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20 pages, 5079 KiB

Open AccessArticle

A Synthetic Formula Amino Acid Diet Leads to Microbiome Dysbiosis, Reduced Colon Length, Inflammation, and Altered Locomotor Activity in C57BL/6J Mice

by Viviana J. Mancilla, Paige N. Braden-Kuhle, Kelly N. Brice, Allison E. Mann, Megan T. Williams, Yan Zhang, Michael J. Chumley, Robert C. Barber, Sabrina N. White, Gary W. Boehm and Michael S. Allen

Microorganisms 2023, 11(11), 2694; https://doi.org/10.3390/microorganisms11112694 - 3 Nov 2023

Viewed by 1579

Abstract

The effects of synthetic, free-amino acid diets, similar to those prescribed as supplements for (phenylketonuria) PKU patients, on gut microbiota and overall health are not well understood. In the current, multidisciplinary study, we examined the effects of a synthetically-derived, low-fiber, amino acid diet [...] Read more.

The effects of synthetic, free-amino acid diets, similar to those prescribed as supplements for (phenylketonuria) PKU patients, on gut microbiota and overall health are not well understood. In the current, multidisciplinary study, we examined the effects of a synthetically-derived, low-fiber, amino acid diet on behavior, cognition, gut microbiome composition, and inflammatory markers. A cohort of 20 male C57BL/6J mice were randomly assigned to either a standard or synthetic diet (n = 10) at post-natal day 21 and maintained for 13 weeks. Sequencing of the 16S rRNA gene from fecal samples revealed decreased bacterial diversity, increased abundance of bacteria associated with disease, such as Prevotella, and a downward shift in gut microbiota associated with fermentation pathways in the synthetic diet group. Furthermore, there were decreased levels of short chain fatty acids and shortening of the colon in mice consuming the synthetic diet. Finally, we measured TNF-α, IL-6, and IL-10 in serum, the hippocampus, and colon, and found that the synthetic diet significantly increased IL-6 production in the hippocampus. These results demonstrate the importance of a multidisciplinary approach to future diet and microbiome studies, as diet not only impacts the gut microbiome composition but potentially systemic health as well. Full article

(This article belongs to the Special Issue Lifestyle, Gut Microbiota and Health)

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23 pages, 6096 KiB

Open AccessArticle

Gut Microbiome and Lipidome Signatures in Irritable Bowel Syndrome Patients from a Low-Income, Food-Desert Area: A Pilot Study

by Nikita Paripati, Lauren Nesi, John D. Sterrett, Lamya’a M. Dawud, Lyanna R. Kessler, Christopher A. Lowry, Lark J. Perez, Joshua DeSipio and Sangita Phadtare

Microorganisms 2023, 11(10), 2503; https://doi.org/10.3390/microorganisms11102503 - 6 Oct 2023

Cited by 1 | Viewed by 1916

Abstract

Irritable bowel syndrome (IBS) is a common gastroenterological disorder with triggers such as fructose. We showed that our IBS patients suffering from socioeconomic challenges have a significantly high consumption of high-fructose corn syrup (HFCS). Here, we characterize gut microbial dysbiosis and fatty acid [...] Read more.

Irritable bowel syndrome (IBS) is a common gastroenterological disorder with triggers such as fructose. We showed that our IBS patients suffering from socioeconomic challenges have a significantly high consumption of high-fructose corn syrup (HFCS). Here, we characterize gut microbial dysbiosis and fatty acid changes, with respect to IBS, HFCS consumption, and socioeconomic factors. Fecal samples from IBS patients and healthy controls were subjected to microbiome and lipidome analyses. We assessed phylogenetic diversity and community composition of the microbiomes, and used linear discriminant analysis effect size (LEfSe), analysis of compositions of microbiomes (ANCOM) on highly co-occurring subcommunities (modules), least absolute shrinkage and selection operator (LASSO) on phylogenetic isometric log-ratio transformed (PhILR) taxon abundances to identify differentially abundant taxa. Based on a Procrustes randomization test, the microbiome and lipidome datasets correlated significantly (p = 0.002). Alpha diversity correlated with economic factors (p < 0.001). Multiple subsets of the phylogenetic tree were associated with HFCS consumption (p < 0.001). In IBS patients, relative abundances of potentially beneficial bacteria such as Monoglobaceae, Lachnospiraceae, and Ruminococcaceae were lower (p = 0.007), and Eisenbergiella, associated with inflammatory disorders, was higher. In IBS patients, certain saturated fatty acids were higher and unsaturated fatty acids were lower (p < 0.05). Our study aims first to underscore the influence of HFCS consumption and socioeconomic factors on IBS pathophysiology, and provides new insights that inform patient care. Full article

(This article belongs to the Special Issue Lifestyle, Gut Microbiota and Health)

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19 pages, 2548 KiB

Open AccessEditor’s ChoiceArticle

Gut Dysbiosis: A Target for Protective Interventions against Parkinson’s Disease

by Illyane S. Lima, Ana C. Pêgo, Ana C. Martins, Ana R. Prada, João Tomás Barros, Gracelino Martins and Raffaella Gozzelino

Microorganisms 2023, 11(4), 880; https://doi.org/10.3390/microorganisms11040880 - 29 Mar 2023

Cited by 7 | Viewed by 2857

Abstract

Sub-chronic inflammation, caused by age-related dysbiosis, primes the brain to neuroinflammation and neurodegenerative diseases. Evidence revealed that Parkinson’s disease (PD) might originate in the gut, demonstrating gastro-intestinal disturbances, as reported by PD patients long before developing motor symptoms. In this study, we conducted [...] Read more.

Sub-chronic inflammation, caused by age-related dysbiosis, primes the brain to neuroinflammation and neurodegenerative diseases. Evidence revealed that Parkinson’s disease (PD) might originate in the gut, demonstrating gastro-intestinal disturbances, as reported by PD patients long before developing motor symptoms. In this study, we conducted comparative analyses in relatively young and old mice maintained in conventional or gnotobiotic conditions. We aimed to confirm that the effects induced by age-related dysbiosis, rather than aging itself, sensitize to PD onset. This hypothesis was confirmed in germ-free (GF) mice, which proved resistant to the pharmacological induction of PD, regardless of their age. Contrary to conventional animals, old GF mice did not develop an inflammatory phenotype or an accumulation of iron in the brain, two catalysts sensitizing to disease onset. The resistance of GF mice to PD is reverted when colonized with stool collected from conventional old animals, but not if receiving bacterial content from young mice. Hence, changes in gut microbiota composition are a risk factor for PD development and can be targeted preventively by iron chelators, shown to protect the brain from pro-inflammatory intestinal priming that sensitizes to neuroinflammation and the development of severe PD. Full article

(This article belongs to the Special Issue Lifestyle, Gut Microbiota and Health)

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14 pages, 1922 KiB

Open AccessArticle

Dietary Microencapsulated Blend of Organic Acids and Plant Essential Oils Affects Intestinal Morphology and Microbiome of Rainbow Trout (Oncorhynchus mykiss)

by David Huyben, Marcia Chiasson, John S. Lumsden, Phuc H. Pham and Mohiuddin A. Kabir Chowdhury

Microorganisms 2021, 9(10), 2063; https://doi.org/10.3390/microorganisms9102063 - 30 Sep 2021

Cited by 19 | Viewed by 3384

Abstract

A study was conducted on 500 juvenile rainbow trout (122 ± 4 g) fed either a control diet or a treatment diet containing 300 mg/kg of a microencapsulated blend of organic acids and essential oils to elucidate effects on intestinal morphology and microbiome. [...] Read more.

A study was conducted on 500 juvenile rainbow trout (122 ± 4 g) fed either a control diet or a treatment diet containing 300 mg/kg of a microencapsulated blend of organic acids and essential oils to elucidate effects on intestinal morphology and microbiome. Proximal intestinal villi length was significantly increased in fish fed the treatment diet. Despite no differences in gut inflammation scores, edema, lamina propria inflammation and apoptosis were completely absent in the distal intestine of fish fed the treatment diet. Next-generation sequencing of the 16S rDNA showed no differences in alpha and beta diversity, and gut bacteria were mainly composed of Firmicutes, Bacteroidetes and Proteobacteria. On the genus level, LefSe analysis of indicator OTUs showed Bacteroides, Sporosarcina, Veillonella, Aeromonas and Acinetobacter were associated with the control diet whereas Streptococcus, Fusobacterium and Escherichia were associated with the treatment diet. Aeromonas hydrophila and Acinetobacter spp. are opportunistic pathogens and several strains have been found to be resistant to antibiotics. The increase in villi length and reduction of specific pathogens indicates that feeding a microencapsulated blend of organic acids and essential oils improves gut health and may serve as a part of an effective strategy to reduce antibiotic use in aquaculture. Full article

(This article belongs to the Special Issue Lifestyle, Gut Microbiota and Health)

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15 pages, 2485 KiB

Open AccessArticle

Degradation Products of Complex Arabinoxylans by Bacteroides intestinalis Enhance the Host Immune Response

by Taro Yasuma, Masaaki Toda, Ahmed M. Abdel-Hamid, Corina D’Alessandro-Gabazza, Tetsu Kobayashi, Kota Nishihama, Valeria Fridman D’Alessandro, Gabriel V. Pereira, Roderick I. Mackie, Esteban C. Gabazza and Isaac Cann

Microorganisms 2021, 9(6), 1126; https://doi.org/10.3390/microorganisms9061126 - 22 May 2021

Cited by 23 | Viewed by 3656

Abstract

Bacteroides spp. of the human colonic microbiome degrade complex arabinoxylans from dietary fiber and release ferulic acid. Several studies have demonstrated the beneficial effects of ferulic acid. Here, we hypothesized that ferulic acid or the ferulic acid-rich culture supernatant of Bacteroides intestinalis, [...] Read more.

Bacteroides spp. of the human colonic microbiome degrade complex arabinoxylans from dietary fiber and release ferulic acid. Several studies have demonstrated the beneficial effects of ferulic acid. Here, we hypothesized that ferulic acid or the ferulic acid-rich culture supernatant of Bacteroides intestinalis, cultured in the presence of complex arabinoxylans, enhances the immune response. Ferulic acid and the culture supernatant of bacteria cultured in the presence of insoluble arabinoxylans significantly decreased the expression of tumor necrosis factor-α and increased the expression of interleukin-10 and transforming growth factor β1 from activated dendritic cells compared to controls. The number of granulocytes in mesenteric lymph nodes, the number of spleen monocytes/granulocytes, and interleukin-2 and interleukin-12 plasma levels were significantly increased in mice treated with ferulic acid or the culture supernatant of bacteria cultured with insoluble arabinoxylans. Ferulic acid or the culture supernatant of bacteria cultured with insoluble arabinoxylans increased the expression of interleukin-12, interferon-α, and interferon-β in intestinal epithelial cell lines. This study shows that ferulic acid or the ferulic acid-rich culture supernatant of the colonic bacterium Bacteroides intestinalis, cultured with insoluble arabinoxylans, exerts anti-inflammatory activity in dendritic cells under inflammatory conditions and enhances the Th1-type immune response under physiological conditions in mice. Full article

(This article belongs to the Special Issue Lifestyle, Gut Microbiota and Health)

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19 pages, 5225 KiB

Open AccessArticle

Gut Microbiome of Indonesian Adults Associated with Obesity and Type 2 Diabetes: A Cross-Sectional Study in an Asian City, Yogyakarta

by Phatthanaphong Therdtatha, Yayi Song, Masaru Tanaka, Mariyatun Mariyatun, Maisaroh Almunifah, Nancy Eka Putri Manurung, Siska Indriarsih, Yi Lu, Koji Nagata, Katsuya Fukami, Tetsuo Ikeda, Yuan-Kun Lee, Endang Sutriswati Rahayu and Jiro Nakayama

Microorganisms 2021, 9(5), 897; https://doi.org/10.3390/microorganisms9050897 - 22 Apr 2021

Cited by 25 | Viewed by 5987

Abstract

Indonesia is a developing country facing the national problem of the growing obesity and diabetes in its population due to recent drastic dietary and lifestyle changes. To understand the link between the gut microbiome, diet, and health of Indonesian people, fecal microbiomes and [...] Read more.

Indonesia is a developing country facing the national problem of the growing obesity and diabetes in its population due to recent drastic dietary and lifestyle changes. To understand the link between the gut microbiome, diet, and health of Indonesian people, fecal microbiomes and metabolomes of 75 Indonesian adults in Yogyakarta City, including obese people (n = 21), type 2 diabetes (T2D) patients (n = 25), and the controls (n = 29) were characterized together with their dietary and medical records. Variations of microbiomes showed a triangular distribution in the principal component analysis, driven by three dominant bacterial genera, namely Bacteroides, Prevotella, and Romboutsia. The Romboutsia-driven microbiome, characterized by low bacterial diversity and high primary bile acids, was associated with fat-driven obesity. The Bacteroides-driven microbiome, which counteracted Prevotella but was associated with Ruminococcaceae concomitantly increased with high-carbohydrate diets, showed positive correlation with T2D indices but negative correlation with body mass index. Notably, Bacteroides fragilis was increased in T2D patients with a decrease in fecal conjugated bile acids, particularly tauroursodeoxycholic acid (TUDCA), a farnesoid X receptor (FXR) antagonist with anti-diabetic activity, while these features disappeared in patients administered metformin. These results indicate that the gut microbiome status of Indonesian adults is differently associated with obesity and T2D under their varied dietary habits. Full article

(This article belongs to the Special Issue Lifestyle, Gut Microbiota and Health)

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Review

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15 pages, 1446 KiB

Open AccessReview

Intestinal Alkaline Phosphatase: A Review of This Enzyme Role in the Intestinal Barrier Function

by Gilberto Maia Santos, Shámila Ismael, Juliana Morais, João R. Araújo, Ana Faria, Conceição Calhau and Cláudia Marques

Microorganisms 2022, 10(4), 746; https://doi.org/10.3390/microorganisms10040746 - 30 Mar 2022

Cited by 28 | Viewed by 8252

Abstract

Intestinal alkaline phosphatase (IALP) has recently assumed a special relevance, being the subject of study in the prevention and treatment of certain diseases related to leaky gut. This brush border enzyme (ecto-enzyme) plays an important role in the maintenance of intestinal microbial homeostasis [...] Read more.

Intestinal alkaline phosphatase (IALP) has recently assumed a special relevance, being the subject of study in the prevention and treatment of certain diseases related to leaky gut. This brush border enzyme (ecto-enzyme) plays an important role in the maintenance of intestinal microbial homeostasis and intestinal barrier function through its ability to dephosphorylate lipopolysaccharide (LPS). This review addresses how IALP and intestinal barrier dysfunction may be implicated in the pathophysiology of specific diseases such as inflammatory bowel disease, necrotizing enterocolitis, and metabolic syndrome. The use of IALP as a possible biomarker to assess intestinal barrier function and strategies to modulate IALP activity are also discussed. Full article

(This article belongs to the Special Issue Lifestyle, Gut Microbiota and Health)

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22 pages, 356 KiB

Open AccessReview

Biliary Diseases from the Microbiome Perspective: How Microorganisms Could Change the Approach to Benign and Malignant Diseases

by Cecilia Binda, Giulia Gibiino, Chiara Coluccio, Monica Sbrancia, Elton Dajti, Emanuele Sinagra, Gabriele Capurso, Vittorio Sambri, Alessandro Cucchetti, Giorgio Ercolani and Carlo Fabbri

Microorganisms 2022, 10(2), 312; https://doi.org/10.3390/microorganisms10020312 - 28 Jan 2022

Cited by 21 | Viewed by 4346

Abstract

Recent evidence regarding microbiota is modifying the cornerstones on pathogenesis and the approaches to several gastrointestinal diseases, including biliary diseases. The burden of biliary diseases, indeed, is progressively increasing, considering that gallstone disease affects up to 20% of the European population. At the [...] Read more.

Recent evidence regarding microbiota is modifying the cornerstones on pathogenesis and the approaches to several gastrointestinal diseases, including biliary diseases. The burden of biliary diseases, indeed, is progressively increasing, considering that gallstone disease affects up to 20% of the European population. At the same time, neoplasms of the biliary system have an increasing incidence and poor prognosis. Framing the specific state of biliary eubiosis or dysbiosis is made difficult by the use of heterogeneous techniques and the sometimes unwarranted invasive sampling in healthy subjects. The influence of the microbial balance on the health status of the biliary tract could also account for some of the complications surrounding the post-liver-transplant phase. The aim of this extensive narrative review is to summarize the current evidence on this topic, to highlight gaps in the available evidence in order to guide further clinical research in these settings, and, eventually, to provide new tools to treat biliary lithiasis, biliopancreatic cancers, and even cholestatic disease. Full article

(This article belongs to the Special Issue Lifestyle, Gut Microbiota and Health)

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