Bioaugmentation as a tool to protect the structure and function of an activated-sludge microbial community against a 3-chloroaniline shock load

Possible role of the gut microbiome in mediating the beneficial effects of the six-herbal formulation STW 5-II on digestive health

BACKGROUND

STW 5-II is a combination of six herbal extracts with clinically proven efficacy in functional dyspepsia (FD) and irritable bowel syndrome (IBS). STW 5-II contains a wide variety of secondary plant constituents that may interact with the human gut microbiome. In addition to complex carbohydrates, secondary plant metabolites, such as polyphenols, are known to exert prebiotic-like effects.

PURPOSE

This study aimed to assess the bidirectional interactions between STW 5-II and the human gut microbiome.

METHODS

STW 5-II was incubated with human fecal microbiota in a short-term colonic model. In the samples, the impact of STW 5-II on microbial fermentation capacity (pH, gas production), short chain fatty acid (SCFA) production, and microbial composition (Illumina 16S rRNA gene sequencing) was analyzed. In addition, the biotransformation of STW 5-II constituents by the fecal microbiota was assessed by UHPLCHRMS-based metabolite profiling. Furthermore, Caco-2/THP1 co-culture assay was used to explore the effect on gut barrier integrity and inflammatory markers.

RESULTS

Fermentation of STW 5-II by fecal microbiota led to consistent changes in pH and gas production and increased production of SCFAs (acetate, propionate, and butyrate). STW 5-II promoted the enrichment of Bifidobacteriaceae, Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, and Eggerthellaceae and suppressed the growth of pathogenic species from the Enterobacteriaceae family. In Caco2/THP1 culture, treatment with STW 5-II-incubated samples resulted in significantly increased transepithelial electrical resistance, indicating enhanced barrier function. Among inflammatory markers, STW 5-II-incubated samples increased LPS-induced secretion of the anti-inflammatory cytokine IL-10, as well as NF-κB activity, and significantly decreased the secretion of the pro-inflammatory chemokine MCP-1. UHPLCHRMS analysis identified 110 constituents of STW 5-II with changed levels during incubation with fecal microbiota: 63 constituents that were metabolized, 22 intermittently increased metabolites, and 25 final metabolites, including compounds with established anti-inflammatory activity, such as 18β-glycyrrhetinic acid.

CONCLUSION

These findings indicate a microbiome-mediated digestive health-promoting effect of STW 5-II via three different routes, namely enhanced microbial SCFA production, microbial production of potentially bioactive metabolites from STW 5-II constituents, and prebiotic-like action by promoting the proliferation/growth of beneficial bacteria.

Ex Vivo Colonic Fermentation of NUTRIOSE® Exerts Immuno-Modulatory Properties and Strong Anti-Inflammatory Effects

NUTRIOSE® (Roquette, Lestrem, France) is a resistant dextrin with well-established prebiotic effects. This study evaluated the indirect effects of pre-digested NUTRIOSE® on host immune response and gut barrier integrity. Fecal samples from eight healthy donors were inoculated in a Colon-on-a-plate® system (ProDigest, Ghent, Belgium) with or without NUTRIOSE® supplementation. Following 48 h fermentation, colonic suspensions were tested in a Caco-2/THP1-Blue™ co-culture system to determine their effects on gut barrier activity (transepithelial electrical resistance) and immune response following lipopolysaccharide stimulation. Additionally, changes in short-chain fatty acid levels (SCFA) and microbial community composition following a 48 h fermentation in the Colon-on-a-plate® system were measured. Across all donors, immune-mediated intestinal barrier damage was significantly reduced with NUTRIOSE®-supplemented colonic suspensions versus blank. Additionally, IL-6 and IL-10 levels were significantly increased, and the level of the neutrophil chemoattractant IL-8 was significantly decreased with NUTRIOSE®-supplemented colonic suspensions versus blank in the co-culture models following lipopolysaccharide stimulation. These beneficial effects of NUTRIOSE® supplementation were likely due to increased acetate and propionate levels and the enrichment of SCFA-producing bacteria. NUTRIOSE® was well fermented by the colonic bacteria of all eight donors and had protective effects on inflammation-induced disruption of the intestinal epithelial barrier and strong anti-inflammatory effects.

Citrus Extract High in Flavonoids Beneficially Alters Intestinal Metabolic Responses in Subjects with Features of Metabolic Syndrome

The objective of this study was to investigate the effects of a citrus extract rich in citrus flavonoids on intestinal metabolic responses in subjects with features of metabolic syndrome, in an in vitro colon fermentation system (TIM-2) and fecal samples obtained from human subjects in an in vivo trial. In the TIM-2 system inoculated with fecal samples of volunteers with features of metabolic syndrome, continuous citrus extract supplementation (500 mg/day) resulted in increased cumulative short-chain fatty acid (SCFA) levels compared to the control condition, which was mainly due to increased production of butyrate, acetate, and valerate. In human volunteers, 12 weeks of daily supplementation with 500 mg citrus extract resulted in a significant shift in the SCFA profile towards more butyrate (p = 0.022) compared to the placebo group. Furthermore, there was a trend towards a reduction in fecal calprotectin levels, a marker for intestinal inflammation, compared to the placebo (p = 0.058). Together, these results suggest that citrus extract intake may have a positive effect on intestinal metabolic responses and through this, on host health in subjects with features of metabolic syndrome. Further research is needed to provide more insight into the potential underlying mechanisms and to study effects on clinical parameters.

The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME® Model

From the estimated 2.2 to 3.8 million fungal species existing on Earth, only a minor fraction actively colonizes the human gastrointestinal tract. In fact, these fungi only represent 0.1% of the gastrointestinal biosphere. Despite their low abundance, fungi play dual roles in human health-both beneficial and detrimental. Fungal infections are often associated with bacterial dysbiosis following antibiotic use, yet our understanding of gut fungi-bacteria interactions remains limited. Here, we used the SHIME® gut model to explore the colonization of human fecal-derived fungi across gastrointestinal compartments. We accounted for the high inter-individual microbial diversity by using fecal samples from healthy adults, healthy babies, and Crohn's disease patients. Using quantitative Polymerase Chain Reaction and targeted next-generation sequencing, we demonstrated that SHIME®-colonized mycobiomes change upon loss of transient colonizers. In addition, SHIME® reactors from Crohn's disease patients contained comparable bacterial levels as healthy adults but higher fungal concentrations, indicating unpredictable correlations between fungal levels and total bacterial counts. Our findings rather link higher bacterial α-diversity to limited fungal growth, tied to colonization resistance. Hence, while healthy individuals had fewer fungi engrafting the colonic reactors, low α-diversity in impaired (Crohn's disease patients) or immature (babies) microbiota was associated with greater fungal abundance. To validate, antibiotic-treated healthy colonic microbiomes demonstrated increased fungal colonization susceptibility, and bacterial taxa that were negatively correlated with fungal expansion were identified. In summary, fungal colonization varied individually and transiently, and bacterial resistance to fungal overgrowth was more related with specific bacterial genera than total bacterial load. This study sheds light on fungal-bacterial dynamics in the human gut.

Development of a reproducible small intestinal microbiota model and its integration into the SHIME®-system, a dynamic in vitro gut model

The human gastrointestinal tract consists of different regions, each characterized by a distinct physiology, anatomy, and microbial community. While the colonic microbiota has received a lot of attention in recent research projects, little is known about the small intestinal microbiota and its interactions with ingested compounds, primarily due to the inaccessibility of this region in vivo. This study therefore aimed to develop and validate a dynamic, long-term simulation of the ileal microbiota using the SHIME®-technology. Essential parameters were identified and optimized from a screening experiment testing different inoculation strategies, nutritional media, and environmental parameters over an 18-day period. Subjecting a synthetic bacterial consortium to the selected conditions resulted in a stable microbiota that was representative in terms of abundance [8.81 ± 0.12 log (cells/ml)], composition and function. Indeed, the observed community mainly consisted of the genera Streptococcus, Veillonella, Enterococcus, Lactobacillus, and Clostridium (qPCR and 16S rRNA gene targeted Illumina sequencing), while nutrient administration boosted lactate production followed by cross-feeding interactions towards acetate and propionate. Furthermore, similarly as in vivo, bile salts were only partially deconjugated and only marginally converted into secondary bile salts. After confirming reproducibility of the small intestinal microbiota model, it was integrated into the established M-SHIME® where it further increased the compositional relevance of the colonic community. This long-term in vitro model provides a representative simulation of the ileal bacterial community, facilitating research of the ileum microbiota dynamics and activity when, for example, supplemented with microbial or diet components. Furthermore, integration of this present in vitro simulation increases the biological relevance of the current M-SHIME® technology.

Capacity of a Microbial Synbiotic To Rescue the In Vitro Metabolic Activity of the Gut Microbiome following Perturbation with Alcohol or Antibiotics

The human gut microbiome contributes crucial bioactive metabolites that support human health and is sensitive to perturbations from the ingestion of alcohol and antibiotics. We interrogated the response and recovery of human gut microbes after acute alcohol or broad-spectrum antibiotic administration in a gut model simulating the luminal and mucosal colonic environment with an inoculated human microbiome. Both alcohol and antibiotic treatments reduced the production of major short-chain fatty acids (SCFAs) (acetate, propionate, and butyrate), which are established modulators of human health. Treatment with a microbial synbiotic restored and enhanced gut function. Butyrate and acetate production increased by up to 29.7% and 18.6%, respectively, relative to untreated, dysbiotic samples. In parallel, treatment led to increases in the relative abundances of beneficial commensal organisms not found in the synbiotic (e.g., Faecalibacterium prausnitzii and the urolithin-producing organism Gordonibacter pamelaeae) as well as species present in the synbiotic (e.g., Bifidobacterium infantis), suggesting synergistic interactions between supplemented and native microorganisms. These results lead us to conclude that functional shifts in the microbiome, evaluated by both metabolite production and specific taxonomic compositional changes, are an appropriate metric to assess microbiome "recovery" following a dysbiosis-inducing disruption. Overall, these findings support the execution of randomized clinical studies to determine whether a microbial synbiotic can help restore microbiome function after a disruption. IMPORTANCE The human gut microbiome is sensitive to disruptions by common stressors such as alcohol consumption and antibiotic treatment. In this study, we used an in vitro system modeling the gut microbiome to investigate whether treatment with a microbial synbiotic can help restore microbiome function after stress. We find that a complex gut community treated with alcohol or antibiotics showed reduced levels of production of short-chain fatty acids, which are critical beneficial molecules produced by a healthy gut microbiota. Treatment of stressed communities with a microbial synbiotic resulted in the recovery of SCFA production as well as an increase in the abundance of beneficial commensal organisms. Our results suggest that treatment with a microbial synbiotic has the potential to restore healthy gut microbiome function after stress and merits further investigation in clinical studies.

Co-Administration of Lactulose Crystals with Amoxicillin Followed by Prolonged Lactulose Treatment Promotes Recovery of the Human Gut Microbiome In Vitro

The validated SHIME model was used to assess the effect of repeated administration of two different lactulose dosages (5 g/d and 10 g/d) on the human gut microbiome during and following amoxicillin–clavulanic acid treatment. First, antibiotic treatment strongly decreased Bifidobacteriaceae levels from 54.4% to 0.6% and from 23.8% to 2.3% in the simulated proximal and distal colon, respectively, coinciding with a marked reduction in butyrate concentrations. Treatment with lactulose enhanced acetate and lactate levels during antibiotic treatment, likely through lactulose fermentation by Lachnospiraceae and Lactobacillaceae. One week after cessation of antibiotic treatment, Bifidobacteriaceae levels re-increased to 20.4% and 7.6% in the proximal and distal colon of the 5 g lactulose/d co-administered unit, as compared with 1.0% and 2.2% in the antibiotic-treated unit, and were even further stimulated upon extension of lactulose administration. Marked butyrogenic effects were observed upon prolonged lactulose supplementation, suggesting the establishment of cross-feeding interactions between Bifidobacteriaceae and butyrate producers. Furthermore, a limited Enterobacteriaceae outgrowth following antibiotic treatment was observed upon dosing with 10 g lactulose/d, indicating inhibition of pathogenic colonization by lactulose following antibiotic therapy. Overall, lactulose seems to be an interesting candidate for limiting the detrimental effects of amoxicillin–clavulanic acid on the human gut microbiome, though further studies are warranted to confirm these findings.

Human Milk Oligosaccharides and Lactose Differentially Affect Infant Gut Microbiota and Intestinal Barrier In Vitro

Background: The infant gut microbiota establishes during a critical window of opportunity when metabolic and immune functions are highly susceptible to environmental changes, such as diet. Human milk oligosaccharides (HMOs) for instance are suggested to be beneficial for infant health and gut microbiota. Infant formulas supplemented with the HMOs 2′-fucosyllactose (2′-FL) and lacto-N-neotetraose (LNnT) reduce infant morbidity and medication use and promote beneficial bacteria in the infant gut ecosystem. To further improve infant formula and achieve closer proximity to human milk composition, more complex HMO mixtures could be added. However, we currently lack knowledge about their effects on infants’ gut ecosystems. Method: We assessed the effect of lactose, 2′-FL, 2′-FL + LNnT, and a mixture of six HMOs (HMO6: consisting of 2′-FL, LNnT, difucosyllactose, lacto-N-tetraose, 3′- and 6′-sialyllactose) on infant gut microbiota and intestinal barrier integrity using a combination of in vitro models to mimic the microbial ecosystem (baby M-SHIME^®) and the intestinal epithelium (Caco-2/HT29-MTX co-culture). Results: All the tested products had bifidogenic potential and increased SCFA levels; however, only the HMOs’ fermented media protected against inflammatory intestinal barrier disruption. 2′-FL/LNnT and HMO6 promoted the highest diversification of OTUs within the Bifidobactericeae family, whereas beneficial butyrate-producers were specifically enriched by HMO6. Conclusion: These results suggest that increased complexity in HMO mixture composition may benefit the infant gut ecosystem, promoting different bifidobacterial communities and protecting the gut barrier against pro-inflammatory imbalances.

A Freeze-Dried Cranberry Powder Consistently Enhances SCFA Production and Lowers Abundance of Opportunistic Pathogens In Vitro

The American cranberry, Vaccinium macrocarpon, contains fibers and (poly)phenols that could exert health-promoting effects through modulation of gut microbiota. This study aimed to investigate how a freeze-dried whole cranberry powder (FCP) modulated metabolite production and microbial composition using both a 48-h incubation strategy and a long-term human gut simulator study with the M-SHIME (Mucosal Simulator of the Human Intestinal Microbial Ecosystem). FCP was repeatedly administered over three weeks. The studies included five and three study subjects, respectively. In both models, FCP significantly increased levels of health-related short-chain fatty acids (SCFA: acetate, propionate and butyrate), while decreased levels of branched-chain fatty acids (markers of proteolytic fermentation). Interestingly, FCP consistently increased luminal Bacteroidetes abundances in the proximal colon of the M-SHIME (+17.5 ± 9.3%) at the expense of Proteobacteria (−10.2 ± 1.5%). At family level, this was due to the stimulation of Bacteroidaceae and Prevotellaceae and a decrease of Pseudomonodaceae and Enterobacteriaceae. Despite of interpersonal differences, FCP also increased the abundance of families of known butyrate producers. Overall, FCP displayed an interesting prebiotic potential in vitro given its selective utilization by host microorganisms and potential health-related effects on inhibition of pathogens and selective stimulation of beneficial metabolites.

The Effect of Amino Acids on Production of SCFA and bCFA by Members of the Porcine Colonic Microbiota

Functional amino acids supplementation to farm animals is considered to not only be beneficial by regulating intestinal barrier, oxidative stress, and immunity, but potentially also by impacting the gut microbiota. The impact of amino acids on a piglet-derived colonic microbiota was evaluated using a 48-h in vitro batch incubation strategy. The combination of 16S rRNA gene profiling with flow cytometry demonstrated that specific microbial taxa were involved in the fermentation of each of the amino acids resulting in the production of specific metabolites. Branched chain amino acids (leucine, isoleucine, valine) strongly increased branched-chain fatty acids (+23.0 mM) and valerate levels (+3.0 mM), coincided with a marked increase of Peptostreptococcaceae. Further, glutamine and glutamate specifically stimulated acetate (~20 mM) and butyrate (~10 mM) production, relating to a stimulation of a range of families containing known butyrate-producing species (Ruminococcaceae, Oscillospiraceae, and Christensenellaceae). Finally, while tryptophan was only fermented to a minor extent, arginine and lysine specifically increased propionate levels (~2 mM), likely produced by Muribaculaceae members. Overall, amino acids were thus shown to be selectively utilized by microbes originating from the porcine colonic microbiota, resulting in the production of health-related short-chain fatty acids, thus confirming the prebiotic potential of specific functional amino acids.

Wild Heterotrophic Nitrifying Strain Pseudomonas BT1 Isolated from Kitchen Waste Sludge Restores Ammonia Nitrogen Removal in a Sewage Treatment Plant Shocked by Thiourea

Thiourea is used in agriculture and industry as a metal scavenger, synthetic intermediate, and nitrification inhibitor. However, in wastewater, it can inhibit the nitrification process and induce the collapse of the nitrification system. In such a case, ammonia-oxidizing bacteria (AOB) lose their ability to remove ammonia. We investigated the nitrification system of a 60,000-t/d municipal sewage treatment plant in Nanjing, which collapsed after receiving 5–15 ppm (5–15 mg/L) thiourea. Ammonia nitrogen removal quickly recovered to more than 95% after inoculation with 10 t high-efficiency nitrification sludge, which was collected from a kitchen waste treatment plant. A heterotrophic nitrification strain was isolated from the inoculated sludge and identified as wild Pseudomonas by 16S rDNA sequencing and named “BT1.” Based on thiourea tolerance tests, BT1 can tolerate a thiourea content of more than 500 ppm. For comparison, the in situ process was imitated by the simulation system, and the wastewater shocked by 10 ppm thiourea could still meet the emission standard after adding 1% (V/V) BT1. High-throughput sequencing analysis was applied to study microbial succession during thiourea shock loading. The results showed that Hydrogenophaga and Thiobacillus grew with the growth of BT1. Pseudomonas BT1 was used for a 6,000-t/d printed circuit board (PCB) wastewater treatment system, the nitrification system returned to normal in 15 days, and the degradation rate stabilized at more than 95%.

Changes in Wastewater Treatment Performance and the Microbial Community during the Bioaugmentation of a Denitrifying Pseudomonas Strain in the Low Carbon–Nitrogen Ratio Sequencing Batch Reactor

The low carbon–nitrogen ratio (C/N) of influent wastewater results in the insufficient carbon source for the process of denitrification in urban wastewater treatment plants (WWTPs). A denitrifying bacterial strain, Pseudomonas sp. JMSTP, was isolated and demonstrated effective denitrification ability under a low C/N ratio of 1.5–4 (w/w) in anoxic conditions. Sequencing batch reactor (SBR) studies were conducted to test the bioaugmentation of JMSTP on total nitrogen (TN) removal under the influent COD/N ratio of 3/1. After the second bioaugmentation, the TN of effluent in the bioaugmented SBR was significantly lower than that in the control SBR. Redundancy analysis results showed that there was a positive correlation between Pseudomonas sp. abundance and TN removal in the bioaugmented SBR. Microbial community analysis showed that, especially after the second bioaugmentation, the abundance of Pseudomonas sp. decreased rapidly, but it was still much higher than that in the control SBR. Correlation network analysis showed that after the addition, Pseudomonas sp. had no significant co-occurrence relationship with other native bacteria, owing to the quick increase and decrease. Our results suggest that JMSTP shows the potential to enhance TN removal through bioaugmentation. Since the effect of bioaugmentation gradually diminishes, further research is still needed to investigate its long-lasting applications.

Consistent Prebiotic Effects of Carrot RG-I on the Gut Microbiota of Four Human Adult Donors in the SHIME® Model despite Baseline Individual Variability

The human gut microbiome is currently recognized to play a vital role in human biology and development, with diet as a major modulator. Therefore, novel indigestible polysaccharides that confer a health benefit upon their fermentation by the microbiome are under investigation. Based on the recently demonstrated prebiotic potential of a carrot-derived pectin extract enriched for rhamnogalacturonan I (cRG-I), the current study aimed to assess the impact of cRG-I upon repeated administration using the M-SHIME technology (3 weeks at 3g cRG-I/d). Consistent effects across four simulated adult donors included enhanced levels of acetate (+21.1 mM), propionate (+17.6 mM), and to a lesser extent butyrate (+4.1 mM), coinciding with a marked increase of OTUs related to Bacteroides dorei and Prevotella species with versatile enzymatic potential likely allowing them to serve as primary degraders of cRG-I. These Bacteroidetes members are able to produce succinate, explaining the consistent increase of an OTU related to the succinate-converting Phascolarctobacterium faecium (+0.47 log₁₀(cells/mL)). While the Bifidobacteriaceae family remained unaffected, a specific OTU related to Bifidobacterium longum increased significantly upon cRG-I treatment (+1.32 log₁₀(cells/mL)). Additional monoculture experiments suggested that Bifidobacterium species are unable to ferment cRG-I structures as such and that B. longum probably feeds on arabinan and galactan side chains of cRG-I, released by aforementioned Bacteroidetes members. Overall, this study confirms the prebiotic potential of cRG-I and additionally highlights the marked consistency of the microbial changes observed across simulated subjects, suggesting the involvement of a specialized consortium in cRG-I fermentation by the human gut microbiome.

Effect of probiotic, prebiotic, and synbiotic on the gut microbiota of autistic children using an in vitro gut microbiome model

Imbalances in gut microbiota composition occur in individuals with autism spectrum disorder (ASD). The administration of probiotics, prebiotics, and synbiotics is emerging as a potential and promising strategy for regulating the gut microbiota and improving ASD-related symptoms. We first investigated the survival of the probiotics Limosilactobacillus (L.) reuteri and Bifidobacterium (B.) longum alone, mixed and combined with a galacto-oligosaccharide (GOS) under simulated gastrointestinal conditions. Next, we evaluated the impact of probiotics (L. reuteri + B. longum), prebiotic (GOS), and synbiotic (L. reuteri + B. longum + GOS) on gut microbiota composition and metabolism of children with ASD using an in vitro fermentation model (SHIME®). The combination of L. reuteri, B. longum, and GOS showed elevated gastrointestinal resistance. The probiotic, prebiotic, and synbiotic treatments resulted in a positive modulation of the gut microbiota and metabolic activity of children with ASD. More specifically, the probiotic treatment increased the relative abundance of Lactobacillus, while the prebiotic treatment increased the relative abundance of Bifidobacterium and decreased the relative abundance of Lachnoclostridium. Changes in microbial metabolism were associated with increased short-chain fatty acid concentrations and reduced ammonium levels, particularly in the prebiotic and synbiotic treatments.

Quantitative detection of human- and canine-associated Bacteroides genetic markers from an urban coastal lagoon

The contamination of water catchments by nonpoint source faecal pollution is a major issue affecting the microbial quality of receiving waters and is associated with the occurrence of a range of enteric illnesses in humans. The potential sources of faecal pollution in surface waters are diverse, including urban sewage leaks, surface runoff and wildlife contamination originating from a range of hosts. The major contributing hosts require identification to allow targeted management of this public health concern. In this study, two high-performing Microbial Source Tracking (MST) assays, HF183/Bac242 and BacCan-UCDmodif, were used for their ability to detect host-specific Bacteroides 16Sr RNA markers for faecal pollution in a 12-month study on an urban coastal lagoon in Sydney, Australia. The lagoon was found to contain year-round high numbers of human and canine faecal markers, as well as faecal indicator bacteria counts, suggesting considerable human and animal faecal pollution. The high sensitivity and specificity of the HF183/Bac242 and BacCan-UCDmodif assays, together with the manageable levels of PCR inhibition and high level DNA extraction efficiency obtained from lagoon water samples make these markers candidates for inclusion in an MST 'toolbox' for investigating host origins of faecal pollution in urban surface waters.

A randomized, placebo-controlled trial investigating the acute and chronic benefits of American Ginseng (Cereboost®) on mood and cognition in healthy young adults, including in vitro investigation of gut microbiota changes as a possible mechanism of action

Purpose

Cereboost®, an American ginseng extract, has shown improved short-term memory and attention/alertness in healthy young and middle-aged individuals, potentially via modulation of the gut microbiome and upregulation of neurotransmitters such as acetylcholine. Here, we explored the effects of Cereboost® on cognition and mood in the first 6 h post intervention (acute), after 2 weeks daily supplementation (chronic), and whether 2 weeks daily supplementation altered the response to a single acute dose (acute-on-chronic). A concurrent in vitro study evaluated effects of repeated Cereboost® administration on human gut microbiota.

Methods

Cognitive effects of Cereboost® were assessed using a double-blind, randomized, placebo-controlled clinical trial, with 61 healthy young adults. Modulation of the gut microbiome was concurrently modelled using the Simulator of the Human Microbial Ecosystem (SHIME®), using a young adult donor.

Results

Consistent with previous findings, Cereboost® improved working memory and attention during the immediate postprandial period; effects that were amplified following two weeks’ treatment (acute-on-chronic) compared to acute testing alone. Chronic supplementation improved cognition on an acetylcholine-sensitive attention task and improved mental fatigue and self-assurance aspects of mood. The parallel in vitro study revealed significantly increased acetate, propionate, and butyrate levels in simulated proximal and distal colon regions, linked with observed increases in Akkermansia muciniphila and Lactobacillus.

Conclusion

This study confirmed the promising effects of Cereboost® on cognitive function and mood, while suggesting a possible link to alterations of the gut microbiome and modulation of acetylcholine. Further studies will be required to unravel the underlying mechanisms that are involved.

Registration

The study was pre-registered at ClinicalTrials.gov on 6th July 2018 (Identifier: NCT03579095).

Supplementary Information

The online version contains supplementary material available at 10.1007/s00394-021-02654-5.

Comparison of protection and release behavior of different capsule polymer combinations based on L. acidophilus survivability and function and caffeine release

Oral administration of active pharmaceutical ingredients, nutraceuticals, enzymes or probiotics requires an appropriate delivery system for optimal bioactivity and absorption. The harsh conditions during the gastrointestinal transit can degrade the administered products, hampering their efficacy. Enteric or delayed-release pharmaceutical formulations may help overcome these issues. In a Simulator of Human Intestinal Microbial Ecosystem model (SHIME) and using caffeine as a marker for release kinetics and L. acidophilus survivability as an indicator for protection, we compared the performance of ten capsule configurations, single or DUOCAP® combinations. The function of L. acidophilus and its impact on the gut microbiota was further tested in three selected capsule types, combinations of DRcaps® capsule in DRcaps® capsule (DR-in-DR) and DRcaps® capsule in Vcaps® capsule (DR-in-VC) and single Vcaps® Plus capsule under colonic conditions. We found that under stomach and small intestine conditions, DR-in-DR and DR-in-VC led to the best performance both under fed and fasted conditions based on the slow caffeine release and the highest L. acidophilus survivability. The Vcaps® Plus capsule however, led to the quickest caffeine and probiotic release. When DR-in-DR, DR-in-VC and single Vcaps® Plus capsules were tested through the whole gastrointestinal tract, including under colonic conditions, caffeine release was found to be slower in capsules containing DRcaps® capsules compared to the single Vcaps® capsules. In addition, colonic survival of L. acidophilus was significantly increased under fasted conditions in DR-in-DR or DR-in-VC formulation compared to Vcaps® Plus capsule. To assess the impact of these formulations on the microbial function, acetate, butyrate and propionate as well as ammonia were measured. L. acidophilus released from DR-in-DR or DR-in-VC induced a significant increase in butyrate and a decrease in ammonia, suggesting a proliferation of butyrate-producing bacteria and reduction in ammonia-producing bacteria. These data suggest that L. acidophilus included in DR-in-DR or DR-in-VC reaching the colon is viable and functional, potentially contributing to changes in colonic microbiota composition and diversity.

2'FL and LNnT Exert Antipathogenic Effects against C. difficile ATCC 9689 In Vitro, Coinciding with Increased Levels of Bifidobacteriaceae and/or Secondary Bile Acids

Clostridioides difficile (formerly Clostridium difficile) infection (CDI) is one of the most common hospital-acquired infections, which is often triggered by a dysbiosed indigenous gut microbiota (e.g., upon antibiotic therapy). Symptoms can be as severe as life-threatening colitis. The current study assessed the antipathogenic potential of human milk oligosaccharides (HMOs), i.e., 2'-O-fucosyllactose (2'FL), lacto-N-neotetraose (LNnT), and a combination thereof (MIX), against C. difficile ATCC 9689 using in vitro gut models that allowed the evaluation of both direct and, upon microbiota modulation, indirect effects. During a first 48 h fecal batch study, dysbiosis and CDI were induced by dilution of the fecal inoculum. For each of the three donors tested, C. difficile levels strongly decreased (with >4 log CFU/mL) upon treatment with 2'FL, LNnT and MIX versus untreated blanks, coinciding with increased acetate/Bifidobacteriaceae levels. Interindividual differences among donors at an intermediate time point suggested that the antimicrobial effect was microbiota-mediated rather than being a direct effect of the HMOs. During a subsequent 11 week study with the PathogutTM model (specific application of the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®)), dysbiosis and CDI were induced by clindamycin (CLI) treatment. Vancomycin (VNC) treatment cured CDI, but the further dysbiosis of the indigenous microbiota likely contributed to CDI recurrence. Upon co-supplementation with VNC, both 2'FL and MIX boosted microbial activity (acetate and to lesser extent propionate/butyrate). Moreover, 2'FL avoided CDI recurrence, potentially because of increased secondary bile acid production. Overall, while not elucidating the exact antipathogenic mechanisms-of-action, the current study highlights the potential of HMOs to combat CDI recurrence, help the gut microbial community recover after antibiotic treatment, and hence counteract the adverse effects of antibiotic therapies.

Lacticaseibacillus rhamnosus GG and Saccharomyces cerevisiae boulardii supplementation exert protective effects on human gut microbiome following antibiotic administration in vitro

Antibiotic-induced dysbiosis of the microbial community has been associated with several gastrointestinal symptoms. The impact of repeated administration of Lacticaseibacillus rhamnosus GG (CNCM-I-4798) (formerly known as Lactobacillus rhamnosus GG), Saccharomyces cerevisiae boulardii (CNCM-I-1079) and their combination (associated in Smebiocta/Smectaflora Protect®) in supporting recovery of gut microbiota functionality and composition during and following amoxicillin:clavulanic acid administration was evaluated in vitro. Antibiotic dosage negatively affected SCFA production, coinciding with detrimental effects on Bacteroidetes, Firmicutes and Bifidobacterium spp. in the simulated proximal colon, while Akkermansia muciniphila was significantly reduced in the distal colon. L. rhamnosus GG and S. boulardii were able to thrive in both colon regions upon dosing, with S. boulardii even showing protective effects on the survival of L. rhamnosus GG during antibiotic administration. The impact of the probiotic strains on microbiome recovery revealed that supplementation with L. rhamnosus GG and/or S. boulardii resulted in a stimulating effect on the most abundant bacterial groups within the bacterial community of each donor. For one of the donors tested, co-dosing of L. rhamnosus GG and S. boulardii resulted in superior short-chain fatty acid recovery accompanied by a stronger increase in abundance of Bifidobacteriaceae. Overall, the current study provides first evidence that combined supplementation of L. rhamnosus GG and S. boulardii might be an interesting candidate in limiting detrimental effects of amoxicillin:clavulanic acid on the human gut microbiome, though further studies are warranted to confirm these findings.

Enhanced Biogas Production by Ligninolytic Strain Enterobacter hormaechei KA3 for Anaerobic Digestion of Corn Straw

Lignin-feeding insect gut is a natural ligninolytic microbial bank for the sustainable conversion of crop straw to biogas. However, limited studies have been done on highly efficient microbes. Here, an efficient ligninolytic strain Enterobacter hormaechei KA3 was isolated from the gut microbiomes of lignin-feeding Hypomeces squamosus Fabricius, and its effects on lignin degradation and anaerobic digestion were investigated. No research has been reported. Results showed that strain KA3 had better lignin-degrading ability for corn straw with a higher lignin-degrading rate (32.05%) and lignin peroxidase activity (585.2 U/L). Furthermore, the highest cumulative biogas yield (59.19 L/kg-VS) and methane yield (14.76 L/kg-VS) were obtained for KA3 inoculation, which increased by 20% and 31%, respectively, compared to CK. Higher removal rates of COD, TS, and vs. of 41.6%, 43.11%, and 66.59% were also found. Moreover, microbial community diversity increased as digestion time prolonged in TG, and bacteria were more diverse than archaea. The dominant genus taxon, for methanogens, was Methanosate in TG, while in CK was Methanosarcina. For bacteria, dominant taxa were similar for all groups, which were Solibacillus and Clostridium. Therefore, strain KA3 improved the methane conversion of the substrate. This study could provide a new microbial resource and practical application base for lignin degradation.

Simultaneous nitrification and phosphate removal by bioaugmented aerobic granules treating a fluoroorganic compound

The presence of toxic compounds in wastewater can cause problems for organic matter and nutrient removal. In this study, the long-term effect of a model xenobiotic, 2-fluorophenol (2-FP), on ammonia-oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB) and phosphate accumulating organisms (PAO) in aerobic granular sludge was investigated. Phosphate (P) and ammonium (N) removal efficiencies were high (>93%) and, after bioaugmentation with 2-FP degrading strain FP1, 2-FP was completely degraded. Neither N nor P removal were affected by 50 mg L^-1 of 2-FP in the feed stream. Changes in the aerobic granule bacterial communities were followed. Numerical analysis of the denaturing gradient gel electrophoresis (DGGE) profiles showed low diversity for the ammonia monooxygenase (amoA) gene with an even distribution of species. PAOs, including denitrifying PAO (dPAO), and AOB were present in the 2-FP degrading granules, although dPAO population decreased throughout the 444 days reactor operation. The results demonstrated that the aerobic granules bioaugmented with FP1 strain successfully removed N, P and 2-FP simultaneously.

Antioxidant Vitamins and Prebiotic FOS and XOS Differentially Shift Microbiota Composition and Function and Improve Intestinal Epithelial Barrier In Vitro

Human gut microbiota (HGM) play a significant role in health and disease. Dietary components, including fiber, fat, proteins and micronutrients, can modulate HGM. Much research has been performed on conventional prebiotics such as fructooligosaccharides (FOS) and galactooligosaccharides (GOS), however, novel prebiotics or micronutrients still require further validation. We assessed the effect of FOS, xylooligosaccharides (XOS) and a mixture of an antioxidant vitamin blend (AOB) on gut microbiota composition and activity, and intestinal barrier in vitro. We used batch fermentations and tested the short-term effect of different products on microbial activity in six donors. Next, fecal inocula from two donors were used to inoculate the simulator of the human microbial ecosystem (SHIME) and after long-term exposure of FOS, XOS and AOB, microbial activity (short- and branched-chain fatty acids and lactate) and HGM composition were evaluated. Finally, in vitro assessment of intestinal barrier was performed in a Transwell setup of differentiated Caco-2 and HT29-MTX-E12 cells exposed to fermentation supernatants. Despite some donor-dependent differences, all three tested products showed beneficial modulatory effects on microbial activity represented by an increase in lactate and SCFA levels (acetate, butyrate and to a lesser extent also propionate), while decreasing proteolytic markers. Bifidogenic effect of XOS was consistent, while AOB supplementation appears to exert a specific impact on reducing F. nucleatum and increasing butyrate-producing B. wexlerae. Functional and compositional microbial changes were translated to an in vitro host response by increases of the intestinal barrier integrity by all the products and a decrease of the redox potential by AOB supplementation.

A Comparison of the In Vitro Effects of 2'Fucosyllactose and Lactose on the Composition and Activity of Gut Microbiota from Infants and Toddlers

Because of the recognized health benefits of breast milk, it is recommended as the sole nutrition source during the first 6 months of life. Among the bioactive components are human milk oligosaccharides (HMOs) that exert part of their activity via the gut microbiota. Here, we investigated the gut microbiota fermentation of HMO 2'fucosyllactose (2'-FL), using two in vitro models (48 h fecal incubations and the long-term mucosal simulator of the human intestinal microbial ecosystem [M-SHIME®]) with fecal samples from 3-month-old breastfed (BF) infants as well as 2-3 year old toddlers. The short-term model allowed the screening of five donors for each group and provided supportive data for the M-SHIME® study. A key finding was the strong and immediate increase in the relative abundance of Bifidobacteriaceae following 2'-FL fermentation by both the BF infant and toddler microbiota in the M-SHIME®. At the metabolic level, while decreasing branched-chain fatty acids, 2'-FL strongly increased acetate production together with increases in the health-related propionate and butyrate whilst gas production only mildly increased. Notably, consistently lower gas production was observed with 2'-FL fermentation as compared to lactose, suggesting that reduced discomfort during the dynamic microbiome establishment in early life may be an advantage along with the bifidogenic effect observed.

In vitro-in vivo Validation of Stimulatory Effect of Oat Ingredients on Lactobacilli

The prebiotic activity of a commercially available oat product and a novel oat ingredient, at similar β-glucan loads, was tested using a validated in vitro gut model (M-SHIME^®). The novel oat ingredient was tested further at lower β-glucan loads in vitro, while the commercially available oat product was assessed in a randomised, single-blind, placebo-controlled, and cross-over human study. Both approaches focused on healthy individuals with mild hypercholesterolemia. In vitro analysis revealed that both oat products strongly stimulated Lactobacillaceae and Bifidobacteriaceae in the intestinal lumen and the simulated mucus layer, and corresponded with enhanced levels of acetate and lactate with cross-feeding interactions leading to an associated increase in propionate and butyrate production. The in vitro prebiotic activity of the novel oat ingredient remained at lower β-glucan levels, indicating the prebiotic potential of the novel oat product. Finally, the stimulation of Lactobacillus spp. was confirmed during the in vivo trial, where lactobacilli abundance significantly increased in the overall population at the end of the intervention period with the commercially available oat product relative to the control product, indicating the power of in vitro gut models in predicting in vivo response of the microbial community to dietary modulation.

Fructans with Varying Degree of Polymerization Enhance the Selective Growth of Bifidobacterium animalis subsp. lactis BB-12 in the Human Gut Microbiome In Vitro

Synbiotics aim to improve gastrointestinal health by combining pre- and probiotics. This study evaluated combinations of Bifidobacterium animalis subsp. lactis BB-12 with seven fructans: oligofructoses (OF1-OF2; low degree of polymerization (DP)), inulins (IN1-IN2-IN3; high DP) and OF/IN mixtures (OF/IN1-OF/IN2). During monoculture incubations, all fructans were fermented by BB-12 as followed from increased BB-12 numbers and increased acetate and lactate concentrations, with most pronounced fermentation for low DP fructans (OF1-OF2). Further, short-term colonic incubations for three human donors revealed that also in presence of a complex microbiota, all fructans (particularly OF1) consistently selectively enhanced the growth of BB-12. While each fructan as such already increased Bifidobacteriaceae numbers with 0.94–1.26 log(cells/mL), BB-12 co-supplementation additionally increased Bifidobacteriaceae with 0.17–0.46 log(cells/mL). Further, when co-supplemented with fructans, BB-12 decreased Enterobacteriaceae numbers (significant except for IN1-IN3). At metabolic level, all fructans decreased pH due to increased acetate and lactate production, while OF/IN2-IN1-IN2-IN3 also stimulated propionate and butyrate production. BB-12 co-supplementation further increased propionate and butyrate for OF/IN2-IN3 and IN1-IN2, respectively. Overall, combinations of BB-12 with fructans are promising synbiotic concepts, likely due to intracellular consumption of low DP-fructans by BB-12 (either present in starting product or released upon fermentation by indigenous microbes), thereby enhancing effects of the co-administered fructan.

Comparison of the Bifidogenic Effects of Goat and Cow Milk-Based Infant Formulas to Human Breast Milk in an in vitro Gut Model for 3-Month-Old Infants

Human milk contains prebiotic components, such as human milk oligosaccharides (HMOs), which stimulate the growth of specific members of the infant gut microbiota (e.g., Bifidobacteria). Plant-based or synthetic oligosaccharides are often added to infant formulas to simulate the bifidogenic effect of HMOs. Cow milk, the most common source of protein in infant formula, and goat milk, used increasingly in the manufacture of infant formula, contain naturally-occurring prebiotics. This study compared the upper gastrointestinal digestion and subsequent colonic fermentation of human milk vs. goat and cow milk-based infant formulas (goat IF and cow IF, respectively), without additional oligosaccharides using an in vitro model for 3-month-old infants based on the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). First, a dialysis approach using 3.5 kDa membranes was demonstrated to simulate small intestinal absorption of carbohydrates in conditions similar to those in vivo. During the in vitro digestion experiment, oligosaccharides were detected in human milk and goat IF but barely detected in the cow IF. Further, all three milk matrices decreased colonic pH by boosting acetate, lactate, and propionate production, which related to increased abundances of acetate/lactate-producing Bifidobacteriaceae for human milk (+25.7%) and especially goat IF (33.8%) and cow IF (37.7%). Only cow IF stimulated butyrate production which correlated with an increase in Lachnospiraceae and Clostridiaceae. Finally, Enterobacteriaceae and Acidaminococcaceae also increased with all three milk matrices, while production of proteolytic metabolites (branched-chain fatty acids) was only detected for the cow IF. Overall, goat and cow milk-based formulas without added oligosaccharides impacted gut microbial activity and composition similarly to human milk. This suggests that even without supplementation of formula with oligosaccharides, whole goat milk, whole cow milk and cow milk ingredients already supply compounds in formulas that exert beneficial bifidogenic effects. Further clinical research is warranted to elucidate the effect of whole goat milk-based formulas on the infant gut microbiome.

Effect of a novel animal milk oligosaccharide biosimilar on the gut microbial communities and metabolites of in vitro incubations using feline and canine fecal inocula

Milk oligosaccharides (MO) confer multiple potential physiological benefits, such as the selective growth promotion of beneficial microbiota, inhibition of enteric pathogen growth and adhesion to enterocytes, maturation of the gut mucosal barrier, and modulation of the gastrointestinal immune system. This study was conducted to determine the fermentation potential of GNU100, an animal MO biosimilar, in an in vitro system using healthy canine and feline fecal inocula. Single feline and single canine fecal samples were used to inoculate a batch fermentation system. Tubes containing a blank control (BNC), GNU100 at 0.5% (5 g/L; GNU1), or GNU100 at 1.0% (10 g/L; GNU2) were incubated for 48 h. Gas pressure, pH, lactate, short-chain fatty acids (SCFA; acetate, propionate, and butyrate), and branched-chain fatty acids (BCFA; isobutyrate, isovalerate, and valerate) were measured after 6, 24, and 48 h. Ammonium and microbiota (total bacteria by flow cytometry and Pet-16Seq; Lactobacillus and Bifidobacterium by quantitative polymerase chain reaction ) were measured after 24 and 48 h. Data were analyzed using the Mixed Models procedure of SAS. Substrates were considered to be a fixed effect and replicates considered to be a random effect. Tukey's multiple comparison analysis was used to compare least squares means, with differences considered significant with P < 0.05. In feline and canine incubations, SCFA increases were greater (P < 0.0001) in GNU100 compared with BNC, with acetate making up the largest SCFA proportion (P < 0.0001). GNU100 cultures led to greater increases (P < 0.0001) in lactate and ammonium than BNC in the feline incubations. GNU100 cultures led to greater increases (P < 0.0001) in ammonium than BNC in canine incubations and greater increases (P < 0.0001) in BCFA than BNC in feline incubations. Pet-16Seq microbial profiles from the feline and canine fecal incubations exhibited a modulation after GNU100 fermentation, with a reduction of the genera Escherichia/Shigella and Salmonella. In feline incubations, Bifidobacterium populations had greater increases (P < 0.0001) in GNU100 than BNC. In feline incubations, Lactobacillus populations had greater increases (P = 0.01) in GNU100 than BNC, with GNU1 leading to greater increases (P = 0.02) in Lactobacillus than BNC tubes in canine incubations. Overall, this study demonstrated that GNU100 was fermented in an in vitro fermentation system inoculated with canine and feline microbiota, resulting in the growth of beneficial bacteria and the production of SCFA, BCFA, and ammonium.

Pollutant removal from landfill leachate via two-stage anoxic/oxic combined membrane bioreactor: Insight in organic characteristics and predictive function analysis of nitrogen-removal bacteria

A two-stage anoxic/oxic combined membrane bioreactor (A/O-A/O-MBR) was operated for 81 d to treat landfill leachate under different reflux ratios (R). The best performance was found under R = 150%, where the chemical oxygen demand (COD), ammonium (NH₄⁺-N) and total nitrogen (TN) removal was 85.6%, 99.3%, and 80.7%, respectively. Particularly, the highest pollutant removal was achieved in the second-stage A/O, where the COD and TN removal capacity was 78.88 and 11.74 g/d, respectively. Meantime, DOM removal was 83.9%, where the removal of aromatic protein substances I and II, fulvic acids-like compounds, soluble microbial products and humic acids-like compounds was 93.4%, 86.4%, 72.0%, 86.6% and 59.4%, respectively. The gene functions of microbial community in the process showed that amoA, hao, nirK and nosZ, etc. were the core genes for nitrification and denitrification. The carbon source for denitrification might come from the conversion of refractory organic matters in landfill leachate.

Yeast-Derived Formulations Are Differentially Fermented by the Canine and Feline Microbiome As Assessed in a Novel In Vitro Colonic Fermentation Model

The current study evaluated the effect of five yeast-derived formulations (T1-T5) on microbial metabolism and composition of the canine and feline gut microbiota using a novel in vitro colonic incubation approach. This novel in vitro model allowed for growth of the entire spectrum of dog- and cat-derived bacteria from the inoculum, thus offering an excellent platform to evaluate effects of nutritional interventions on the gut microbiota. Further, yeast-derived ingredients differentially increased production of acetate, propionate, butyrate, ammonium, and branched short-chain fatty acids, with T5 and T1 consistently stimulating propionate and butyrate, respectively. 16S-targeted Illumina sequencing coupled with flow cytometry provided unprecedented high-resolution quantitative insights in canine and feline microbiota modulation by yeast-derived ingredients, revealing that effects on propionate production were related to Prevotellaceae, Tannerellaceae, Bacteroidaceae, and Veillonellaceae members, while effects on butyrate production were related to Erysipelotrichaceae, Lachnospiraceae, Ruminococcaceae, and Fusobacteriaceae. Overall, these findings strengthen the health-promoting potential of yeast-derived ingredients.

Effects of Human Milk Oligosaccharides on the Adult Gut Microbiota and Barrier Function

Human milk oligosaccharides (HMOs) shape the gut microbiota in infants by selectively stimulating the growth of bifidobacteria. Here, we investigated the impact of HMOs on adult gut microbiota and gut barrier function using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®), Caco2 cell lines, and human intestinal gut organoid-on-chips. We showed that fermentation of 2'-O-fucosyllactose (2'FL), lacto-N-neotetraose (LNnT), and combinations thereof (MIX) led to an increase of bifidobacteria, accompanied by an increase of short chain fatty acid (SCFA), in particular butyrate with 2'FL. A significant reduction in paracellular permeability of FITC-dextran probe was observed using Caco2 cell monolayers with fermented 2'FL and MIX, which was accompanied by an increase in claudin-8 gene expression as shown by qPCR, and a reduction in IL-6 as determined by multiplex ELISA. Using gut-on-chips generated from human organoids derived from proximal, transverse, and distal colon biopsies (Colon Intestine Chips), we showed that claudin-5 was significantly upregulated across all three gut-on-chips following treatment with fermented 2'FL under microfluidic conditions. Taken together, these data show that, in addition to their bifidogenic activity, HMOs have the capacity to modulate immune function and the gut barrier, supporting the potential of HMOs to provide health benefits in adults.

The Fate of Anthropogenic Nanoparticles, nTiO2 and nCeO2, in Waste Water Treatment

Wastewater treatment is one of the main end-of-life scenarios, as well as a possible reentry point into the environment, for anthropogenic nanoparticles (NP). These can be released from consumer products such as sunscreen or antibacterial clothing, from health-related applications or from manufacturing processes such as the use of polishing materials (nCeO2) or paints (nTiO2). The use of NP has dramatically increased over recent years and initial studies have examined the possibility of toxic or environmentally hazardous effects of these particles, as well as their behavior when released. This study focuses on the fate of nTiO2 and nCeO2 during the wastewater treatment process using lab scale wastewater treatment systems to simulate the NP mass flow in the wastewater treatment process. The feasibility of single particle mass spectroscopy (sp-ICP-MS) was tested to determine the NP load. The results show that nTiO2 and nCeO2 are adsorbed to at least 90 percent of the sludge. Furthermore, the results indicate that there are processes during the passage of the treatment system that lead to a modification of the NP shape in the effluent, as NP are observed to be partially smaller in effluent than in the added solution. This observation was made particularly for nCeO2 and might be due to dissolution processes or sedimentation of larger particles during the passage of the treatment system.

In Vitro Modulation of Gut Microbiota and Metabolism by Cooked Cowpea and Black Bean

Legumes are a rich source of a wide range of compounds that may represent an important tool to overcome gut dysbiosis. In this work, the prebiotic potential of two cooked legumes (cowpea and black bean) was investigated in comparison with potato:beef mixture, as substrates in batch faecal culture fermentation. Prior to the fermentation, all the samples were in vitro digested, passing through three phases, namely mouth, gastric and small intestine simulation, and then in vitro fermented for 6, 24 and 48 h. The shift of pH, production of gas and short-chain fatty acids (SCFAs) and changes in gut microbiota were evaluated along the fermentation time. The pH decreased significantly over time in all media with fermentable sources when compared with the negative control. Gas production was higher in the media containing fermentable source than in the negative control and decreased with fermentation time. The concentration of SCFAs increased over time and it was significantly higher for both legumes than in inulin (positive control) and potato:beef meal. Acetate was the major SCFAs produced during fermentation, particularly in media containing legumes. Both legumes presented a strong prebiotic effect on gut microbiota, showing a significant increase in Bifidobacterium and Lactobacillus. These results suggest that consumption of cooked cowpea and black bean, used alone or as an ingredient of novel functional foods, may contribute to improving intestinal health and therefore human health promotion.

Immobilized-microbial bioaugmentation protects aerobic denitrification from heavy metal shock in an activated-sludge reactor

The inhibition of denitrification by heavy metals is a problem in nitrogen wastewater treatment, but the solutions are rarely studied. In this study, Pseudomonas brassicacearum LZ-4, immobilized in sodium alginate-kaolin, was applied in an activated-sludge reactor to protect denitrifiers from hexavalent chromium (Cr(VI)). Q-PCR result showed that the strain LZ-4 was incorporated into activated sludge under the help of immobilization. In the non-bioaugmentation system, the removal efficiency of nitrate was decreased by 86.07% by 30 mg/L Cr(VI). Whereas, denitrification was protected and 95% of nitrate was removed continuously in immobilized-cell bioaugmentation system. Miseq sequencing data showed that bioaugmentation decreased the impact of Cr(VI) on microbial communities and increased the abundance of denitrifiers. Based on the results of biomass and extracellular polymers, activated sludge was protected from Cr(VI) toxicity. This discovery will provide a feasible technique for nitrogen wastewater treatment in the presence of distressing heavy metals.

A Novel Non-Digestible, Carrot-Derived Polysaccharide (cRG-I) Selectively Modulates the Human Gut Microbiota while Promoting Gut Barrier Integrity: An Integrated in Vitro Approach

Modulation of the gut microbiome as a means to improve human health has recently gained increasing interest. In this study, it was investigated whether cRG-I, a carrot-derived pectic polysaccharide, enriched in rhamnogalacturonan-I (RG-I) classifies as a potential prebiotic ingredient using novel in vitro models. First, digestion methods involving α-amylase/brush border enzymes demonstrated the non-digestibility of cRG-I by host-derived enzymes versus digestible (starch/maltose) and non-digestible controls (inulin). Then, a recently developed short-term (48 h) colonic incubation strategy was applied and revealed that cRG-I fermentation increased levels of health-promoting short-chain fatty acids (SCFA; mainly acetate and propionate) and lactate comparable but not identical to the reference prebiotic inulin. Upon upgrading this fermentation model by inclusion of a simulated mucosal environment while applying quantitative 16S-targeted Illumina sequencing, cRG-I was additionally shown to specifically stimulate operational taxonomic units (OTUs) related to health-associated species such as Bifidobacterium longum, Bifidobacterium adolescentis, Bacteroides dorei, Bacteroides ovatus, Roseburia hominis, Faecalibacterium prausnitzii, and Eubacterium hallii. Finally, in a novel model to assess host–microbe interactions (Caco-2/peripheral blood mononuclear cells (PBMC) co-culture) fermented cRG-I increased barrier integrity while decreasing markers for inflammation. In conclusion, by using novel in vitro models, cRG-I was identified as a promising prebiotic candidate to proceed to clinical studies.

Responses of Exogenous Bacteria to Soluble Extracellular Polymeric Substances in Wastewater: A Mechanistic Study and Implications on Bioaugmentation

Compared with the chemically defined synthetic wastewater (SynWW), real wastewater has been reported to exhibit distinct effects on microbial community development. Whether and how soluble microbial products in real wastewater contribute to different effects of synthetic and real wastewater on the fate of exogenous bacteria remains elusive. In this study, using a model wastewater bacterium Comamonas testosteroni, we first examined the influences of microfiltration filter-sterilized real wastewater (MF-WW) and SynWW on the retention of C. testosteroni in established wastewater flocs during bioaugmentation. In bioreactors fed with MF-WW, augmentation of C. testosteroni to wastewater flocs resulted in a substantially higher abundance of the augmented bacterial cells than those fed with SynWW. To identify the soluble microbial products in MF-WW contributing to the observed differences between bioaugmentation reactors fed with MF-WW and SynWW, we examined the effect of MF-WW and SynWW on the growth, floc formation, and biofilm development of C. testosteroni. When C. testosteroni grew in MF-WW, visible flocs formed within 2 h, which is in contrast to cell growth in SynWW where floc formation was not observed. We further demonstrated that the observed differences were mainly attributed to the high molecular weight fraction of the soluble extracellular polymeric substances (EPS) in MF-WW, in particular, proteins and extracellular DNA. The DLVO analysis suggested that, in the presence of soluble EPS, the bacterial cell surface exhibits an increased hydrophobicity and a diminished energy barrier, leading to irreversible attachment of planktonic cells and floc formation. The RNA-seq based transcriptional analysis revealed that, in the presence of soluble EPS, genes involved in nonessential metabolisms were downregulated while genes coding for Cco (cbb3-type) and Cox (aa3-type) oxidases with different oxygen affinities were upregulated, facilitating bacterial survival in flocs. Taken together, this study reveals the mechanisms underlying the contribution of soluble EPS in real wastewater to the recruitment of exogenous bacteria by microbial aggregates and provides implications to bioaugmentation.

Effects of transient 3-chloroaniline shock loading on the performance, microbial community and enzymatic activity of sequencing batch reactor

Chloroanilines from industrial wastewater can produce adverse effects on biological wastewater treatment systems due to their potential biotoxicity. The performance, nitrogen removal rate, microbial community and enzymatic activity of a sequencing batch reactor (SBR) were evaluated under transient 3-chloroaniline shock loading. After 40 mg/L 3-chloroaniline shock loading of 24 h on day 9, the chemical oxygen demand (COD) removal efficiency decreased from 90.71% on day 8 to 80.57% on day 11, and the NH₄⁺-N removal efficiency reduced from 98.96% on day 8 to 35.51% on day 12. Subsequently, the COD and NH₄⁺-N removal efficiencies gradually recovered to normal value. Compared with the absence of 3-chloroaniline shock loading, the ammonia-oxidizing rate (SAOR), nitrite-oxidizing rate (SNOR), nitrite-reducing rate (SNIRR) and nitrate-reducing rate (SNRR) decreased by 66.19%, 14.49%, 16.20% and 49.38% on day 11, respectively, and then they gradually recovered to normal value. The SAOR, SNOR, SNIRR and SNRR displayed the similar varying trends to the activities of ammonia monooxygenase, nitrite oxidoreductase, nitrite reductase and nitrate reductase, respectively. The appearance of 3-chloroaniline promoted the microbial reactive oxygen species production and lactate dehydrogenase release. The transient 3-chloroaniline shock loading distinctly impacted the microbial richness and diversity. The present research results can provide theoretical basis and technical support for evaluating the effects of transient 3-chloroaniline shock on biological wastewater treatment systems, which is beneficial to take reasonable preventable measures to decrease the adverse effects on the bioreactor performance.

Effects of Olive and Pomegranate By-Products on Human Microbiota: A Study Using the SHIME® in Vitro Simulator

Two by-products containing phenols and polysaccharides, a “pâté” (OP) from the extra virgin olive oil milling process and a decoction of pomegranate mesocarp (PM), were investigated for their effects on human microbiota using the SHIME^® system. The ability of these products to modulate the microbial community was studied simulating a daily intake for nine days. Microbial functionality, investigated in terms of short chain fatty acids (SCFA) and NH₄⁺, was stable during the treatment. A significant increase in Lactobacillaceae and Bifidobacteriaceae at nine days was induced by OP mainly in the proximal tract. Polyphenol metabolism indicated the formation of tyrosol from OP mainly in the distal tract, while urolithins C and A were produced from PM, identifying the human donor as a metabotype A. The results confirm the SHIME^® system as a suitable in vitro tool to preliminarily investigate interactions between complex botanicals and human microbiota before undertaking more challenging human studies.

Effects of 2,4,6-trichlorophenol on simultaneous nitrification and denitrification: Performance, possible degradation pathway and bacterial community structure

This study aimed to investigate the effect of different 2,4,6-trichlorophenol (TCP) concentrations on the performance of simultaneous nitrification and denitrification processes established in a sequential batch biofilm reactor. And the degradation and the possible degradation pathway of 2,4,6-TCP and microbial community structure were also explored. Results indicated that 2,4,6-TCP inhibited the nitrification with the decrease in ammonium nitrogen removal. However, 2,4,6-TCP had different effects on denitrification. Nitrate accumulation showed the tendency to decrease first and then increase, whilst nitrite accumulation showed the opposite with a small change. The adaptation and recovery time of 25 mg/l 2,4,6-TCP was longest. In addition, the process had a good degradation effect on 2,4,6-TCP. Comparing the degradation of 2,4,6-TCP under different concentrations, the result showed that 2,4,6-TCP was mainly reduced to 2,4-dichlorophenol. With the increase in 2,4,6-TCP concentration, the differences in the bacterial community in the reactor were significant.

Gut microbiome patterns depending on children's psychosocial stress: Reports versus biomarkers

AIM

Chronic stress increases disease vulnerability factors including inflammation, a pathological characteristic potentially regulated by the gut microbiota. We checked the association between the gut microbiome and psychosocial stress in children/adolescents and investigated which stress parameter (negative versus positive emotion, self-report versus parental report, events versus emotions, biomarker cortisol versus parasympathetic activity) is the most relevant indicator herein.

METHODS

Gut microbiome sequencing was completed in fecal samples from 93 Belgian 8-16y olds. Stress measures included negative events, negative emotions, emotional problems reported by parents, happiness, hair cortisol and heart rate variability (pnn50 parameter reflecting parasympathetic activity). Alpha diversity, beta diversity and linear discriminant analysis were the unadjusted analyses. Age, sex, socio-economic status, diet, physical activity, sleep and weight status were adjusted for via a redundancy analysis and differential abundance via zero-inflated negative binomial regression.

RESULTS

High stress as reflected by low pnn50 and more negative events were associated with a lower alpha diversity as indicated by the Simpson index. Happiness and pnn50 showed significant differences between high and low stress groups based on weighted UniFrac distance, and this remained significant after confounder adjustment. Adjusted and unadjusted taxonomic differences were also most pronounced for happiness and pnn50 being associated respectively with 24 OTU (=11.8% of bacterial counts) and 31 OTU (=13.0%). As a general pattern, high stress was associated with lower Firmicutes at the phylum level and higher Bacteroides, Parabacteroides, Rhodococcus, Methanobrevibacter and Roseburia but lower Phascolarctobacterium at genus level. Several genera gave conflicting results between different stress measures e.g. Ruminococcaceae UCG014, Tenericutes, Eubacterium coprostanoligenes, Prevotella 9 and Christensenellaceae R7. Differential results in preadolescents versus adolescents were also evident.

CONCLUSION

Even in this young healthy population, stress parameters were cross-sectionally associated with gut microbial composition but this relationship was instrument specific. Positive emotions and parasympathetic activity appeared the strongest parameters and should be integrated in future microbiota projects amongst other stress measures.

Trait-based life-history strategies explain succession scenario for complex bacterial communities under varying disturbance

Trait-based approaches are increasingly gaining importance in community ecology, as a way of finding general rules for the mechanisms driving changes in community structure and function under the influence of perturbations. Frameworks for life-history strategies have been successfully applied to describe changes in plant and animal communities upon disturbance. To evaluate their applicability to complex bacterial communities, we operated replicated wastewater treatment bioreactors for 35 days and subjected them to eight different disturbance frequencies of a toxic pollutant (3-chloroaniline), starting with a mixed inoculum from a full-scale treatment plant. Relevant ecosystem functions were tracked and microbial communities assessed through metagenomics and 16S rRNA gene sequencing. Combining a series of ordination, statistical and network analysis methods, we associated different life-history strategies with microbial communities across the disturbance range. These strategies were evaluated using tradeoffs in community function and genotypic potential, and changes in bacterial genus composition. We further compared our findings with other ecological studies and adopted a semi-quantitative competitors, stress-tolerants, ruderals (CSR) classification. The framework reduces complex data sets of microbial traits, functions and taxa into ecologically meaningful components to help understand the system response to disturbance and hence represents a promising tool for managing microbial communities.

A synbiotic concept containing spore-forming Bacillus strains and a prebiotic fiber blend consistently enhanced metabolic activity by modulation of the gut microbiome in vitro

A standardized in vitro simulation of the human gastrointestinal tract (M-SHIME®) was used to assess the effect of repeated daily administration of a synbiotic formulation, containing five spore-forming Bacillus strains and a prebiotic fiber blend, on the microbial activity and composition of three simulated human subjects. Firstly, while confirming recent findings, deeper phylogenetic insight was obtained in the resident M-SHIME® microbiota, demonstrating that the model maintains a diverse and representative, colon region-specific luminal and mucosal microbial community. Supplementation of the synbiotic concept increased microbial diversity in the distal colon areas, whereas specific enhancement of Bacillaceae levels was observed in the ascending colon suggesting a successful engraftment of the Bacillus spores, which probably resulted in a stimulatory effect on, among others, Bifidobacteriaceae, Lactobacillaceae, Prevotellaceae, Tannerellaceae and Faecalibacterium prausnitzii contributing directly or indirectly to stimulation of acetate, propionate and butyrate production. When compared with a previous study investigating the Bacillus strains, the generated data suggest a synergistic effect on the intestinal microbiota for the synbiotic formulation. Given the fact that the probiotic strains have been shown to impact post-prandial metabolic endotoxemia in human individuals, it might be interesting to further investigate the efficacy of the synbiotic concept in protecting against obesity-related disorders.

Bioaugmentation of membrane bioreactor with Achromobacter denitrificans strain PR1 for enhanced sulfamethoxazole removal in wastewater

Achromobacter denitrificans strain PR1, previously found to harbour specific degradation pathways with high sulfamethoxazole (SMX) degradation rates, was bioaugmented into laboratory-scale membrane bioreactors (MBRs) operated under aerobic conditions to treat SMX-containing real domestic wastewater. Different hydraulic retention times (HRTs), which is related to reaction time and loading rates, were considered and found to affect the SMX removal efficiency. The availability of primary substrates was important in both bioaugmented and non-bioaugmented activated sludge (AS) for cometabolism of SMX. High HRT (24 h) resulted in low food to microorganism ratio (F/M) and low SMX removal, due to substrate limitation. Decrease in HRT from 24 h to 12 h, 6 h and finally 4 h led to gradual increases in primary substrates availability, e.g. organic compounds and ammonia, resulted in increased SMX removal efficiency and degradation rate, and is more favorable for high-rate wastewater treatment processes. After inoculation into the MBRs, the bioaugmentation strain was sustained in the reactor for a maximum of 31 days even though a significant decrease in abundance was observed. The bioaugmented MBRs showed enhanced SMX removal, especially under SMX shock loads compared to the control MBRs. The results of this study indicate that re-inoculation is required regularly after a period of time to maintain the removal efficiency of the target compound.

Different Oat Ingredients Stimulate Specific Microbial Metabolites in the Gut Microbiome of Three Human Individuals in Vitro

We used a standardized in vitro simulation of the intestinal environment of three human donors to investigate the effect of six oat ingredients, which were produced by the application of different processing techniques, on the gut microbial community. Fructooligosaccharide was used as the positive control. Consistent changes in pH and gas production, on average -0.4 pH units and +32 kPa, indicated the high fermentability of the oat ingredients, and the resulting increased production of metabolites that are considered as beneficial for human health. These metabolites included acetate and lactate, but mostly propionate (+13.6 mM on average). All oat ingredients resulted in increased bifidobacteria levels with an average increase of 0.73 log. Moreover, a decreased production of proteolytic markers was observed, including branched short-chain fatty acids and ammonium. The results were donor-specific and product-specific. The results suggested an association between the total amounts of dietary fiber and the prebiotic potentials of different ingredients. Furthermore, as mechanical processing of oat products has previously been linked to increased extractability of dietary fibers, the obtained results suggest that different processing techniques might have impacted the potential functional properties of the final ingredients.

Responses of atrazine degradation and native bacterial community in soil to Arthrobacter sp. strain HB-5

The bioremediation of soil contaminated with organic pesticides is a safe and effective approach to remove pollutants from the soil. However, whether the invasion of foreign aid organisms affects the local organisms has received increasing attention in recent years. Therefore, the purpose of this study was to examine the degradation ability of atrazine by the strain HB-5 and evaluate its effects on natural bacterial communities in a miniature pot experiment. Results showed that HB-5 accelerated the degradation of atrazine and the degradation half-life of atrazine was 3.3 times less than the natural soil. Additionally, HB-5 increased the quantities of indigenous bacteria, the microbial biomass carbon and the Shannon, Simpson and McIntosh diversity indices of soil microbes in its early stage of use, But these parameters in soil treated with HB-5 decreased to values as low as those found in the control at the later stage of incubation. These suggested that the bacteria vanished as atrazine was completely removed. These results demonstrated that Arthrobacter sp. strain HB-5 had great potential and would be an effective and environmental friendly technique to remove atrazine from the contaminated soil.

Taking the technical microbiome into the next decade

The 'microbiome' has become a buzzword. Multiple new technologies allow to gather information about microbial communities as they evolve under stable and variable environmental conditions. The challenge of the next decade will be to develop strategies to compose and manage microbiomes. Here, key aspects are considered that will be of crucial importance for future microbial technological developments. First, the need to deal not only with genotypes but also particularly with phenotypes is addressed. Microbial technologies are often highly dependent on specific core organisms to obtain the desired process outcome. Hence, it is essential to combine omics data with phenotypic information to invoke and control specific phenotypes in the microbiome. Second, the development and application of synthetic microbiomes is evaluated. The central importance of the core species is a no-brainer, but the implementation of proper satellite species is an important route to explore. Overall, for the next decade, microbiome research should no longer almost exclusively focus on its capacity to degrade and dissipate but rather on its remarkable capability to capture disordered components and upgrade them into high-value microbial products. These products can become valuable commodities in the cyclic economy, as reflected in the case of 'reversed sanitation', which is introduced here.