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Barker-Tejeda TC, Zubeldia-Varela E, Macías-Camero A, Alonso L, Martín-Antoniano IA, Rey-Stolle MF, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Shanmuganathan M, Britz-McKibbin P, Ubeda C, Francino MP, Barber D, Ibáñez-Sandín MD, Barbas C, Pérez-Gordo M, Villaseñor A. Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach. Nat Commun 2024; 15:3004. [PMID: 38589361 PMCID: PMC11001937 DOI: 10.1038/s41467-024-47182-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024] Open
Abstract
The human gut microbiome establishes and matures during infancy, and dysregulation at this stage may lead to pathologies later in life. We conducted a multi-omics study comprising three generations of family members to investigate the early development of the gut microbiota. Fecal samples from 200 individuals, including infants (0-12 months old; 55% females, 45% males) and their respective mothers and grandmothers, were analyzed using two independent metabolomics platforms and metagenomics. For metabolomics, gas chromatography and capillary electrophoresis coupled to mass spectrometry were applied. For metagenomics, both 16S rRNA gene and shotgun sequencing were performed. Here we show that infants greatly vary from their elders in fecal microbiota populations, function, and metabolome. Infants have a less diverse microbiota than adults and present differences in several metabolite classes, such as short- and branched-chain fatty acids, which are associated with shifts in bacterial populations. These findings provide innovative biochemical insights into the shaping of the gut microbiome within the same generational line that could be beneficial in improving childhood health outcomes.
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Affiliation(s)
- Tomás Clive Barker-Tejeda
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Elisa Zubeldia-Varela
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Andrea Macías-Camero
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Lola Alonso
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Isabel Adoración Martín-Antoniano
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Instituto de Estudios de las Adicciones IEA-CEU, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - María Fernanda Rey-Stolle
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Leticia Mera-Berriatua
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Raphaëlle Bazire
- Department of Allergy, Hospital Infantil Niño Jesús, Fib-HNJ, Madrid, Spain
- Instituto de Investigación Sanitaria-La Princesa, Madrid, Spain
| | - Paula Cabrera-Freitag
- Pedriatic Allergy Unit, Allergy Service, Hospital General Universitario Gregorio Marañón, and Gregorio Marañón Health Research Institute, Madrid, Spain
| | - Meera Shanmuganathan
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Philip Britz-McKibbin
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Carles Ubeda
- Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO), Valencia, Spain
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
| | - M Pilar Francino
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
- Joint Research Unit in Genomics and Health, Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO) and Institut de Biologia Integrativa de Sistemes (Universitat de València / Consejo Superior de Investigaciones Científicas), València, Spain
| | - Domingo Barber
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - María Dolores Ibáñez-Sandín
- Department of Allergy, Hospital Infantil Niño Jesús, Fib-HNJ, Madrid, Spain
- Instituto de Investigación Sanitaria-La Princesa, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Marina Pérez-Gordo
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain.
| | - Alma Villaseñor
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain.
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain.
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Correia BSB, Sandby K, Krarup T, Magkos F, Geiker NRW, Bertram HC. Changes in Plasma, Urine, and Fecal Metabolome after 16 Weeks of Consuming Dairy With Different Food Matrixes - A Randomized Controlled Trial. Mol Nutr Food Res 2024; 68:e2300363. [PMID: 38299443 DOI: 10.1002/mnfr.202300363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 01/03/2024] [Indexed: 02/02/2024]
Abstract
SCOPE Understanding the mode-of-action by which fermented dairy consumption influences health is of interest. The aim of this study is to elucidate the impact of the chemical-physical properties of the dairy matrix and postbiotic effects on the metabolomics response to fermented dairy consumption. METHODS AND RESULTS Hundred males (Body Mass Index (BMI) 28.0-45.0 kg m-2, waist circumference ≥ 102 cm) are included in the study. During a 16-week intervention, the study subjects are instructed to consume 400 g per day of either 1) milk, 2) yogurt, 3) heat-treated yogurt, or 4) chemically acidified milk as part of their habitual diet. Nuclear Magnetic Resonance (NMR)-based metabolomics is conducted on plasma, urine, and fecal samples collected before and after the intervention. Both consumption of acidified milk and heat-treated yogurt resulted in changes in the fecal metabolome including decreases in the level of amino acids (leucine, valine, and threonine), and the branched-chain fatty acid (BCFA) isobutyrate that indicated an altered protein putrefaction, and proteolytic metabolism in the gut. In the plasma metabolome, an increased citrate is found for yogurt consumption. No difference in the urine metabolome is found. CONCLUSIONS Our metabolomics analyses indicate that consumption of heat-treated yogurt and acidified milk exerted similar effects on the metabolic activity in the gut as yogurt consumption.
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Affiliation(s)
- Banny S B Correia
- Department of Food Science, Aarhus University, Aarhus, Midtjylland, 8200, Denmark
| | - Karoline Sandby
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, 1958, Denmark
| | - Thure Krarup
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, 1958, Denmark
- Department of Endocrinology, Copenhagen University Hospital Bispebjerg, Copenhagen, 2400, Denmark
| | - Faidon Magkos
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, 1958, Denmark
| | - Nina R W Geiker
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, 1958, Denmark
- Center for Childhood Health, Copenhagen, 2300, Denmark
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Sisk-Hackworth L, Brown J, Sau L, Levine AA, Tam LYI, Ramesh A, Shah RS, Kelley-Thackray ET, Wang S, Nguyen A, Kelley ST, Thackray VG. Genetic hypogonadal mouse model reveals niche-specific influence of reproductive axis and sex on intestinal microbial communities. Biol Sex Differ 2023; 14:79. [PMID: 37932822 PMCID: PMC10626657 DOI: 10.1186/s13293-023-00564-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The gut microbiome has been linked to many diseases with sex bias including autoimmune, metabolic, neurological, and reproductive disorders. While numerous studies report sex differences in fecal microbial communities, the role of the reproductive axis in this differentiation is unclear and it is unknown how sex differentiation affects microbial diversity in specific regions of the small and large intestine. METHODS We used a genetic hypogonadal mouse model that does not produce sex steroids or go through puberty to investigate how sex and the reproductive axis impact bacterial diversity within the intestine. Using 16S rRNA gene sequencing, we analyzed alpha and beta diversity and taxonomic composition of fecal and intestinal communities from the lumen and mucosa of the duodenum, ileum, and cecum from adult female (n = 20) and male (n = 20) wild-type mice and female (n = 17) and male (n = 20) hypogonadal mice. RESULTS Both sex and reproductive axis inactivation altered bacterial composition in an intestinal section and niche-specific manner. Hypogonadism was significantly associated with bacteria from the Bacteroidaceae, Eggerthellaceae, Muribaculaceae, and Rikenellaceae families, which have genes for bile acid metabolism and mucin degradation. Microbial balances between males and females and between hypogonadal and wild-type mice were also intestinal section-specific. In addition, we identified 3 bacterial genera (Escherichia Shigella, Lachnoclostridium, and Eggerthellaceae genus) with higher abundance in wild-type female mice throughout the intestinal tract compared to both wild-type male and hypogonadal female mice, indicating that activation of the reproductive axis leads to female-specific differentiation of the gut microbiome. Our results also implicated factors independent of the reproductive axis (i.e., sex chromosomes) in shaping sex differences in intestinal communities. Additionally, our detailed profile of intestinal communities showed that fecal samples do not reflect bacterial diversity in the small intestine. CONCLUSIONS Our results indicate that sex differences in the gut microbiome are intestinal niche-specific and that sampling feces or the large intestine may miss significant sex effects in the small intestine. These results strongly support the need to consider both sex and reproductive status when studying the gut microbiome and while developing microbial-based therapies.
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Affiliation(s)
- Laura Sisk-Hackworth
- University of California San Diego, La Jolla, CA, USA
- San Diego State University, San Diego, CA, USA
| | - Jada Brown
- University of California San Diego, La Jolla, CA, USA
| | - Lillian Sau
- University of California San Diego, La Jolla, CA, USA
| | | | | | | | - Reeya S Shah
- University of California San Diego, La Jolla, CA, USA
| | | | - Sophia Wang
- University of California San Diego, La Jolla, CA, USA
| | - Anita Nguyen
- University of California San Diego, La Jolla, CA, USA
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Kim SY, Shin SY, Park SJ, Im JP, Kim HJ, Lee KM, Kim JW, Jung SA, Lee J, Kang SB, Shin SJ, Kim ES, Kim YS, Kim TO, Kim HS, Park DI, Kim HK, Kim ES, Kim YH, Teng D, Kim JH, Kim W, Saeed M, Moon JM, Kim K, Choi CH, Choi HK. Changes in fecal metabolic and lipidomic features by anti-TNF treatment and prediction of clinical remission in patients with ulcerative colitis. Therap Adv Gastroenterol 2023; 16:17562848231168199. [PMID: 37153496 PMCID: PMC10161336 DOI: 10.1177/17562848231168199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 03/21/2023] [Indexed: 05/09/2023] Open
Abstract
Background Therapeutic targets for ulcerative colitis (UC) and prediction models of antitumor necrosis factor (TNF) therapy outcomes have not been fully reported. Objective Investigate the characteristic metabolite and lipid profiles of fecal samples of UC patients before and after adalimumab treatment and develop a prediction model of clinical remission following adalimumab treatment. Design Prospective, observational, multicenter study was conducted on moderate-to-severe UC patients (n = 116). Methods Fecal samples were collected from UC patients at 8 and 56 weeks of adalimumab treatment and from healthy controls (HC, n = 37). Clinical remission was assessed using the Mayo score. Metabolomic and lipidomic analyses were performed using gas chromatography mass spectrometry and nano electrospray ionization mass spectrometry, respectively. Orthogonal partial least squares discriminant analysis was performed to establish a remission prediction model. Results Fecal metabolites in UC patients markedly differed from those in HC at baseline and were changed similarly to those in HC during treatment; however, lipid profiles did not show these patterns. After treatment, the fecal characteristics of remitters (RM) were closer to those of HC than to those of non-remitters (NRM). At 8 and 56 weeks, amino acid levels in RM were lower than those in NRM and similar to those in HC. After 56 weeks, levels of 3-hydroxybutyrate, lysine, and phenethylamine decreased, and dodecanoate level increased in RM similarly to those in HC. The prediction model of long-term remission in male patients based on lipid biomarkers showed a higher performance than clinical markers. Conclusion Fecal metabolites in UC patients markedly differ from those in HC, and the levels in RM are changed similarly to those in HC after anti-TNF therapy. Moreover, 3-hydroxybutyrate, lysine, phenethylamine, and dodecanoate are suggested as potential therapeutic targets for UC. A prediction model of long-term remission based on lipid biomarkers may help implement personalized treatment.
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Affiliation(s)
- Seok-Young Kim
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Seung Yong Shin
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Soo Jung Park
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, South Korea
| | - Jong Pil Im
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyo Jong Kim
- Department of Gastroenterology, Kyung Hee University Hospital, Seoul, South Korea
| | - Kang-Moon Lee
- Department of Gastroenterology, The Catholic University of Korea St. Vincent’s Hospital, Suwon, South Korea
| | - Ji Won Kim
- Department of Gastroenterology, SMG-SNU Boramae Medical Center, Seoul, South Korea
| | - Sung-Ae Jung
- Department of Gastroenterology, Ewha Woman’s University College of Medicine, Seoul, South Korea
| | - Jun Lee
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, South Korea
| | - Sang-Bum Kang
- Department of Gastroenterology, The Catholic University of Korea Daejeon St. Mary’s Hospital, Daejeon, South Korea
| | - Sung Jae Shin
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, South Korea
| | - Eun Sun Kim
- Department of Gastroenterology, Korea University Anam Hospital, Seoul, South Korea
| | - You Sun Kim
- Department of Gastroenterology, Inje University Seoul Paik Hospital, Seoul, South Korea
| | - Tae Oh Kim
- Department of Gastroenterology, Inje University Haeundae Paik Hospital, Busan, South Korea
| | - Hyun-Soo Kim
- Department of Gastroenterology, Chonnam National University Hospital, Gwangju, South Korea
| | - Dong Il Park
- Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University, Seoul, South Korea
| | - Hyung Kil Kim
- Department of Gastroenterology, Inha University Hospital, Incheon, South Korea
| | - Eun Soo Kim
- Department of Internal Medicine, Kyungpook National University, School of Medicine, Daegu, South Korea
| | - Young-Ho Kim
- Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | | | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University, College of Medicine, Seoul, South Korea
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University, College of Medicine, Seoul, South Korea
| | - Maham Saeed
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Jung Min Moon
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Kisung Kim
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Chang Hwan Choi
- Professor of Medicine, Internal Medicine, Chung-Ang University College of Medicine, 102 Heukseok-ro, Dongjak-gu, Seoul 06973, Republic of Korea
| | - Hyung-Kyoon Choi
- Professor of College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
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Igudesman D, Crandell J, Corbin KD, Zaharieva DP, Addala A, Thomas JM, Bulik CM, Pence BW, Pratley RE, Kosorok MR, Maahs DM, Carroll IM, Mayer-Davis EJ. Associations of disordered eating with the intestinal microbiota and short-chain fatty acids among young adults with type 1 diabetes. Nutr Metab Cardiovasc Dis 2023; 33:388-398. [PMID: 36586772 PMCID: PMC9925402 DOI: 10.1016/j.numecd.2022.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 11/05/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND AND AIMS Disordered eating (DE) in type 1 diabetes (T1D) includes insulin restriction for weight loss with serious complications. Gut microbiota-derived short chain fatty acids (SCFA) may benefit host metabolism but are reduced in T1D. We evaluated the hypothesis that DE and insulin restriction were associated with reduced SCFA-producing gut microbes, SCFA, and intestinal microbial diversity in adults with T1D. METHODS AND RESULTS We collected stool samples at four timepoints in a hypothesis-generating gut microbiome pilot study ancillary to a weight management pilot in young adults with T1D. 16S ribosomal RNA gene sequencing measured the normalized abundance of SCFA-producing intestinal microbes. Gas-chromatography mass-spectrometry measured SCFA (total, acetate, butyrate, and propionate). The Diabetes Eating Problem Survey-Revised (DEPS-R) assessed DE and insulin restriction. Covariate-adjusted and Bonferroni-corrected generalized estimating equations modeled the associations. COVID-19 interrupted data collection, so models were repeated restricted to pre-COVID-19 data. Data were available for 45 participants at 109 visits, which included 42 participants at 65 visits pre-COVID-19. Participants reported restricting insulin "At least sometimes" at 53.3% of visits. Pre-COVID-19, each 5-point DEPS-R increase was associated with a -0.34 (95% CI -0.56, -0.13, p = 0.07) lower normalized abundance of genus Anaerostipes; and the normalized abundance of Lachnospira genus was -0.94 (95% CI -1.5, -0.42), p = 0.02 lower when insulin restriction was reported "At least sometimes" compared to "Rarely or Never". CONCLUSION DE and insulin restriction were associated with a reduced abundance of SCFA-producing gut microbes pre-COVID-19. Additional studies are needed to confirm these associations to inform microbiota-based therapies in T1D.
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Affiliation(s)
- Daria Igudesman
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA; AdventHealth Translational Research Institute, Orlando, 32804, USA.
| | - Jamie Crandell
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA
| | - Karen D Corbin
- AdventHealth Translational Research Institute, Orlando, 32804, USA
| | - Dessi P Zaharieva
- Department of Pediatrics, Division of Endocrinology, Stanford University, Stanford, 94304, USA
| | - Ananta Addala
- Department of Pediatrics, Division of Endocrinology, Stanford University, Stanford, 94304, USA
| | - Joan M Thomas
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA
| | - Cynthia M Bulik
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA; Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, USA; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Brian W Pence
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA
| | | | - Michael R Kosorok
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA
| | - David M Maahs
- Department of Pediatrics, Division of Endocrinology, Stanford University, Stanford, 94304, USA
| | - Ian M Carroll
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA
| | - Elizabeth J Mayer-Davis
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA
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Hussain A, Patwekar U, Mongad DS, Shouche YS. Strategizing the human microbiome for small molecules: Approaches and perspectives. Drug Discov Today 2023; 28:103459. [PMID: 36435302 DOI: 10.1016/j.drudis.2022.103459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 11/03/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022]
Abstract
Studies of the human microbiome are providing a deeper understanding of its significance to human health, and increasing evidence links the microbiota with several diseases. Nevertheless, the exact mechanisms involved in human-microbe interactions are mostly undefined. The genomic potential of the human microbiome to biosynthesize distinct molecules outmatches its known chemical space, and small-molecule discovery in this context remains in its infancy. The profiling of microbiome-derived small molecules and their contextualization through cause-effect mechanistic studies may provide a better understanding of host-microbe interactions, guide new therapeutic interventions, and modulate microbiome-based therapies. This review describes the advances, approaches, and allied challenges in mining new microbial scaffolds from the human microbiome using genomic, microbe cultivation, and chemical analytic platforms. In the future, the complete biological characterization of a single microbe-derived molecule that has a specific therapeutic application could resolve the current limitations of microbiota-modulating therapies.
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Affiliation(s)
- Aehtesham Hussain
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India.
| | - Umera Patwekar
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India
| | - Dattatray S Mongad
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India
| | - Yogesh S Shouche
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India
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Sisk-Hackworth L, Kelley ST, Thackray VG. Sex, puberty, and the gut microbiome. Reproduction 2023; 165:R61-R74. [PMID: 36445259 PMCID: PMC9847487 DOI: 10.1530/rep-22-0303] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/28/2022] [Indexed: 11/30/2022]
Abstract
In brief Sex differences in the gut microbiome may impact multiple aspects of human health and disease. In this study, we review the evidence for microbial sex differences in puberty and adulthood and discuss potential mechanisms driving differentiation of the sex-specific gut microbiome. Abstract In humans, the gut microbiome is strongly implicated in numerous sex-specific physiological processes and diseases. Given this, it is important to understand how sex differentiation of the gut microbiome occurs and how these differences contribute to host health and disease. While it is commonly believed that the gut microbiome stabilizes after 3 years of age, our review of the literature found considerable evidence that the gut microbiome continues to mature during and after puberty in a sex-dependent manner. We also review the intriguing, though sparse, literature on potential mechanisms by which host sex may influence the gut microbiome, and vice versa, via sex steroids, bile acids, and the immune system. We conclude that the evidence for the existence of a sex-specific gut microbiome is strong but that there is a dearth of research on how host-microbe interactions lead to this differentiation. Finally, we discuss the types of future studies needed to understand the processes driving the maturation of sex-specific microbial communities and the interplay between gut microbiota, host sex, and human health.
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Affiliation(s)
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, California 92182
| | - Varykina G. Thackray
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California 92093
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Kono G, Yoshida K, Kokubo E, Ikeda M, Matsubara T, Koyama T, Iwamoto H, Miyaji K. Fermentation Supernatant of Elderly Feces with Inulin and Partially Hydrolyzed Guar Gum Maintains the Barrier of Inflammation-Induced Caco-2/HT29-MTX-E12 Co-Cultured Cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:1510-1517. [PMID: 36622307 PMCID: PMC9880993 DOI: 10.1021/acs.jafc.2c06232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/22/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Intestinal barrier function declines with aging. We evaluated the effect of dietary fibers and indigestible oligosaccharides on intestinal barrier function by altering the microbiota of the elderly. The feces were anaerobically cultured with indigestible dextrin, inulin, partially hydrolyzed guar gum (PHGG), lactulose, raffinose, or alginate, and the fermented supernatant was added to inflammation-induced Caco-2/HT29-MTX-E12 co-cultured cells. Our data showed that inulin- and PHGG-derived supernatants exerted a protective effect on the intestinal barrier. The protective effect was significantly positively correlated with total short-chain fatty acids (SCFAs) and butyric acid production in the supernatant and negatively correlated with the claudin-2 (CLDN2) gene expression in the cultured cells. Furthermore, we showed that the CLDN2 levels are regulated by butyric acid. Thus, inulin and PHGG can change the intestinal environment of the elderly and maintain the intestinal barrier by accelerating the production of SCFAs and modifying the expression levels of barrier function-related genes.
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Lower plasma concentrations of short-chain fatty acids (SCFAs) in patients with ADHD. J Psychiatr Res 2022; 156:36-43. [PMID: 36228390 DOI: 10.1016/j.jpsychires.2022.09.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/21/2022] [Accepted: 09/23/2022] [Indexed: 01/20/2023]
Abstract
Short-chain fatty acids (SCFAs), produced during bacterial fermentation, have been shown to be mediators in the microbiota-gut-brain axis. This axis has been proposed to influence psychiatric symptoms seen in attention deficit hyperactivity disorder (ADHD). However, there is no report of plasma SCFA concentrations in ADHD. The aim of this study was to explore the plasma concentrations of SCFAs in children and adults with ADHD and the possible factors that could influence those levels. We collected data on age group, sex, serum vitamin D levels, delivery mode, body mass index, diet, medication and blood samples from 233 ADHD patients and 36 family-related healthy controls. The concentrations of SCFAs and the intermediary metabolite succinic acid, were measured using liquid chromatography-mass spectrometry. Adults with ADHD had lower plasma concentrations of formic, acetic, propionic and succinic acid than their healthy family members. When adjusting for SCFA-influential factors among those with ADHD, children had lower concentrations of formic, propionic and isovaleric acid than adults, and those who had more antibiotic medications during the last 2 years had lower concentrations of formic, propionic and succinic acid. When adjusting for antibiotic medication, we found that among children, those currently on stimulant medication had lower acetic and propionic acid levels, and adults with ADHD had lower formic and propionic acid concentrations than adult healthy family members. In all, our findings show lower-than-normal plasma concentrations of SCFAs in ADHD explained in-part by antibiotic medication, age and stimulant medication. Whether or not this is of clinical significance is yet to be explored.
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Untargeted Metabolomics Pilot Study Using UHPLC-qTOF MS Profile in Sows' Urine Reveals Metabolites of Bladder Inflammation. Metabolites 2022; 12:metabo12121186. [PMID: 36557224 PMCID: PMC9784506 DOI: 10.3390/metabo12121186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/07/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Urinary tract infections (UTI) of sows (characterized by ascending infections of the urinary bladder (cyst), ureters, and renal pelvis), are major health issues with a significant economic impact to the swine industry. The current detection of UTI incidents lacks sensitivity; thus, UTIs remain largely under-diagnosed. The value of metabolomics in unraveling the mechanisms of sow UTI has not yet been established. This study aims to investigate the urine metabolome of sows for UTI biomarkers. Urine samples were collected from 58 culled sows from a farrow-to-finish herd in Greece. Urine metabolomic profiles in 31 healthy controls and in 27 inflammatory ones were evaluated. UHPLC-qTOF MS/MS was applied for the analysis with a combination of multivariate and univariate statistical analysis. Eighteen potential markers were found. The changes in several urine metabolites classes (nucleosides, indoles, isoflavones, and dipeptides), as well as amino-acids allowed for an adequate discrimination between the study groups. Identified metabolites were involved in purine metabolism; phenylalanine; tyrosine and tryptophan biosynthesis; and phenylalanine metabolism. Through ROC analysis it was shown that the 18 identified metabolite biomarkers exhibited good predictive accuracy. In summary, our study provided new information on the potential targets for predicting early and accurate diagnosis of UTI. Further, this information also sheds light on how it could be applied in live animals.
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Nardone V, Giannicola R, Giannarelli D, Saladino RE, Azzarello D, Romeo C, Bianco G, Rizzo MR, Di Meo I, Nesci A, Pastina P, Falzea AC, Caracciolo D, Reginelli A, Caraglia M, Luce A, Mutti L, Giordano A, Cappabianca S, Pirtoli L, Barbieri V, Tassone P, Tagliaferri P, Correale P. Distinctive Role of the Systemic Inflammatory Profile in Non-Small-Cell Lung Cancer Younger and Elderly Patients Treated with a PD-1 Immune Checkpoint Blockade: A Real-World Retrospective Multi-Institutional Analysis. Life (Basel) 2021; 11:life11111235. [PMID: 34833111 PMCID: PMC8621400 DOI: 10.3390/life11111235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/01/2021] [Accepted: 11/12/2021] [Indexed: 12/17/2022] Open
Abstract
An immune checkpoint blockade with mAbs to PD-1 and PD-L1 is an expanding therapeutic option for mNSCLC patients. This treatment strategy is based on the use of mAbs able to restore the anti-tumor activity of intratumoral T cells inhibited by PD-1 binding to PD-L1/2 on tumor and inflammatory cells. It has been speculated that a chronic status of systemic inflammation as well as the immunosenescence physiologically occurring in elderly patients may affect the efficacy of the treatment and the occurrence of irAEs. We performed a multi-institutional retrospective study aimed at evaluating the effects of these mAbs (nivolumab or atezolizumab) in 117 mNSCLC patients younger (90 cases) and older (27 cases) than 75 years in correlation with multiple inflammatory parameters (NLR, CRP, ESR, LDH and PCT). No differences were observed when the cohorts were compared in terms of the frequency of PFS, OS, inflammatory markers and immune-related adverse events (irAEs). Similarly, the occurrence of irAEs was strictly correlated with a prolonged OS survival in both groups. On the contrary, a negative correlation between the high baseline levels of inflammatory markers and OS could be demonstrated in the younger cohort only. Overall, PD-1/PD-L1-blocking mAbs were equally effective in young and elderly mNSCLC patients; however, the detrimental influence of a systemic inflammation at the baseline was only observed in young patients, suggesting different aging-related inflammation immunoregulative effects.
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Affiliation(s)
- Valerio Nardone
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (A.R.); (M.C.); (A.L.); (S.C.)
- Correspondence:
| | - Rocco Giannicola
- Medical Oncology Unit, Grand Metropolitan Hospital “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (R.G.); (D.A.); (C.R.); (G.B.); (A.C.F.); (P.C.)
| | - Diana Giannarelli
- Biostatistical Unit, National Cancer Institute “Regina Elena”, IRCCS, 00161 Rome, Italy;
| | - Rita Emilena Saladino
- Tissue typing Unit, Grand Metropolitan Hospital “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy;
| | - Domenico Azzarello
- Medical Oncology Unit, Grand Metropolitan Hospital “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (R.G.); (D.A.); (C.R.); (G.B.); (A.C.F.); (P.C.)
| | - Caterina Romeo
- Medical Oncology Unit, Grand Metropolitan Hospital “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (R.G.); (D.A.); (C.R.); (G.B.); (A.C.F.); (P.C.)
| | - Giovanna Bianco
- Medical Oncology Unit, Grand Metropolitan Hospital “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (R.G.); (D.A.); (C.R.); (G.B.); (A.C.F.); (P.C.)
| | - Maria Rosaria Rizzo
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.R.R.); (I.D.M.)
| | - Irene Di Meo
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.R.R.); (I.D.M.)
| | - Antonio Nesci
- Unit of Pharmacy, Grand Metropolitan Hospital “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy;
| | - Pierpaolo Pastina
- Section of Radiation Oncology, Medical School, University of Siena, 53100 Siena, Italy;
| | - Antonia Consuelo Falzea
- Medical Oncology Unit, Grand Metropolitan Hospital “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (R.G.); (D.A.); (C.R.); (G.B.); (A.C.F.); (P.C.)
| | - Daniele Caracciolo
- Medical and Translational Oncology Unit, Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy; (D.C.); (V.B.); (P.T.); (P.T.)
| | - Alfonso Reginelli
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (A.R.); (M.C.); (A.L.); (S.C.)
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (A.R.); (M.C.); (A.L.); (S.C.)
- BiogemScarl, Institute of Genetic Research, Precision and Molecular Oncology Laboratory, Ariano Irpino, 83031 Avellino, Italy
| | - Amalia Luce
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (A.R.); (M.C.); (A.L.); (S.C.)
| | - Luciano Mutti
- Sbarro Institute for Cancer Research and Molecular Medicine and Center of Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA; (L.M.); (A.G.); (L.P.)
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine and Center of Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA; (L.M.); (A.G.); (L.P.)
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Salvatore Cappabianca
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (A.R.); (M.C.); (A.L.); (S.C.)
| | - Luigi Pirtoli
- Sbarro Institute for Cancer Research and Molecular Medicine and Center of Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA; (L.M.); (A.G.); (L.P.)
| | - Vito Barbieri
- Medical and Translational Oncology Unit, Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy; (D.C.); (V.B.); (P.T.); (P.T.)
| | - Pierfrancesco Tassone
- Medical and Translational Oncology Unit, Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy; (D.C.); (V.B.); (P.T.); (P.T.)
| | - Pierosandro Tagliaferri
- Medical and Translational Oncology Unit, Department of Experimental and Clinical Medicine, Magna Graecia University, 88100 Catanzaro, Italy; (D.C.); (V.B.); (P.T.); (P.T.)
| | - Pierpaolo Correale
- Medical Oncology Unit, Grand Metropolitan Hospital “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (R.G.); (D.A.); (C.R.); (G.B.); (A.C.F.); (P.C.)
- Sbarro Institute for Cancer Research and Molecular Medicine and Center of Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA; (L.M.); (A.G.); (L.P.)
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Cui M, Trimigno A, Castro-Mejía JL, Reitelseder S, Bülow J, Bechshøft RL, Nielsen DS, Holm L, Engelsen SB, Khakimov B. Human Fecal Metabolome Reflects Differences in Body Mass Index, Physical Fitness, and Blood Lipoproteins in Healthy Older Adults. Metabolites 2021; 11:717. [PMID: 34822375 PMCID: PMC8620003 DOI: 10.3390/metabo11110717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 12/12/2022] Open
Abstract
This study investigated how body mass index (BMI), physical fitness, and blood plasma lipoprotein levels are related to the fecal metabolome in older adults. The fecal metabolome data were acquired using proton nuclear magnetic resonance spectroscopy and gas chromatography-mass spectrometry on 163 healthy older adults (65-80 years old, 80 females and 83 males). Overweight and obese subjects (BMI ≥ 27) showed higher levels of fecal amino acids (AAs) (valine, alanine, and phenylalanine) compared to normal-weight subjects (BMI ≤ 23.5). Adults classified in the high-fitness group displayed slightly lower concentrations of fecal short-chain fatty acids, propionic acid, and AAs (methionine, leucine, glutamic acid, and threonine) compared to the low-fitness group. Subjects with lower levels of cholesterol in low-density lipoprotein particles (LDLchol, ≤2.6 mmol/L) displayed higher fecal levels of valine, glutamic acid, phenylalanine, and lactic acid, while subjects with a higher level of cholesterol in high-density lipoprotein particles (HDLchol, ≥2.1 mmol/L) showed lower fecal concentration of isovaleric acid. The results from this study suggest that the human fecal metabolome, which primarily represents undigested food waste and metabolites produced by the gut microbiome, carries important information about human health and should be closely integrated to other omics data for a better understanding of the role of the gut microbiome and diet on human health and metabolism.
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Affiliation(s)
- Mengni Cui
- Chemometrics and Analytical Technology Section, Department of Food Science University of Copenhagen Rolighedsvej 26, 1958 Frederiksberg C, Denmark; (M.C.); (A.T.)
| | - Alessia Trimigno
- Chemometrics and Analytical Technology Section, Department of Food Science University of Copenhagen Rolighedsvej 26, 1958 Frederiksberg C, Denmark; (M.C.); (A.T.)
| | - Josue L. Castro-Mejía
- Food Microbiology & Fermentation Section, Department of Food Science University of Copenhagen Rolighedsvej 26, 1958 Frederiksberg C, Denmark; (J.L.C.-M.); (D.S.N.)
| | - Søren Reitelseder
- Institute of Sports Medicine, Department of Orthopedic Surgery, Bispebjerg and Frederiksberg Hospital, Nielsine Nielsens Vej 11, 2400 Copenhagen, Denmark; (S.R.); (J.B.); (R.L.B.); (L.H.)
| | - Jacob Bülow
- Institute of Sports Medicine, Department of Orthopedic Surgery, Bispebjerg and Frederiksberg Hospital, Nielsine Nielsens Vej 11, 2400 Copenhagen, Denmark; (S.R.); (J.B.); (R.L.B.); (L.H.)
| | - Rasmus Leidesdorff Bechshøft
- Institute of Sports Medicine, Department of Orthopedic Surgery, Bispebjerg and Frederiksberg Hospital, Nielsine Nielsens Vej 11, 2400 Copenhagen, Denmark; (S.R.); (J.B.); (R.L.B.); (L.H.)
| | - Dennis Sandris Nielsen
- Food Microbiology & Fermentation Section, Department of Food Science University of Copenhagen Rolighedsvej 26, 1958 Frederiksberg C, Denmark; (J.L.C.-M.); (D.S.N.)
| | - Lars Holm
- Institute of Sports Medicine, Department of Orthopedic Surgery, Bispebjerg and Frederiksberg Hospital, Nielsine Nielsens Vej 11, 2400 Copenhagen, Denmark; (S.R.); (J.B.); (R.L.B.); (L.H.)
- School of Sport, Exercise and Rehabilitation Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Søren Balling Engelsen
- Chemometrics and Analytical Technology Section, Department of Food Science University of Copenhagen Rolighedsvej 26, 1958 Frederiksberg C, Denmark; (M.C.); (A.T.)
| | - Bekzod Khakimov
- Chemometrics and Analytical Technology Section, Department of Food Science University of Copenhagen Rolighedsvej 26, 1958 Frederiksberg C, Denmark; (M.C.); (A.T.)
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