Levan Enhances Associated Growth of Bacteroides, Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota

Shifts in the microbial community and metabolome in rumen ecological niches during antler growth

Antlers are hallmark organ of deer, exhibiting a relatively high growth rate among mammals, and requiring large amounts of nutrients to meet its development. The rumen microbiota plays key roles in nutrient metabolism. However, changes in the microbiota and metabolome in the rumen during antler growth are largely unknown. We investigated rumen microbiota (liquid, solid, ventral epithelium, and dorsal epithelium) and metabolic profiles of sika deer at the early (EG), metaphase (MG) and fast growth (FG) stages. Our data showed greater concentrations of acetate and propionate in the rumens of sika deer from the MG and FG groups than in those of the EG group. However, microbial diversity decreased during antler growth, and was negatively correlated with short-chain fatty acid (SCFA) levels. Prevotella, Ruminococcus, Schaedlerella and Stenotrophomonas were the dominant bacteria in the liquid, solid, ventral epithelium, and dorsal epithelium fractions. The proportions of Stomatobaculum, Succiniclasticum, Comamonas and Anaerotruncus increased significantly in the liquid or dorsal epithelium fractions. Untargeted metabolomics analysis revealed that the metabolites also changed significantly, revealing 237 significantly different metabolites, among which the concentrations of γ-aminobutyrate and creatine increased during antler growth. Arginine and proline metabolism and alanine, aspartate and glutamate metabolism were enhanced. The co-occurrence network results showed that the associations between the rumen microbiota and metabolites different among the three groups. Our results revealed that the different rumen ecological niches were characterized by distinct microbiota compositions, and the production of SCFAs and the metabolism of specific amino acids were significantly changed during antler growth.

Reproducible chemostat cultures to minimize eukaryotic viruses from fecal transplant material

Recent studies indicate an important role of bacteriophages for successful fecal microbiota transplantation (FMT). However, wider clinical applications of FMT are hampered by to donor variability and concerns of infection risks by bacteria and human viruses. To overcome these challenges, mouse cecal and human fecal material were propagated in a chemostat fermentation setup supporting multiplication of bacteria, and phages, while propagation of eukaryotic viruses will be prevented in the absence of eukaryotic host cells. The results showed decrease of the median relative abundance of viral contigs of classified eukaryotic viruses below 0.01%. The corresponding virome profiles showed dilution rate dependency, a reproducibility between biological replicates, and maintained high diversity regarding both the human and mouse inocula. This proof-of-concept cultivation approach may constitute the first step of developing novel therapeutic tools with high reproducibility and with low risk of infection from the donor material to target gut-related diseases.

Endo- and exo-levanases from Bacillus subtilis HM7: Catalytic components, synergistic cooperation, and application in fructooligosaccharide synthesis

Levan-type fructooligosaccharides (LFOS) exhibit significant biological activities and selectively promote the growth of certain beneficial bacteria. Levanase is an important enzyme for LFOS production. In this study, two isoforms of levanases, exo- and endo-type depolymerizing enzymes, from Bacillus subtilis HM7 isolated from Dynastes hercules larvae excrement were cloned, expressed, and characterized. The synergistic effect on the levan hydrolysis and kinetic properties of both isoforms were evaluated, indicating their cooperation in levan metabolism, where the endo-levanase catalyzes a rate-limiting step. In addition, homology models and molecular dynamics simulations revealed the key amino residues of the enzymes for levan binding and catalysis. It was found that both isoforms possessed distinct binding residues in the active sites, suggesting the importance of the specificity of the enzymes. Finally, we demonstrated the potential of endo-type levanase in LFOS synthesis using a one-pot reaction with levansucrase. Overall, this study fills the knowledge gap in understanding levanase's mechanism, making an important contribution to the fields of food science and biotechnology.

Effects of Salmonella Outer Membrane Vesicles on Intestinal Microbiota and Intestinal Barrier Function

Salmonella enterica is one of the most important zoonotic pathogens causing foodborne gastroenteritis worldwide. Outer membrane vesicles (OMVs) are lipid-bilayer vesicles produced by Gram-negative bacteria, which contain biologically active components. We hypothesized that OMVs are an important weapon of S. enterica to initiate enteric diseases pathologies. In this study, the effects of S. enterica OMVs (SeOMVs) on intestinal microbiota and intestinal barrier function were investigated. In vitro fecal culture experiments showed that alpha diversity indexes and microbiota composition were altered by SeOMV supplementation. SeOMV supplementation showed an increase of pH, a decrease of OD630 and total short chain fatty acid (SCFA) concentrations. In vitro IPEC-J2 cells culture experiments showed that SeOMV supplementation did not affect the IPEC-J2 cell viability and the indicated genes expression. In vivo experiments in mice showed that SeOMVs had adverse effects on average daily gain (p < 0.05) and feed:gain ratio (p < 0.05), and had a tendency to decrease the final body weight (p = 0.073) in mice. SeOMV administration decreased serum interleukin-10 level (p < 0.05), decreased the relative abundance of bacteria belonging to the genera BacC-u-018 and Akkermansia (p < 0.05). Furthermore, SeOMV administration damaged the ileum mucosa (p < 0.05). These findings suggest that SeOMVs play an important role in the activation of intestinal inflammatory response induced by S. enterica, and downregulation of SCFA-producing bacteria is a possible mechanism.

Simulated Digestion and Fecal Fermentation Behaviors of Levan and Its Impacts on the Gut Microbiota

Levan is a microbial fructan widely explored in various fields owing to its excellent physical and biochemical properties. However, little is known about its digestion and fermentation characteristics in vitro. This study evaluated the potential prebiotic properties of levan obtained by enzymatic synthesis. Scanning electron microscopy, Fourier transform infrared spectroscopy, and nuclear magnetic resonance spectroscopy showed that the primary structures of levan remained stable after saliva-gastrointestinal digestion. The microtopography, molecular weight, and functional group of levan were seriously damaged during fecal fermentation. Moreover, the total short-chain fatty acid levels increased significantly, especially for propionic acid, butyric acid, and valeric acid. The 16S rDNA sequencing showed that levan mainly increased the abundance of Firmicutes; in genus levels, certain beneficial bacteria such as Megasphaera and Megamonas genera were remarkably promoted, and the proliferation of harmful genera was inhibited (such as Cedecea and Klebsiella). Overall, this study provided new insights into the potential probiotic mechanism of levan.

Biofilm-based delivery approaches and specific enrichment strategies of probiotics in the human gut

The use of probiotics has been one of the effective strategies to restructure perturbed human gut microbiota following a disease or metabolic disorder. One of the biggest challenges associated with the use of probiotic-based gut modulation strategies is to keep the probiotic cells viable and stable during the gastrointestinal transit. Biofilm-based probiotics delivery approaches have emerged as fascinating modes of probiotic delivery in which probiotics show significantly greater tolerance and biotherapeutic potential, and interestingly probiotic biofilms can be developed on food-grade surfaces too, which is ideal for the growth and proliferation of bacterial cells for incorporation into food matrices. In addition, biofilms can be further encapsulated with food-grade materials or with bacterial self-produced biofilms. This review presents a newly emerging and unprecedently discussed techniques for the safe delivery of probiotics based on biofilms and further discusses newly emerging prebiotic materials which target specific gut microbiota groups for growth and proliferation.

Structural and compositional segregation of the gut microbiota in HCV and liver cirrhotic patients: A clinical pilot study

Gut microbial dysbiosis during the development of Hepatitis C virus and liver-related diseases is not well studied. Nowadays, HCV and liver cirrhosis are the major concerns that cause gut bacterial alteration, which leads to dysbiosis. For this purpose, the present study was aimed at correlating the gut bacterial community of the control group in comparison to HCV and liver cirrhotic patients. A total of 23 stool samples were collected, including control (9), liver cirrhotic (8), and HCV (6). The collected samples were subjected to 16S rRNA Illumina gene sequencing. In comparison with control, a significant gut bacterial alteration was observed in the progression of HCV and liver cirrhosis. Overall, Firmicutes were significantly abundant in the whole study. No significant difference was observed in the alpha diversity of the control and patient studies. Additionally, the beta diversity based on non-metric multidimensional scaling (NMDS) has a significant difference (p = 0.005) (ANOSIM R² = 0.14) in all groups. The discriminative results based on the LEfSe tool revealed that the HCV-infected patients had higher Enterobacteriaceae and Enterobacterial, as well as Lactobacillus and Bacilli in comparison than the liver-cirrhotic patients. These taxa were significantly different from the control group (p < 0.05). Regarding prospects, a detailed analysis of the function through metagenomics and transcriptomics is needed.

Functional Characterization of Recombinant Endo-Levanase (LevBk) from Bacillus koreensis HL12 on Short-Chain Levan-Type Fructooligosaccharides Production

Levan-type fructooligosaccharides (L-FOSs) are a prominent class of non-digestible oligosaccharides with potential as nutritional prebiotics. Endo-levanase, which randomly hydrolyzes β-(2,6)-linkages in fructans, is a promising enzyme for short-chain FOS production. In this work, a recombinant levanase (LevBk) from Bacillus koreensis strain HL12 was characterized. Soluble LevBk protein was produced in Escherichia coli BL21(DE3) system at 40 mg/L of culture medium. Based on sequence and structural analysis, LevBk was classified as a member of endo-levanase in GH32 family containing N-terminal substrate binding pocket and C-terminal β-sandwich domains. LevBk optimally worked at 45 °C, pH 6.0 with the specific activity of 2.43 U/mg. Based on enzymatic hydrolysis, short-chain L-FOSs with degree of polymerization (DP) of 2-4 were produced from hydrolysis of timothy grass levan under optimal conditions for 9-24 h. With its ability to produce L-FOSs with specific chain lengths, LevBk could be attractively applied for converting of levan containing material to high value-added sweetener in the biorefinery industry.

Production of a high molecular weight levan by Bacillus paralicheniformis, an industrially and agriculturally important isolate from the buffalo grass rhizosphere

A new exopolysaccharide (EPS) producing Gram-positive bacterium was isolated from the rhizosphere of Bouteloua dactyloides (buffalo grass) and its EPS product was structurally characterized. The isolate, designated as LB1-1A, was identified as Bacillus paralicheniformis based on 16S rRNA gene sequence and phylogenetic tree analysis. The EPS produced by LB1-1A was identified as a levan, having β(2 → 6) linked backbone with β(2 → 1) linkages at the branch points (4.66%). The isolate LB1-1A yielded large amount (~ 42 g/l) of levan having high weight average molecular weight (Mw) of 5.517 × 10⁷ Da. The relatively low degree of branching and high molecular weight of this levan makes B. paralicheniformis LB1-1A a promising candidate for industrial applications.

Evaluation of Microbial-Fructo-Oligosaccharides Metabolism by Human Gut Microbiota Fermentation as Compared to Commercial Inulin-Derived Oligosaccharides

The prebiotic potential of fructo-oligosaccharides (microbial-FOS) produced by a newly isolated Aspergillus ibericus, and purified by Saccharomyces cerevisiae YIL162 W, was evaluated. Their chemical structure and functionality were compared to a non-microbial commercial FOS sample. Prebiotics were fermented in vitro by fecal microbiota of five healthy volunteers. Microbial-FOS significantly stimulated the growth of Bifidobacterium probiotic strains, triggering a beneficial effect on gut microbiota composition. A higher amount of total short-chain fatty acids (SCFA) was produced by microbial-FOS fermentation as compared to commercial-FOS, particularly propionate and butyrate. Inulin neoseries oligosaccharides, with a degree of polymerization (DP) up to 5 (e.g., neokestose and neonystose), were identified only in the microbial-FOS mixture. More than 10% of the microbial-oligosaccharides showed a DP higher than 5. Differences identified in the structures of the FOS samples may explain their different functionalities. Results indicate that microbial-FOS exhibit promising potential as nutraceutical ingredients for positive gut microbiota modulation.

Antitumor bioactivity and gut microbiota modulation of polyhydroxybutyrate (PHB) in a rat animal model for colorectal cancer

Polyhydroxybutyrate (PHB) is a non-toxic polyhydroxyalkanoate polymer produced by several microorganisms, widely used as a biological substitute for plastics derived from fossil hydrocarbons. In this work, PHB polymer has been tested in an animal model for colorectal cancer. In the animal model, PHB has been able to reduce the number of polyps by 48,1%, and the tumoral extension area by 58,1%. Also, PHB induces a selective increase in beneficial gut bacterial taxons in this animal model, and a selective reduction in pro-inflammatory taxons, demonstrating its value as a nutraceutical compound. This antitumor effect is caused by gut production of 3-hydroxybutyrate and butyrate. In this animal model, 3-hydroxybutyrate is also observed in plasma and in brain tissue, after PHB consumption, making PHB supplementation interesting as a bioactive compound in other extraintestinal conditions, as 3-hydroxybutyrate has been reported to enhance brain and cognitive function, cardiac performance, appetite suppression and diabetes. Therefore, PHB could be postulated as an interesting non-polysaccharide antitumor prebiotic, paving the way towards its future use in functional foods.

Synergistic enzyme cocktail between levansucrase and inulosucrase for superb levan-type fructooligosaccharide synthesis

Inulosucrase (ISC) and levansucrase (LSC) utilise sucrose and produce inulin- and levan-type fructans, respectively. This study aims to propose a new strategy to improve levan-type fructooligosaccharide (L-FOS) production. The effect of ISC/ LSC -mixed reaction was elucidated on L-FOS production. The presence of ISC in the LSC reaction significantly leads to the higher production of L-FOSs as the main products. Furthermore, the different ratios between ISC and LSC affected the distribution of L-FOSs. A greater amount of ISC compared to LSC promoted the synthesis of short-chain L-FOSs. Conversely, when LSC was increased, the synthesis of longer-chain L-FOSs was enhanced. The addition of trisaccharide mixtures obtained from either a single ISC or LSC reaction could enhance L-FOSs synthesis in the LSC reaction. Analysis of these trisaccharides revealed that most species of the oligosaccharides were similar, with 1-kestose being the major one. The supplement of only 1-kestose in the LSC reaction showed similar results to those of the reaction in the presence of trisaccharide mixtures. Moreover, the results were supported by molecular dynamics simulations. This work not only provides an improvement in L-FOS production but also revealed and supported some insights into the mechanism of fructansucrases.

Effects of Combinations of Goat Milk and Oligosaccharides on Altering the Microbiota, Immune Responses, and Short Chain Fatty Acid Levels in the Small Intestines of Mice

Goat milk and oligosaccharides play important roles in gastrointestinal health. A combination of goat milk with three oligosaccharides, stachyose (STS), fructo-oligosaccharide (FOS), and a prebiotics mixture (FGS), was fed to mice. Changes and functions of the microbiota, short chain fatty acid (SCFA) concentrations, and immune gene expression in the small intestines were determined. The FOS treatment increased the beneficial bacteria Lactobacillus and Bifidobacterium, the FGS treatment helped stabilize the microbial community, and the STS treatment significantly enhanced microbial diversity and the growth of Bacteroidetes. The oligosaccharide treatments regulated the gene expression levels of the immune factors tumor necrosis factor alpha (Tnfα), granzyme B (Gzmb), perforin (Prf), and aryl hydrocarbon receptor (Ahr). Stachyose significantly increased the concentrations of acetate and propionate compared with other treatments. These findings demonstrate that STS is the preferred carbon source for microbiota, slightly modulates SCFA production, and results in low immunogenicity in the small intestines of mice.

Acidic pH enhances butyrate production from pectin by faecal microbiota

Environmental pH and gut transit rate are the key factors determining the dynamics of colonic microbiota. In this study, the effect of changing pH on the composition and metabolism of pooled faecal microbiota was elucidated at physiologically relevant dilution rates Dhigh = 0.2 and Dlow = 0.05 1/h. The results showed the best adaptability of Bacteroides ovatus within the pH range 6.0-8.0 at both dilution rates. The butyrate producing Faecalibacterium and Coprococcus comes were extremely sensitive to pH > 7.5, while the abundance of Akkermansia muciniphila increased significantly at pH >7 at Dhigh, causing a pH-dependant shift in the dynamics of mucin degrading species. Increased gas formation was observed at pH < 6.5. Substantially more CO2 was produced at Dlow than at Dhigh (18-29 vs 12-23 mmol per L medium, respectively). Methane was produced only at Dlow and pH > 7, consistent with the simultaneous increased abundance of Methanobrevibacter smithii. Our study confirmed the importance of pH in the development of faecal microbiota in pectin-supplemented medium. Fermentation of other dietary fibres can be studied using the same approach. The significance of pH should be more emphasized in gut research and diagnostics.

The Immunomodulatory Properties of β-2,6 Fructans: A Comprehensive Review

Polysaccharides such as β-2,1-linked fructans including inulin or fructose oligosaccharides are well-known prebiotics with recognised immunomodulatory properties. In recent years, other fructan types covering β-2,6-linked fructans, particularly microbial levans, have gained increasing interest in the field. β-2,6-linked fructans of different degrees of polymerisation can be synthesised by plants or microbes including those that reside in the gastrointestinal tract. Accumulating evidence suggests a role for these β-2,6 fructans in modulating immune function. Here, we provide an overview of the sources and structures of β-2,6 fructans from plants and microbes and describe their ability to modulate immune function in vitro and in vivo along with the suggested mechanisms underpinning their immunomodulatory properties. Further, we discuss the limitations and perspectives pertinent to current studies and the potential applications of β-2,6 fructans including in gut health.

Causal effects in microbiomes using interventional calculus

Causal inference in biomedical research allows us to shift the paradigm from investigating associational relationships to causal ones. Inferring causal relationships can help in understanding the inner workings of biological processes. Association patterns can be coincidental and may lead to wrong conclusions about causality in complex systems. Microbiomes are highly complex, diverse, and dynamic environments. Microbes are key players in human health and disease. Hence knowledge of critical causal relationships among the entities in a microbiome, and the impact of internal and external factors on microbial abundance and their interactions are essential for understanding disease mechanisms and making appropriate treatment recommendations. In this paper, we employ causal inference techniques to understand causal relationships between various entities in a microbiome, and to use the resulting causal network to make useful computations. We introduce a novel pipeline for microbiome analysis, which includes adding an outcome or "disease" variable, and then computing the causal network, referred to as a "disease network", with the goal of identifying disease-relevant causal factors from the microbiome. Internventional techniques are then applied to the resulting network, allowing us to compute a measure called the causal effect of one or more microbial taxa on the outcome variable or the condition of interest. Finally, we propose a measure called causal influence that quantifies the total influence exerted by a microbial taxon on the rest of the microiome. Our pipeline is robust, sensitive, different from traditional approaches, and able to predict interventional effects without any controlled experiments. The pipeline can be used to identify potential eubiotic and dysbiotic microbial taxa in a microbiome. We validate our results using synthetic data sets and using results on real data sets that were previously published.

Biosynthesis and prebiotic activity of a linear levan from a new Paenibacillus isolate

Levan, a type of β (2→6)-linked fructan, is a promising biopolymer with distinct properties and extensive applications in the fields of food, pharmaceutical, cosmetics, etc. However, the commercial availability of levan is still limited due to the relatively high production costs. Here, a new Paenibacillus sp. strain FP01 was isolated and identified as an efficient fructan producer with high yield (around 89.5 g/L fructan was obtained under 180 g/L sucrose) and conversation rate (49.7%). The fructan named Plev was structurally characterized as a linear levan-type fructan with a molecular mass of 3.11 × 10⁶ Da. Aqueous solutions of Plev exhibited a non-Newtonian behavior at concentrations 3-5%. Heating and chilling had no obvious effects on apparent viscosities of Plev solutions. Plev also had good rheological stabilities toward pH (3-11) and metal salts (Na⁺, K⁺, Ca²⁺, Mg²⁺). Microbiome and metabolome analysis showed that Plev intervention increased the abundance of beneficial bacteria and elevated the levels of short-chain fatty acids (SCFAs) in feces of mice. Taken together, Plev could be considered a potential thickener and prebiotic supplement in food industry.Key points• Paenibacillus sp. strain FP01 was identified as a high-efficient levan producer.• The levan Plev from FP01 exhibited good rheological properties and stabilities.• The in vivo prebiotic activities of linear levan were revealed.

Antibacterial and probiotic promotion potential of a new soluble soybean polysaccharide‑iron(III) complex

In this study soluble soybean polysaccharide‑iron(III) (SSPS-Fe(III)) was synthesized to investigate the effects on the growth of Escherichia coli, Staphylococcus aureus and Bacillus licheniformis. Two new detection methods of real-time fluorescence quantitative polymerase chain reaction (qRT-PCR) and microcalorimetry were used to evaluate the effects of different concentrations of SSPS-Fe(III) on the growth of three bacteria. The copy numbers of three bacteria showed that SSPS-Fe(III) had different impacts on the growth of E. coli, S. aureus and B. licheniformis. E. coli growth was inhibited by SSPS-Fe(III) in the higher concentration range and S. aureus growth was inhibited at any concentration, however B. licheniformis growth was promoted. The thermogenic curves for growth metabolism of E. coli and S. aureus presented peak shapes while those of B. licheniformis did platform shapes. As SSPS-Fe(III) concentration increased, the peak heights lowered for E. coli and S. aureus, and the time reaching stationary phase advanced for B. licheniformis. These findings demonstrate that SSPS-Fe(III) has an inhibitory effect on the foodborne pathogens of E. coli and S. aureus, and an enhancement on the probiotics of B. licheniformis.

The Combination of Lead and Bacillus coagulans R11 Increased the Concentration of Alpha-Solanine in the Cecum of Laying Hens and the Pathogens Abundance Decreased

Alpha-solanine is an alkaloid that can inhibit the growth of pathogens and cancer cells, the present study proved that feeding with Bacillus coagulans R11 increases the concentration of alpha-solanine in the cecum of laying hens, which also decreases the abundance of potential pathogens. In addition, the bacteria genera, metabolism pathways and its proteins involved in the biosynthesis of alpha-solanine in the cecum were also characterized. The results showed that B. coagulans R11 feeding could increase the concentration of alpha-solanine, even with lead exposure. Mevalonic acid and MEP/DOXP pathways were both participated in the biosynthesis of alpha-solanine; at the same time, the gut metabolites (S)-2-amino-6-oxohexanoate, N2-succinyl-L-ornithine and the bacteria proteins atoB, ispH were shown to be crucial role in the biosynthesis of alpha-solanine in the gut. The genera Faecalibacterium sp. An77 and Faecalibacterium sp. An58 2 were important in the biosynthesis of alpha-solanine, which provided the key proteins atoB and ispH. In addition, alpha-solanine could decrease the abundance of Prevotella sp. 109 and Prevotella marshii. In conclusion, alpha-solanine could be biosynthesized by cecal microorganisms with the stimulation of B. coagulans R11 in the intestine of laying hens, in addition, alpha-solanine was the main compound which also decreased the abundance of gut potential.

First crystal structure of an endo-levanase - the BT1760 from a human gut commensal Bacteroides thetaiotaomicron

The endo-levanase BT1760 of a human gut commensal Bacteroides thetaiotaomicron randomly cuts a β-2,6-linked fructan, levan, into fructo-oligosaccharides providing a prebiotic substrate for gut microbiota. Here we introduce the crystal structure of BT1760 at resolution of 1.65 Å. The fold of the enzyme is typical for GH32 family proteins: a catalytic N-terminal five-bladed β-propeller connected with a C-terminal β-sandwich domain. The levantetraose-bound structure of catalytically inactive mutant E221A at 1.90-Å resolution reveals differences in substrate binding between the endo-acting fructanases. A shallow substrate-binding pocket of the endo-inulinase INU2 of Aspergillus ficuum binds at least three fructose residues at its flat bottom. In the levantetraose-soaked crystal of the endo-levanase E221A mutant the ligand was bent into the pond-like substrate pocket with its fructose residues making contacts at −3, −2, −1 and + 1 subsites residing at several pocket depths. Binding of levantetraose to the β-sandwich domain was not detected. The N- and C-terminal modules of BT1760 did not bind levan if expressed separately, the catalytic domain lost its activity and both modules tended to precipitate. We gather that endo-levanase BT1760 requires both domains for correct folding, solubility and stability of the protein.

Chemical Structure and Localization of Levan, the Predominant Fructan Type in Underground Systems of Gomphrena marginata (Amaranthaceae)

Gomphrena marginata Seub. (Amaranthaceae) is an endemic species from Brazilian campos rupestres with a fructan accumulating underground reserve system. Analyses of high performance anion exchange chromatography (HPAEC-PAD) revealed the presence of the soluble carbohydrates glucose, fructose, sucrose, 1-kestose, 6-kestose, nystose and fructans with degree of polymerization (DP) up to approximately 40 fructose units. Data of ¹H and ¹³C Nuclear Magnetic Resonance (NMR) spectroscopy, including Heteronuclear Single-Quantum Correlation (HSQC) and Heteronuclear Multiple-Bonds Correlation (HMBC) showed the presence of β (2,6) linkages, characteristic of the linear molecule of levan-type fructan(2,6). These results confirmed previous studies suggesting that the reserve carbohydrate in the underground system of this species was levan-type fructans, similar to that of G. macrocephala. Structural analyses of the thickened underground system using light microscopy revealed a mixed origin system consisting mainly of a gemmiferous tuberous root with the upper region formed by short branched stems, both presenting vascular cylinders with unusual growth patterns. Fructan spherocrystals were visualized under polarized light and scanning electron microscopy (SEM) mostly in the cortex and vascular cylinder in both thickened stem and root. In addition to data reported in the literature concerning the occurrence of fructans in the Amaranthaceae, the results presented here suggest that fructans are a trait in this family while the levan-type fructan prevail in Gomphrena species.

Selection of fast and slow growing bacteria from fecal microbiota using continuous culture with changing dilution rate

Background: Nutrient and energy metabolism in human colon depends on bacterial growth rate that is determined by the colonic transit rate. Objective: A novel approach, De-stat culture was used to distinguish the fast and slow growing sub-populations from fecal microbiota. Design: The enrichment and metabolism of bacteria from pooled fecal cultures of children was studied at dilution rates D = 0.2-0.0 1/h in mucin-supplemented media containing either arabinogalactan or apple pectin. Results: The study revealed clear differentiation of the fecal microbiota at higher (above 0.1 1/h) and lower (below 0.1 1/h) dilution rates, along with metabolic changes. Similarity of the fast and slow growing bacteria was observed in two different fecal pools and on both substrates, suggesting the dilution rate as the main triggering parameter for selection of bacteria. At high dilution rates, the species Collinsella aerofaciens, Dorea longicatena, Escherichia coli, Lachnoclostridium torques, and different Bacteroides (B. caccae, B. fragilis, B. ovatus, B. thetaiotaomicron, B. vulgatus) were dominant in both media variants. At low dilution rates, Akkermansia muciniphila, Eisenbergiella tayi, Negativicoccus succinivorans, and a group of Ruminococcaceae became dominant in both media and in both fecal pools. This change in bacterial population accompanied by the increased production of propionic and butyric acids as well as higher consumption of alanine and branched chain amino acids at low dilution rates. Conclusions: The study suggests that specific growth rate has important effect on the dynamics of colon microbiota. Manipulation of the proportions of fast and slow growing gut bacteria through modulation of the transit rate could be a target in human nutrition studies. The De-stat study would enable to predict changes in microbiota composition associated with the decrease or increase of the colonic transit rate.

Influence of acid depolymerization parameters on levan molar mass distribution and its utilization by bacteria

Levan is a fructan composed of β -(2, 6) linkages in its main chain. Its health properties, especially its prebiotic potential can be partially modified by changing its molar mass distribution. Given that native levan is rarely fermented by probiotic bacteria, especially lactic acid bacteria (LAB), levanoligosaccharides (LOS) were produced by mild acid hydrolysis. The response surface methodology (RSM) was applied to determine the optimum parameters for depolymerization. Gel permeation chromatography (GPC) was used to characterize the LOS produced and to show the differences between inulin and levan. The prebiotic potential of four fractions of LOS with different molar mass distributions was investigated. MRS (Mann Rogosa Sharpe) medium supplemented with the LOS were inoculated with bacterial strains and growth was monitored by measuring the turbidity of the cultures. The utilization of oligofructans was also confirmed by RP-UHPLC-UV-ESI-MS (liquid chromatography coupled with mass spectrometry) measurements of LOS derivatized with 1-phenyl-3-methyl-5-pyrazolone (PMP). It was observed that the degree of polymerization of LOS has an influence on the growth of the tested bacteria.

Conventional wastewater treatment and reuse site practices modify bacterial community structure but do not eliminate some opportunistic pathogens in reclaimed water

Water recycling continues to expand across the United States, from areas that have access to advanced, potable-level treated reclaimed water, to those having access only to reclaimed water treated at conventional municipal wastewater treatment plants. This expansion makes it important to further characterize the microbial quality of these conventionally-treated water sources. Therefore, we used 16S rRNA gene sequencing to characterize total bacterial communities present in differentially-treated wastewater and reclaimed water (n = 67 samples) from four U.S. wastewater treatment plants and one associated spray irrigation site conducting on-site ultraviolet treatment and open-air storage. The number of observed operational taxonomic units was significantly lower (p < 0.01) in effluent, compared to influent, after conventional treatment. Effluent community structure was influenced more by treatment method than by influent community structure. The abundance of Legionella spp. increased as treatment progressed in one treatment plant that performed chlorination and in another that seasonally chlorinated. Overall, the alpha-diversity of bacterial communities in reclaimed water decreased (p < 0.01) during wastewater treatment and spray irrigation site ultraviolet treatment (p < 0.01), but increased (p < 0.01) after open-air storage at the spray irrigation site. The abundance of Legionella spp. was higher at the sprinkler system pumphouse at the spray irrigation site than in the influent from the treatment plant supplying the site. Legionella pneumophila was detected in conventionally treated effluent samples and in samples collected after ultraviolet treatment at the spray irrigation site, while Legionella feeleii persisted throughout on-site treatment at the spray irrigation site, and, along with Mycobacterium gordonae, was also detected at the sprinkler system pumphouse at the spray irrigation site. These data could inform the development of future treatment technologies and reuse guidelines that address a broader assemblage of the bacterial community of reclaimed water, resulting in reuse practices that may be more protective of public health.

Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans

The aim of the study was to investigate the metabolism of non-digestible oligo- and polysaccharides by fecal microbiota, using isothermal microcalorimetry. The five tested substrates were raffinose, melibiose, a mixture of oligo- and polysaccharides produced from raffinose by levansucrase, levan synthesized from raffinose, and levan from timothy grass. Two inocula were comprised of pooled fecal samples from overweight or normal-weight children, from healthy adult volunteers and a pure culture of Bacteroides thetaiotaomicron as a reference bacterium for colon microbiota. The growth was analyzed based on the heat evolution curves, and the production of organic acids and gases. Taxonomic profiles of the microbiota were assessed by 16S rDNA sequencing. Raffinose and melibiose promoted the growth of bifidobacteria in all fecal pools. Several pool-specific substrate-related responses to raffinose and melibiose were revealed. Lactate-producing bacteria (Streptococcus and Enterococcus) became enriched in the pool of overweight children resulting in lactic acid as the major fermentation product on short saccharides. Acetic and butyric acids were prevalent at fermentation in the normal-weight pool coinciding with the enrichment of Catenibacterium. In the adult pool, the specific promotion of Bacteroides and Lachnospiraceae by levans was disclosed. In the fecal pool of normal-weight children, levans stimulated the growth of Senegalimassilia and Lachnoclostridium and this particular pool also showed the highest maximum heat production rate at levan fermentation. Levans and raffinose-derived oligosaccharides, but not raffinose and melibiose were completely fermented by a pure culture of Bacteroides thetaiotaomicron. The main conclusion from the study is that fecal microbiota of normal and overweight children have different compositions and they respond in specific manners to non-digestible oligo- and polysaccharides: raffinose, melibiose, raffinose-derived oligosaccharides and levans. The potential of the tested saccharides to support a healthy balance of colon microbiota requires further studies.

The composition and metabolism of faecal microbiota is specifically modulated by different dietary polysaccharides and mucin: an isothermal microcalorimetry study

The metabolic activity of colon microbiota is specifically affected by fibres with various monomer compositions, degree of polymerisation and branching. The supply of a variety of dietary fibres assures the diversity of gut microbial communities considered important for the well-being of the host. The aim of this study was to compare the impact of different oligo- and polysaccharides (galacto- and fructooligosaccharides, resistant starch, levan, inulin, arabinogalactan, xylan, pectin and chitin), and a glycoprotein mucin on the growth and metabolism of faecal microbiota in vitro by using isothermal microcalorimetry (IMC). Faecal samples from healthy donors were incubated in a phosphate-buffered defined medium with or without supplementation of a single substrate. The generation of heat was followed on-line, microbiota composition (V3-V4 region of the 16S rRNA using Illumina MiSeq v2) and concentrations of metabolites (HPLC) were determined at the end of growth. The multiauxic power-time curves obtained were substrate-specific. More than 70% of all substrates except chitin were fermented by faecal microbiota with total heat generation of up to 8 J/ml. The final metabolite patterns were in accordance with the microbiota changes. For arabinogalactan, xylan and levan, the fibre-affected distribution of bacterial taxa showed clear similarities (e.g. increase of Bacteroides ovatus and decrease of Bifidobacterium adolescentis). The formation of propionic acid, an important colon metabolite, was enhanced by arabinogalactan, xylan and mucin but not by galacto- and fructooligosaccharides or inulin. Mucin fermentation resulted in acetate, propionate and butyrate production in ratios previously observed for faecal samples, indicating that mucins may serve as major substrates for colon microbial population. IMC combined with analytical methods was shown to be an effective method for screening the impact of specific dietary fibres on functional changes in faecal microbiota.

Animal nutrition and breeding conditions modify the physiology of isolated primary cells

Animal primary cell cultures are widely used in biomedical research to investigate cell metabolism, diseases and to devise novel treatments. Modern animal breeding techniques are developed to unify, control and reduce the amount of microorganisms that the animals are being exposed to. Furthermore, health monitoring and strict caging and handling protocols allow animals to be exposed only to a selected spectrum of microbes. We are starting to appreciate that nutrition can influence composition of gut microbiota that can impact hosting organism's physiology and can even result in development of pathological changes. Evidence is also emerging that acute as well as chronic stresses can profoundly influence the physiology of certain organs, especially heart and liver. Our preliminary data imply that changes in animal nutrition and stress levels initiated up to minutes before the cell isolation could alter the cell stress response of cultured primary hepatocytes after isolation, leading to differences in sensitivity of apoptosis triggering. Therefore, we propose the hypothesis that conditions of animal breeding, especially diet and stress levels, are reflected in the physiology of the isolated primary cells. Variations in animal breeding conditions may influence experimental results on isolated cells and their applicability for studying human disorders.

A Highly Active Endo-Levanase BT1760 of a Dominant Mammalian Gut Commensal Bacteroides thetaiotaomicron Cleaves Not Only Various Bacterial Levans, but Also Levan of Timothy Grass

Bacteroides thetaiotaomicron, an abundant commensal of the human gut, degrades numerous complex carbohydrates. Recently, it was reported to grow on a β-2,6-linked polyfructan levan produced by Zymomonas mobilis degrading the polymer into fructooligosaccharides (FOS) with a cell surface bound endo-levanase BT1760. The FOS are consumed by B. thetaiotaomicron, but also by other gut bacteria, including health-promoting bifidobacteria and lactobacilli. Here we characterize biochemical properties of BT1760, including the activity of BT1760 on six bacterial levans synthesized by the levansucrase Lsc3 of Pseudomonas syringae pv. tomato, its mutant Asp300Asn, levansucrases of Zymomonas mobilis, Erwinia herbicola, Halomonas smyrnensis as well as on levan isolated from timothy grass. For the first time a plant levan is shown as a perfect substrate for an endo-fructanase of a human gut bacterium. BT1760 degraded levans to FOS with degree of polymerization from 2 to 13. At optimal reaction conditions up to 1 g of FOS were produced per 1 mg of BT1760 protein. Low molecular weight (<60 kDa) levans, including timothy grass levan and levan synthesized from sucrose by the Lsc3Asp300Asn, were degraded most rapidly whilst levan produced by Lsc3 from raffinose least rapidly. BT1760 catalyzed finely at human body temperature (37°C) and in moderately acidic environment (pH 5–6) that is typical for the gut lumen. According to differential scanning fluorimetry, the T_m of the endo-levanase was 51.5°C. All tested levans were sufficiently stable in acidic conditions (pH 2.0) simulating the gastric environment. Therefore, levans of both bacterial and plant origin may serve as a prebiotic fiber for B. thetaiotaomicron and contribute to short-chain fatty acids synthesis by gut microbiota. In the genome of Bacteroides xylanisolvens of human origin a putative levan degradation locus was disclosed.

Microbial communities mediating algal detritus turnover under anaerobic conditions

BACKGROUND

Algae encompass a wide array of photosynthetic organisms that are ubiquitously distributed in aquatic and terrestrial habitats. Algal species often bloom in aquatic ecosystems, providing a significant autochthonous carbon input to the deeper anoxic layers in stratified water bodies. In addition, various algal species have been touted as promising candidates for anaerobic biogas production from biomass. Surprisingly, in spite of its ecological and economic relevance, the microbial community involved in algal detritus turnover under anaerobic conditions remains largely unexplored.

RESULTS

Here, we characterized the microbial communities mediating the degradation of Chlorella vulgaris (Chlorophyta), Chara sp. strain IWP1 (Charophyceae), and kelp Ascophyllum nodosum (phylum Phaeophyceae), using sediments from an anaerobic spring (Zodlteone spring, OK; ZDT), sludge from a secondary digester in a local wastewater treatment plant (Stillwater, OK; WWT), and deeper anoxic layers from a seasonally stratified lake (Grand Lake O' the Cherokees, OK; GL) as inoculum sources. Within all enrichments, the majority of algal biomass was metabolized within 13-16 weeks, and the process was accompanied by an increase in cell numbers and a decrease in community diversity. Community surveys based on the V4 region of the 16S rRNA gene identified different lineages belonging to the phyla Bacteroidetes, Proteobacteria (alpha, delta, gamma, and epsilon classes), Spirochaetes, and Firmicutes that were selectively abundant under various substrate and inoculum conditions. Within all kelp enrichments, the microbial communities structures at the conclusion of the experiment were highly similar regardless of the enrichment source, and were dominated by the genus Clostridium, or family Veillonellaceae within the Firmicutes. In all other enrichments the final microbial community was dependent on the inoculum source, rather than the type of algae utilized as substrate. Lineages enriched included the uncultured groups VadinBC27 and WCHB1-69 within the Bacteroidetes, genus Spirochaeta and the uncultured group SHA-4 within Spirochaetes, Ruminococcaceae, Lachnospiraceae, Yongiibacter, Geosporobacter, and Acidaminobacter within the Firmicutes, and genera Kluyvera, Pantoea, Edwardsiella and Aeromonas, and Buttiauxella within the Gamma-Proteobaceteria order Enterobacteriales.

CONCLUSIONS

Our results represent the first systematic survey of microbial communities mediating turnover of algal biomass under anaerobic conditions, and highlights the diversity of lineages putatively involved in the degradation process.

Performance of an anaerobic membrane bioreactor in which granular sludge and dynamic filtration are integrated

To alleviate the fouling of a filter, simple substrates, dynamic filtration, and granular sludge were applied in an anaerobic membrane bioreactor (AnMBR). The results showed that under a transmembrane pressure < 20 kPa, the filter flux ranged between 15 and 20 l (m^-2 h)^-1 for a period of 30 days. The flux was higher than the typical flux of AnMBRs with conventional membranes and most current dynamic filters. In addition, the low cost of the filter avoided the need for a higher flux. Moreover, a stable granular sludge bed, which consumed all volatile fatty acids, was maintained. A compact fouling/filtration layer formed on the filter, which contributed to low effluent chemical oxygen demand concentrations and turbidity. In addition, substrate scarcity in the filtration zone resulted in the evolution of diverse bacteria on the filter.

Dysbiosis of small intestinal microbiota in liver cirrhosis and its association with etiology

Cirrhosis-associated duodenal dysbiosis is not yet clearly defined. In this research, duodenal mucosal microbiota was analyzed in 30 cirrhotic patients and 28 healthy controls using 16S rRNA gene pyrosequencing methods. The principal coordinate analysis revealed that cirrhotic patients were colonized by remarkable different duodenal mucosal microbiota in comparison with controls. At the genus level, Veillonella, Megasphaera, Dialister, Atopobium, and Prevotella were found overrepresented in cirrhotic duodenum. And the duodenal microbiota of healthy controls was enriched with Neisseria, Haemophilus, and SR1 genera incertae sedis. On the other hand, based on predicted metagenomes analyzed, gene pathways related to nutrient absorption (e.g. sugar and amino acid metabolism) were highly abundant in cirrhosis duodenal microbiota, and functional modules involved in bacterial proliferation and colonization (e.g. bacterial motility proteins and secretion system) were overrepresented in controls. When considering the etiology of cirrhosis, two operational taxonomic units (OTUs), OTU-23 (Neisseria) and OTU-36 (Gemella), were found discriminative between hepatitis-B-virus related cirrhosis and primary biliary cirrhosis. The results suggest that the structure of duodenal mucosa microbiota in cirrhotic patients is dramatically different from healthy controls. The duodenum dysbiosis might be related to alterations of oral microbiota and changes in duodenal micro-environment.