Food Starch Structure Impacts Gut Microbiome Composition

ABSTRACT Starch is a major source of energy in the human diet and is consumed in diverse forms. Resistant starch (RS) escapes small intestinal digestion and is fermented in the colon by the resident microbiota, with beneficial impacts on colonic function and host health, but the impacts of the micro- and nanoscale structure of different physical forms of food starch on the broader microbial community have not been described previously. Here, we use a porcine in vitro fermentation model to establish that starch structure dramatically impacts microbiome composition, including the key amylolytic species, and markedly alters both digestion kinetics and fermentation outcomes. We show that three characteristic food forms of starch that survive digestion in the small intestine each give rise to substantial and distinct changes in the microbiome and in fermentation products. Our results highlight the complexity of starch fermentation processes and indicate that not all forms of RS in foods are degraded or fermented in the same way. This work points the way for the design of RS with tailored degradation by defined microbial communities, informed by an understanding of how substrate structure influences the gut microbiome, to improve nutritive value and/or health benefits. IMPORTANCE Dietary starch is a major component in the human diet. A proportion of the starch in our diet escapes digestion in the small intestine and is fermented in the colon. In this study, we use a model of the colon, seeded with porcine feces, in which we investigate the fermentation of a variety of starches with structures typical of those found in foods. We show that the microbial community changes over time in our model colon are highly dependent on the structure of the substrate and how accessible the starch is to colonic microbes. These findings have important implications for how we classify starches reaching the colon and for the design of foods with improved nutritional properties.

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The phyllosphere microbiome of host trees contributes more than leaf phytochemicals to variation in the Agrilus planipennis Fairmaire gut microbiome structure

Scientific Reports ◽

10.1038/s41598-021-95146-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Judith Mogouong ◽

Philippe Constant ◽

Pierre Legendre ◽

Claude Guertin

Keyword(s):

Microbial Community ◽

Gut Microbiome ◽

Strong Predictor ◽

Emerald Ash Borer ◽

Agrilus Planipennis ◽

Food Sources ◽

Microbiome Composition ◽

Living Organisms ◽

Insect Gut ◽

Gut Microbial Community

AbstractThe microbiome composition of living organisms is closely linked to essential functions determining the fitness of the host for thriving and adapting to a particular ecosystem. Although multiple factors, including the developmental stage, the diet, and host-microbe coevolution have been reported to drive compositional changes in the microbiome structures, very few attempts have been made to disentangle their various contributions in a global approach. Here, we focus on the emerald ash borer (EAB), an herbivorous pest and a real threat to North American ash tree species, to explore the responses of the adult EAB gut microbiome to ash leaf properties, and to identify potential predictors of EAB microbial variations. The relative contributions of specific host plant properties, namely bacterial and fungal communities on leaves, phytochemical composition, and the geographical coordinates of the sampling sites, to the EAB gut microbial community was examined by canonical analyses. The composition of the phyllosphere microbiome appeared to be a strong predictor of the microbial community structure in EAB guts, explaining 53 and 48% of the variation in fungi and bacteria, respectively. This study suggests a potential covariation of the microorganisms associated with food sources and the insect gut microbiome.

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The sugar composition of the fibre in selected plant foods modulates weaning infants’ gut microbiome composition and fermentation metabolites in vitro

Scientific Reports ◽

10.1038/s41598-021-88445-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Shanthi G. Parkar ◽

Jovyn K. T. Frost ◽

Doug Rosendale ◽

Halina M. Stoklosinski ◽

Carel M. H. Jobsis ◽

...

Keyword(s):

Gut Microbiome ◽

Gas Production ◽

Sugar Composition ◽

Microbiome Composition ◽

Fibre Concentration ◽

Microbiome Profile ◽

Infant Gut Microbiome ◽

Immune Health ◽

Faecal Bacteria

AbstractEight plant-based foods: oat flour and pureed apple, blackcurrant, carrot, gold- and green-fleshed kiwifruit, pumpkin, sweetcorn, were pre-digested and fermented with pooled inocula of weaning infants’ faecal bacteria in an in vitro hindgut model. Inulin and water were included as controls. The pre-digested foods were analysed for digestion-resistant fibre-derived sugar composition and standardised to the same total fibre concentration prior to fermentation. The food-microbiome interactions were then characterised by measuring microbial acid and gas metabolites, microbial glycosidase activity and determining microbiome structure. At the physiologically relevant time of 10 h of fermentation, the xyloglucan-rich apple and blackcurrant favoured a propiogenic metabolic and microbiome profile with no measurable gas production. Glucose-rich, xyloglucan-poor pumpkin caused the greatest increases in lactate and acetate (indicative of high fermentability) commensurate with increased bifidobacteria. Glucose-rich, xyloglucan-poor oats and sweetcorn, and arabinogalactan-rich carrot also increased lactate and acetate, and were more stimulatory of clostridial families, which are indicative of increased microbial diversity and gut and immune health. Inulin favoured a probiotic-driven consortium, while water supported a proteolytic microbiome. This study shows that the fibre-derived sugar composition of complementary foods may shape infant gut microbiome structure and metabolic activity, at least in vitro.

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Muribaculaceae Genomes Assembled from Metagenomes Suggest Genetic Drivers of Differential Response to Acarbose Treatment in Mice

mSphere ◽

10.1128/msphere.00851-21 ◽

2021 ◽

Author(s):

Byron J. Smith ◽

Richard A. Miller ◽

Thomas M. Schmidt

Keyword(s):

Small Intestine ◽

Gut Microbiome ◽

Differential Response ◽

Fermentation Products ◽

Fermentation Product ◽

The Family ◽

Acarbose Treatment

The drug acarbose is used to treat diabetes by preventing the breakdown of starch in the small intestine, resulting in dramatic changes in the abundance of some members of the gut microbiome and its fermentation products. In mice, several of the bacteria that respond most positively are classified in the family Muribaculaceae , members of which produce propionate as a primary fermentation product.

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Method for Modeling the Small Intestine and Resident Microbiome Through in Vitro Fermentation (P20-001-19)

Current Developments in Nutrition ◽

10.1093/cdn/nzz040.p20-001-19 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

Author(s):

Laurel Doherty ◽

Jordan Whitman ◽

Steven Arcidiacono ◽

Karen Conca ◽

Jason Soares

Keyword(s):

Small Intestine ◽

Microbial Community ◽

Nutrient Absorption ◽

Model Design ◽

In Vitro Fermentation ◽

Fed State ◽

Food Components ◽

Physiological Relevance ◽

Fermentation Model

Abstract Objectives The human small intestine is a complex and dynamic organ tasked with enzymatic digestion and absorption of nutrients. Design of a small intestine model can provide detailed systematic knowledge of these processes; model design challenges include differential pH and oxygen availability along the length of the small intestine, food-dependent host secretion of digestive compounds, complex nutrient absorption processes, and microbiome interactions with both food and host. Numerous in vitro models have been developed to simulate the small intestine, but physiological relevance is limited. Here, we present an in vitro fermentation model of the small intestine to include microbiota and enhance physiological relevance. Methods A stepwise biofidelic model design approach was implemented with initial stages consisting of simulating ileum conditions, including pH and residence time, utilizing an automated bioreactor system for real-time monitoring and control of fermentation parameters, with incorporation of digestive enzymes and bile acids for breakdown of food inputs. Nutrient absorption, simulated using hollow-fiber columns to emulate passive diffusion, was initially optimized using small molecules to mimic dietary digestion byproducts; validation with food components, such as starch or whey powder, is planned. A mock microbial community, with organisms selected to represent major phyla and functions of the small intestine microbiota, was designed, implemented, and characterized in fermentations representing “fed-state” ileum conditions. Results Design and validation of the model with mock food components will be presented, along with steps taken to integrate in situ nutrient absorption and mock microbial community. Initial characterization of the microbial community indicates synergistic growth dynamics and nutrient utilization under “fed-state” conditions. Conclusions These efforts will be the foundation for our long-term goal of simulating the small intestine to complement our large intestine fermentation model, jA2COB, creating a complete in vitro fermentation model of the lower GI tract. Insight gleaned from this model, alone or in concert with in vivo studies, can inform nutritional strategies to restore and maintain host gut homeostasis. Funding Sources Funded by U.S. Army NSRDEC core applied research funds.

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Characteristics of the Gut Microbiome and IL-13/TGF-β1 Mediated Fibrosis in Post-Kasai Cholangitis of Biliary Atresia

Frontiers in Pediatrics ◽

10.3389/fped.2021.751204 ◽

2021 ◽

Vol 9 ◽

Author(s):

Lingdu Meng ◽

Jia Liu ◽

Junfeng Wang ◽

Min Du ◽

Shouhua Zhang ◽

...

Keyword(s):

Biliary Atresia ◽

Gut Microbiome ◽

Expression Patterns ◽

Rna Seq ◽

Microbiome Composition ◽

Kasai Procedure ◽

Rdna Sequencing ◽

Liver Organoids ◽

Tgf Β1

Aims: Cholangitis in biliary atresia (BA), which accelerates liver fibrosis progression, is among the most common serious complications after Kasai surgery; however, its etiology remains elusive. Gut microbiome migration may contribute to post-Kasai cholangitis. Further, there is no appropriate model of BA post-Kasai cholangitis for use in investigation of its pathogenesis.Methods: We explored the characteristics of gut microbiome in patients with BA before and after Kasai procedure based on 16S rDNA sequencing. We isolated the dominant strain from patient stool samples and established an in vitro model by infecting patient-derived liver organoids. Bulk RNA-seq was performed, and we conducted qPCR, ELISA, and western blot to explore the mechanism of fibrosis.Results: Gut microbiome diversity was lower in patients after, relative to before, Kasai procedure, while the relative abundance of Klebsiella was higher. Patients who developed cholangitis within 1 month after discharge tended to have simpler gut microbiome composition, dominated by Klebsiella. Klebsiella pneumoniae (KPN) was isolated and used for modeling. RNA-seq showed that BA liver organoids expressed markers of hepatic progenitor cells (KRT19, KRT7, EPCAM, etc.) and that organoids were more stable and less heterogeneous among individuals than liver tissues. After infection with KPN, gene expression patterns in BA liver organoids were enriched in pathways related to infection, apoptosis, and fibrosis. Preliminary experiments indicated the presence of IL-13/TGF-β1-mediated fibrosis in post-Kasai cholangitis.Conclusions: Our findings using a newly-developed model, demonstrate a key role for Klebsiella, and a potential mechanism underlying fibrosis in post-Kasai cholangitis, mediated by the IL-13/TGF-β1 pathway.

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Imidacloprid Decreases Honey Bee Survival Rates but Does Not Affect the Gut Microbiome

Applied and Environmental Microbiology ◽

10.1128/aem.00545-18 ◽

2018 ◽

Vol 84 (13) ◽

Cited By ~ 26

Author(s):

Kasie Raymann ◽

Erick V. S. Motta ◽

Catherine Girard ◽

Ian M. Riddington ◽

Jordan A. Dinser ◽

...

Keyword(s):

Honey Bee ◽

Gut Microbiome ◽

Honey Bees ◽

Microbiome Composition ◽

Susceptibility To Infection ◽

Bee Colony ◽

Colony Loss ◽

Honey Bee Colony ◽

The Impact

ABSTRACT Accumulating evidence suggests that pesticides have played a role in the increased rate of honey bee colony loss. One of the most commonly used pesticides in the United States is the neonicotinoid imidacloprid. Although the primary mode of action of imidacloprid is on the insect nervous system, it has also been shown to cause changes in insects' digestive physiology and alter the microbiota of Drosophila melanogaster larvae. The honey bee gut microbiome plays a major role in bee health. Although many studies have shown that imidacloprid affects honey bee behavior, its impact on the microbiome has not been fully elucidated. Here, we investigated the impact of imidacloprid on the gut microbiome composition, survivorship, and susceptibility to pathogens of honey bees. Consistent with other studies, we show that imidacloprid exposure results in an elevated mortality of honey bees in the hive and increases the susceptibility to infection by pathogens. However, we did not find evidence that imidacloprid affects the gut bacterial community of honey bees. Our in vitro experiments demonstrated that honey bee gut bacteria can grow in the presence of imidacloprid, and we found some evidence that imidacloprid can be metabolized in the bee gut environment. However, none of the individual bee gut bacterial species tested could metabolize imidacloprid, suggesting that the observed metabolism of imidacloprid within in vitro bee gut cultures is not caused by the gut bacteria. Overall, our results indicate that imidacloprid causes increased mortality in honey bees, but this mortality does not appear to be linked to the microbiome. IMPORTANCE Growing evidence suggests that the extensive use of pesticides has played a large role in the increased rate of honey bee colony loss. Despite extensive research on the effects of imidacloprid on honey bees, it is still unknown whether it impacts the community structure of the gut microbiome. Here, we investigated the impact of imidacloprid on the gut microbiome composition, survivorship, and susceptibility to pathogens of honey bees. We found that the exposure to imidacloprid resulted in an elevated mortality of honey bees and increased the susceptibility to infection by opportunistic pathogens. However, we did not find evidence that imidacloprid affects the gut microbiome of honey bees. We found some evidence that imidacloprid can be metabolized in the bee gut environment in vitro , but because it is quickly eliminated from the bee, it is unlikely that this metabolism occurs in nature. Thus, imidacloprid causes increased mortality in honey bees, but this does not appear to be linked to the microbiome.

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pH-Mediated Microbial and Metabolic Interactions in Fecal Enrichment Cultures

mSphere ◽

10.1128/msphere.00047-17 ◽

2017 ◽

Vol 2 (3) ◽

Cited By ~ 23

Author(s):

Zehra Esra Ilhan ◽

Andrew K. Marcus ◽

Dae-Wook Kang ◽

Bruce E. Rittmann ◽

Rosa Krajmalnik-Brown

Keyword(s):

Fatty Acids ◽

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Short Chain Fatty Acids ◽

Human Gut ◽

Fermentation Products ◽

Metabolic Products ◽

Metabolic Interactions

ABSTRACT The human gut is a dynamic environment in which microorganisms consistently interact with the host via their metabolic products. Some of the most important microbial metabolic products are fermentation products such as short-chain fatty acids. Production of these fermentation products and the prevalence of fermenting microbiota depend on pH, alkalinity, and available dietary sugars, but details about their metabolic interactions are unknown. Here, we show that, for in vitro conditions, pH was the strongest driver of microbial community structure and function and microbial and metabolic interactions among pH-sensitive fermentative species. The balance between bicarbonate alkalinity and formation of fatty acids by fermentation determined the pH, which controlled microbial community structure. Our results underscore the influence of pH balance on microbial function in diverse microbial ecosystems such as the human gut. pH and fermentable substrates impose selective pressures on gut microbial communities and their metabolisms. We evaluated the relative contributions of pH, alkalinity, and substrate on microbial community structure, metabolism, and functional interactions using triplicate batch cultures started from fecal slurry and incubated with an initial pH of 6.0, 6.5, or 6.9 and 10 mM glucose, fructose, or cellobiose as the carbon substrate. We analyzed 16S rRNA gene sequences and fermentation products. Microbial diversity was driven by both pH and substrate type. Due to insufficient alkalinity, a drop in pH from 6.0 to ~4.5 clustered pH 6.0 cultures together and distant from pH 6.5 and 6.9 cultures, which experienced only small pH drops. Cellobiose yielded more acidity than alkalinity due to the amount of fermentable carbon, which moved cellobiose pH 6.5 cultures away from other pH 6.5 cultures. The impact of pH on microbial community structure was reflected by fermentative metabolism. Lactate accumulation occurred in pH 6.0 cultures, whereas propionate and acetate accumulations were observed in pH 6.5 and 6.9 cultures and independently from the type of substrate provided. Finally, pH had an impact on the interactions between lactate-producing and -consuming communities. Lactate-producing Streptococcus dominated pH 6.0 cultures, and acetate- and propionate-producing Veillonella, Bacteroides, and Escherichia dominated the cultures started at pH 6.5 and 6.9. Acid inhibition on lactate-consuming species led to lactate accumulation. Our results provide insights into pH-derived changes in fermenting microbiota and metabolisms in the human gut. IMPORTANCE The human gut is a dynamic environment in which microorganisms consistently interact with the host via their metabolic products. Some of the most important microbial metabolic products are fermentation products such as short-chain fatty acids. Production of these fermentation products and the prevalence of fermenting microbiota depend on pH, alkalinity, and available dietary sugars, but details about their metabolic interactions are unknown. Here, we show that, for in vitro conditions, pH was the strongest driver of microbial community structure and function and microbial and metabolic interactions among pH-sensitive fermentative species. The balance between bicarbonate alkalinity and formation of fatty acids by fermentation determined the pH, which controlled microbial community structure. Our results underscore the influence of pH balance on microbial function in diverse microbial ecosystems such as the human gut.

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673. Novel Delayed-Release Formulation of an Oral β-Lactamase Prevents Gut Microbiome Damage and Attenuates Antibiotic Resistance Caused by Oral Amoxicillin/Clavulanate without Interfering with Amoxicillin Systemic Absorption in Dogs

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz360.741 ◽

2019 ◽

Vol 6 (Supplement_2) ◽

pp. S307-S307

Author(s):

Sheila Connelly ◽

Christian Furlan-Freguia ◽

Brian Fanelli ◽

Nur A Hasan ◽

Rita R Colwell ◽

...

Keyword(s):

Antibiotic Resistance ◽

Small Intestine ◽

Gut Microbiome ◽

Clinical Stage ◽

Serum Levels ◽

Systemic Absorption ◽

Release Formulation ◽

Microbiome Composition ◽

Delayed Release ◽

Oral Amoxicillin

Abstract Background Exposure of the gut microbiota to antibiotics can alter the composition of the microbiome and lead to the emergence and spread of antibiotic resistance. SYN-004 (ribaxamase) is a clinical-stage β-lactamase intended to degrade certain IV β-lactam antibiotics in the GI tract to preserve the gut microbiome. In a phase 2b clinical study, ribaxamase significantly reduced C. difficile infection in patients treated with IV ceftriaxone. A new delayed-release ribaxamase formulation, SYN-007, intended for use with oral β-lactams, was evaluated in dogs that received oral amoxicillin plus the β-lactamase inhibitor, clavulanate (amox/clav). Methods SYN-007 was engineered for release in the lower small intestine, distal to the site of antibiotic absorption. Dogs received amox/clav (40 mg/kg amox/5.7 mg/kg clav, PO, TID) +/- SYN-007 (10 mg, PO, TID) for 16 doses. Amoxicillin serum levels were measured by LC/MS/MS after the first and last doses. DNA, isolated from feces collected before and after antibiotic treatment, was analyzed by whole-genome shotgun sequencing using CosmosID, Inc. metagenomics software. Results Serum amoxicillin levels were not significantly different +/- SYN-007 after the first and last doses of amox/clav. Microbiome analyses revealed that amox/clav disrupted the gut microbiome resulting in loss of some species and overgrowth of other taxa. SYN-007 attenuated changes to gut microbiome composition. Amox/clav exposure resulted in the emergence of many, mainly TEM β-lactamase genes that was reduced with SYN-007. Conclusion Oral amox/clav disrupted the gut microbiome in dogs and resulted in the emergence of β-lactamase genes. SYN-007 diminished amox/clav-mediated microbiome disruption and attenuated emergence of β-lactamase genes. SYN-007 did not interfere with amox systemic absorption indicating that the β-lactamase was not released in the upper small intestine, the site of oral amoxicillin absorption. Antibiotic inactivation represents a potential new treatment paradigm for preservation of the gut microbiome and reduction of antibiotic resistance. SYN-007 has the potential to expand β-lactamase-mediated microbiome protection to oral as well as IV β-lactam antibiotics. Disclosures All authors: No reported disclosures.

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Differences in Gut Microbiome Composition Between Sympatric Wild and Allopatric Laboratory Populations of Omnivorous Cockroaches

Frontiers in Microbiology ◽

10.3389/fmicb.2021.703785 ◽

2021 ◽

Vol 12 ◽

Author(s):

Kara A. Tinker ◽

Elizabeth A. Ottesen

Keyword(s):

Microbial Community ◽

Gut Microbiome ◽

Periplaneta Americana ◽

Laboratory Environment ◽

Microbiome Composition ◽

Relative Contribution ◽

Microbiome Diversity ◽

Before And After ◽

Laboratory Populations ◽

Gut Microbial Community

Gut microbiome composition is determined by a complex interplay of host genetics, founder’s effects, and host environment. We are using omnivorous cockroaches as a model to disentangle the relative contribution of these factors. Cockroaches are a useful model for host–gut microbiome interactions due to their rich hindgut microbial community, omnivorous diet, and gregarious lifestyle. In this study, we used 16S rRNA sequencing to compare the gut microbial community of allopatric laboratory populations of Periplaneta americana as well as sympatric, wild-caught populations of P. americana and Periplaneta fuliginosa, before and after a 14 day period of acclimatization to a common laboratory environment. Our results showed that the gut microbiome of cockroaches differed by both species and rearing environment. The gut microbiome from the sympatric population of wild-captured cockroaches showed strong separation based on host species. Laboratory-reared and wild-captured cockroaches from the same species also exhibited distinct gut microbiome profiles. Each group of cockroaches had a unique signature of differentially abundant uncharacterized taxa still present after laboratory cultivation. Transition to the laboratory environment resulted in decreased microbiome diversity for both species of wild-caught insects. Interestingly, although laboratory cultivation resulted in similar losses of microbial diversity for both species, it did not cause the gut microbiome of those species to become substantially more similar. These results demonstrate how competing factors impact the gut microbiome and highlight the need for a greater understanding of host–microbiome interactions.

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Complementary Food Ingredients Alter Infant Gut Microbiome Composition and Metabolism In Vitro

Microorganisms ◽

10.3390/microorganisms9102089 ◽

2021 ◽

Vol 9 (10) ◽

pp. 2089

Author(s):

Shanthi G. Parkar ◽

Doug I. Rosendale ◽

Halina M. Stoklosinski ◽

Carel M. H. Jobsis ◽

Duncan I. Hedderley ◽

...

Keyword(s):

Gut Microbiome ◽

Milk Powder ◽

Free Water ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Water Control ◽

Food Ingredients ◽

Microbiome Composition ◽

Infant Gut Microbiome

We examined the prebiotic potential of 32 food ingredients on the developing infant microbiome using an in vitro gastroileal digestion and colonic fermentation model. There were significant changes in the concentrations of short-chain fatty-acid metabolites, confirming the potential of the tested ingredients to stimulate bacterial metabolism. The 16S rRNA gene sequencing for a subset of the ingredients revealed significant increases in the relative abundances of the lactate- and acetate-producing Bifidobacteriaceae, Enterococcaceae, and Lactobacillaceae, and lactate- and acetate-utilizing Prevotellaceae, Lachnospiraceae, and Veillonellaceae. Selective changes in specific bacterial groups were observed. Infant whole-milk powder and an oat flour enhanced Bifidobacteriaceae and lactic acid bacteria. A New Zealand-origin spinach powder enhanced Prevotellaceae and Lachnospiraceae, while fruit and vegetable powders increased a mixed consortium of beneficial gut microbiota. All food ingredients demonstrated a consistent decrease in Clostridium perfringens, with this organism being increased in the carbohydrate-free water control. While further studies are required, this study demonstrates that the selected food ingredients can modulate the infant gut microbiome composition and metabolism in vitro. This approach provides an opportunity to design nutrient-rich complementary foods that fulfil infants’ growth needs and support the maturation of the infant gut microbiome.

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