 proteins originating from the host organism. Taxonomic information derived from metaproteomics data surpassed previous 16S RNA analysis, and reached species resolutions for moderately abundant taxonomic groups. In particular, the Ruminococcaceae family becomes well resolved-with butyrate producers and amylolytic species such as R. bromii clearly visible and significantly higher while fibrolytic species such as R. flavefaciens are significantly lower with resistant starch feeding. The observed changes in protein patterns are consistent with fiber-associated improvement in CKD phenotype. Several known host CKD-associated proteins and biomarkers of impaired kidney function were significantly reduced with resistant starch supplementation. Data are available via ProteomeXchange with identifier PXD008845.

CONCLUSIONS

Metaproteomics analysis of cecum contents of CKD rats with and without resistant starch supplementation reveals changes within gut microbiota at unprecedented resolution, providing both functional and taxonomic information. Proteins and organisms differentially abundant with RS supplementation point toward a shift from mucin degraders to butyrate producers.

RNA-Based Stable Isotope Probing (RNA-SIP) in the Gut Environment

The RNA-SIP technology allows for linking the structure and function of complex microbial communities, that is, the identification of microbial key players involved in distinct degradation and assimilation processes under in situ conditions. Being dependent on RNA, this technique is particularly suited for environments with high numbers of very active, that is, significantly RNA-expressing microorganisms, such as intestinal tract samples. We use RNA-SIP for the identification of bacteria involved in the degradation and assimilation of prebiotic carbohydrates in order to better understand the functionality of these medically and economically important nutrients in human and animal intestinal environments.

Stable-Isotope Probing of Human and Animal Microbiome Function

Humans and animals host diverse communities of microorganisms important to their physiology and health. Despite extensive sequencing-based characterization of host-associated microbiomes, there remains a dramatic lack of understanding of microbial functions. Stable-isotope probing (SIP) is a powerful strategy to elucidate the ecophysiology of microorganisms in complex host-associated microbiotas. Here, we suggest that SIP methodologies should be more frequently exploited as part of a holistic functional microbiomics approach. We provide examples of how SIP has been used to study host-associated microbes in vivo and ex vivo. We highlight recent developments in SIP technologies and discuss future directions that will facilitate deeper insights into the function of human and animal microbiomes.

RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions

The RNA-SIP technology, introduced into molecular microbial ecology in 2002, is an elegant technique to link the structure and function of complex microbial communities, i.e. to identify microbial key-players involved in distinct degradation and assimilation processes under in-situ conditions. Due to its dependence of microbial RNA, this technique is particularly suited for environments with high numbers of very active, i.e. significantly RNA-expressing, bacteria. So far, it was mainly used in environmental studies using microbiotas from soil or water habitats. Here we outline and summarize our application of RNA-SIP for the identification of bacteria involved in the degradation and assimilation of prebiotic carbohydrates in intestinal samples of human and animal origin. Following an isotope label from a prebiotic substrate into the RNA of distinct bacterial taxa will help to better understand the functionality of these medically and economically important nutrients in an intestinal environment.

In Vivo Assessment of Resistant Starch Degradation by the Caecal Microbiota of Mice Using RNA-Based Stable Isotope Probing-A Proof-of-Principle Study

Resistant starch (RS) is the digestion resistant fraction of complex polysaccharide starch. By reaching the large bowel, RS can function as a prebiotic carbohydrate, i.e., it can shape the structure and activity of bowel bacterial communities towards a profile that confers health benefits. However, knowledge about the fate of RS in complex intestinal communities and the microbial members involved in its degradation is limited. In this study, 16S ribosomal RNA (rRNA)-based stable isotope probing (RNA-SIP) was used to identify mouse bowel bacteria involved in the assimilation of RS or its derivatives directly in their natural gut habitat. Stable-isotope [U¹³C]-labeled native potato starch was administrated to mice, and caecal contents were collected before 0 h and 2 h and 4 h after administration. 'Heavy', isotope-labeled [¹³C]RNA species, presumably derived from bacteria that have metabolized the labeled starch, were separated from 'light', unlabeled [¹²C]RNA species by fractionation of isolated total RNA in isopycnic-density gradients. Inspection of different density gradients showed a continuous increase in 'heavy' 16S rRNA in caecal samples over the course of the experiment. Sequencing analyses of unlabeled and labeled 16S amplicons particularly suggested a group of unclassified Clostridiales, Dorea, and a few other taxa (Bacteroides, Turicibacter) to be most actively involved in starch assimilation in vivo. In addition, metabolic product analyses revealed that the predominant ¹³C-labeled short chain fatty acid (SCFA) in caecal contents produced from the [U¹³C] starch was butyrate. For the first time, this study provides insights into the metabolic transformation of RS by intestinal bacterial communities directly within a gut ecosystem, which will finally help to better understand its prebiotic potential and possible applications in human health.