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Brickman CE, Agnello M, Imam N, Camejo P, Pino R, Carroll LN, Chein A, Palefsky JM. Distinct anal microbiome is correlated with anal cancer precursors in MSM with HIV. AIDS 2024; 38:1476-1484. [PMID: 38691018 PMCID: PMC11239087 DOI: 10.1097/qad.0000000000003920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 03/03/2024] [Accepted: 03/27/2024] [Indexed: 05/03/2024]
Abstract
OBJECTIVES Anal cancer risk is elevated in MSM with HIV (MSMWH). Anal high-risk human papillomavirus (hr-HPV) infection is necessary but insufficient to develop high-grade squamous intraepithelial lesion (HSIL), the anal cancer precursor, suggesting additional factors. We sought to determine whether the microbiome of the anal canal is distinct by comparing it with the microbiome of stool. We also sought to determine whether changes in the anal microbiome are associated with HSIL among MSMWH. DESIGN Cross-sectional comparison of the microbiome of the anal canal with the microbiome of stool in MSMWH and cross-sectional comparison of the anal microbiome of MSMWH with anal HSIL with the anal microbiome of MSMWH without anal HSIL. METHODS Sterile swabs were used to sample the anus of MSMWH for microbiome and HPV testing, followed by high-resolution anoscopy. Stool samples were mailed from home. 16S sequencing was used for bacterial identification. Measures of alpha diversity, beta diversity, and differential abundance analysis were used to compare samples. RESULTS One hundred sixty-six anal samples and 103 matching stool samples were sequenced. Beta diversity showed clustering of stool and anal samples. Of hr-HPV-positive MSMWH, 31 had HSIL and 13 had no SIL. Comparison of the microbiome between these revealed 28 different species. The highest-fold enrichment among MSMWH/hr-HPV/HSIL included pro-inflammatory and carcinogenic Prevotella, Parasuterella, Hungatella, Sneathia, and Fusobacterium species. The anti-inflammatory Anaerostipes caccae showed the greatest reduction among MSMWH/hr-HPV/HSIL. CONCLUSION The anal microbiome is distinct from stool. A pro-inflammatory and carcinogenic environment may be associated with anal HSIL.
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Affiliation(s)
| | - Melissa Agnello
- uBiome, Medical Affairs, San Francisco, California, USA
- Komodo Health, Inc., San Francisco, California
| | - Nabeel Imam
- uBiome, Medical Affairs, Santiago, Chile
- Psomagen, Inc., Rockville, Maryland, USA
| | | | - Rodolfo Pino
- uBiome, Medical Affairs, Santiago, Chile
- Sociedad Química y Minera de Chile, Santiago, Chile
| | - Lauren N Carroll
- uBiome, Medical Affairs, San Francisco, California, USA
- ApotheCom, San Francisco, California, USA
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2
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMSF, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host Microbe 2024; 32:506-526.e9. [PMID: 38479397 PMCID: PMC11022754 DOI: 10.1016/j.chom.2024.02.012] [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: 12/05/2023] [Revised: 01/23/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlate across body sites, suggesting systemic dynamics influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals show altered microbial stability and associations among microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.
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Affiliation(s)
- Xin Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Xiaotao Shen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Jethro S Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, UK
| | - Daniel J Spakowicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Division of Medical Oncology, Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH 43210, USA
| | | | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Monica Avina
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Honkala
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Faye Chleilat
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirley Jingyi Chen
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kexin Cha
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shana Leopold
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Chenchen Zhu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lei Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Lin Lyu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Daniel Hornburg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xinyue Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chao Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Liuyiqi Jiang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew W Brooks
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meng Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peng Gao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | - Hoan Nguyen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Alessandra Celli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bo-Young Hong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Woody L Hunt School of Dental Medicine, Texas Tech University Health Science Center, El Paso, TX 79905, USA
| | - Eddy J Bautista
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Headquarters-Mosquera, Cundinamarca 250047, Colombia
| | - Yair Dorsett
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Paula B Kavathas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yanjiao Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA.
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3
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Beckers KF, Flanagan JP, Sones JL. Microbiome and pregnancy: focus on microbial dysbiosis coupled with maternal obesity. Int J Obes (Lond) 2024; 48:439-448. [PMID: 38145995 PMCID: PMC10978494 DOI: 10.1038/s41366-023-01438-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 12/27/2023]
Abstract
Obesity is becoming a worldwide pandemic with over one billion people affected. Of women in the United States, who are of childbearing age, two-thirds of them are considered overweight/obese. Offspring of women with obesity have a greater likelihood of developing cardiometabolic disease later in life, therefore making obesity a transgenerational issue. Emerging topics such as maternal microbial dysbiosis with altered levels of bacterial phyla and maternal obesity programming offspring cardiometabolic disease are a novel area of research discussed in this review. In the authors' opinion, beneficial therapeutics will be developed from knowledge of bacterial-host interactions at the most specific level possible. Although there is an abundance of obesity-related microbiome research, it is not concise, readily available, nor easy to interpret at this time. This review details the current knowledge regarding the relationship between obesity and the gut microbiome, with an emphasis on maternal obesity.
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Affiliation(s)
- Kalie F Beckers
- Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Juliet P Flanagan
- Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Jenny L Sones
- Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA.
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, USA.
- Clinical Sciences, Colorado State University College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, USA.
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4
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Xu J, Wang H, Xu R, Li Q, Li L, Su Y, Liu J, Zhu W. Daily fluctuation of Lactobacillus species and their antibiotic resistome in the colon of growing pigs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170821. [PMID: 38336077 DOI: 10.1016/j.scitotenv.2024.170821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
There are various types of bacteria inhabiting the intestine that help maintain the balance of the intestinal microbiota. Lactobacillus is one of the important beneficial bacteria and is widely used as a food starter and probiotic. In this study, we investigated the daily fluctuation of the colonic Lactobacillus species and their distribution of antibiotic resistance genes (ARGs) as well as antibiotic susceptibility in pigs. Metagenomic analysis revealed that genus Lactobacillus was one of the most dominant genera in the colon of growing pigs. Rhythmicity analysis revealed that 84 out of 285 Lactobacillus species exhibited rhythmic patterns. Lactobacillus johnsonii and Lactobacillus reuteri were the two most abundant lactobacilli with circadian oscillation, which increased during the day and decreased at night. The profile of the antibiotic resistome was modified over time within 24-h period. Elfamycin resistance genes were the most enriched class found in Lactobacillus. Furthermore, the seven strains of Lactobacillus isolated from the pig intestine mainly exhibited resistance to gentamicin, erythromycin, and lincomycin. The whole genome annotation of four Lactobacillus strains indicated the presence of multiple ARGs, including elfamycin resistance genes, however, the most abundant ARG was optrA in genome of four strains. These results indicate the presence of various Lactobacillus species harboring a large number of ARGs in the swine intestine. This implies that when using animal-derived lactobacilli, it is essential to assess antibiotic resistance to prevent further transmission between animals and the environment.
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Affiliation(s)
- Jianjian Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongyu Wang
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Rongying Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiuke Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Lian Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yong Su
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jinxin Liu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
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5
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Hogue T, Hampton‐Marcell J, Carroll IM, Purdom T, Colleran H, Exford TJ, Brown M, Cook MD. Gut microbiota are differentially correlated with blood pressure status in African American collegiate athletes: A pilot study. Physiol Rep 2024; 12:e15982. [PMID: 38514894 PMCID: PMC10957718 DOI: 10.14814/phy2.15982] [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: 12/29/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Hypertension (HTN) is common among athletes and the most recent epidemiologic data reports that cardiovascular (CV) sudden death is significantly greater in African Americans (AAs). Gut microbial dysbiosis (a poorly diverse stool microbial profile) has been associated with HTN in sedentary people but microbial characteristics of athletes with HTN are unknown. Our purpose was to differentiate microbiome characteristics associated with BP status in AA collegiate athletes. Thirty AA collegiate athletes were stratified by normal BP (systolic BP (SBP) ≤130 mmHg; n = 15) and HTN (SBP ≥130 mmHg; n = 15). 16S rRNA gene sequencing was performed on stool samples to identify microbes at the genus level. We did not observe any significant differences in alpha diversity, but beta diversity was different between groups. Principal coordinate analysis was significantly different (PERMANOVA, p < 0.05, R = 0.235) between groups. Spearman rank correlations showed a significant (p < 0.05) correlation between systolic BP and abundances for Adlercreutzia (R = 0.64), Coprococcus (R = 0.49), Granulicatella (R = 0.63), and Veillonella (R = 0.41). Gut microbial characteristics were associated with differentially abundant microbial genus' and BP status. These results will direct future studies to define the functions of these microbes associated with BP in athletes.
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Affiliation(s)
- Taylor Hogue
- Department of KinesiologyNorth Carolina Agriculture and Technical State UniversityGreensboroNorth CarolinaUSA
| | | | - Ian M. Carroll
- Department of NutritionUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Troy Purdom
- Department of KinesiologyNorth Carolina Agriculture and Technical State UniversityGreensboroNorth CarolinaUSA
| | - Heather Colleran
- Department of NutritionNorth Carolina Agriculture and Technical State UniversityGreensboroNorth CarolinaUSA
| | - T. J. Exford
- Education & Research DepartmentDayton VA Medical CenterDaytonOhioUSA
| | - Michael Brown
- Department of KinesiologyUniversity of MarylandCollege ParkMarylandUSA
| | - Marc D. Cook
- Department of KinesiologyNorth Carolina Agriculture and Technical State UniversityGreensboroNorth CarolinaUSA
- Center for Integrative Health Disparity & Equity Research (CIHDER)North Carolina Agricultural and Technical State UniversityGreensboroNorth CarolinaUSA
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6
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Bu L, Wang C, Bai J, Song J, Zhang Y, Chen H, Suo H. Gut microbiome-based therapies for alleviating cognitive impairment: state of the field, limitations, and future perspectives. Food Funct 2024; 15:1116-1134. [PMID: 38224464 DOI: 10.1039/d3fo02307a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Cognitive impairment (CI) is a multifaceted neurological condition that can trigger negative emotions and a range of concurrent symptoms, imposing significant public health and economic burdens on society. Therefore, it is imperative to discover a remedy for CI. Nevertheless, the mechanisms behind the onset of this disease are multifactorial, which makes the search for effective amelioration difficult and complex, hindering the search for effective measures. Intriguingly, preclinical research indicates that gut microbiota by influencing brain function, plays an important role in the progression of CI. Furthermore, numerous preclinical studies have highlighted the potential of probiotics, prebiotics, fecal microbiota transplantation (FMT), and diet in modulating the gut microbiota, thereby ameliorating CI symptoms. This review provides a comprehensive evaluation of CI pathogenesis, emphasizing the contribution of gut microbiota disorders to CI development. It also summarizes and discusses current strategies and mechanisms centered on the synergistic role of gut microbiota modulation in the microbiota-gut-brain axis in CI development. Finally, problems with existing approaches are contemplated and the development of microbial modulation strategies as therapeutic approaches to promote and restore brain cognition is discussed. Further research considerations and directions are highlighted to provide ideas for future CI prevention and treatment strategies.
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Affiliation(s)
- Linli Bu
- College of Food Science, Southwest University, Chongqing 400715, China.
- Modern "Chuan Cai Yu Wei" Food Industry Innovation Research Institute, Chongqing 400715, China
| | - Chen Wang
- College of Food Science, Southwest University, Chongqing 400715, China.
- Modern "Chuan Cai Yu Wei" Food Industry Innovation Research Institute, Chongqing 400715, China
| | - Junying Bai
- Citrus Research Institute, Southwest University, Chongqing 400715, China
| | - Jiajia Song
- College of Food Science, Southwest University, Chongqing 400715, China.
- Modern "Chuan Cai Yu Wei" Food Industry Innovation Research Institute, Chongqing 400715, China
| | - Yuhong Zhang
- Institute of Food Sciences and Technology, Tibet Academy of Agricultural and Animal Husbandry Sciences, Xizang 850000, China
| | - Hongyu Chen
- College of Food Science, Southwest University, Chongqing 400715, China.
- Modern "Chuan Cai Yu Wei" Food Industry Innovation Research Institute, Chongqing 400715, China
| | - Huayi Suo
- College of Food Science, Southwest University, Chongqing 400715, China.
- Modern "Chuan Cai Yu Wei" Food Industry Innovation Research Institute, Chongqing 400715, China
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7
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Schüssler-Fiorenza Rose SM, Binh Tran TD, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas P, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.577565. [PMID: 38352363 PMCID: PMC10862915 DOI: 10.1101/2024.02.01.577565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
To understand dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune and clinical markers of microbiomes from four body sites in 86 participants over six years. We found that microbiome stability and individuality are body-site-specific and heavily influenced by the host. The stool and oral microbiome were more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. Also, we identified individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlated across body sites, suggesting systemic coordination influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals showed altered microbial stability and associations between microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease. Study Highlights The stability of the human microbiome varies among individuals and body sites.Highly individualized microbial genera are more stable over time.At each of the four body sites, systematic interactions between the environment, the host and bacteria can be detected.Individuals with insulin resistance have lower microbiome stability, a more diversified skin microbiome, and significantly altered host-microbiome interactions.
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8
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Geng ZH, Zhu Y, Chen WF, Fu PY, Xu JQ, Wang TY, Yao L, Liu ZQ, Li XQ, Zhang ZC, Wang Y, Ma LY, Lin SL, He MJ, Zhao C, Li QL, Zhou PH. The role of type II esophageal microbiota in achalasia: Activation of macrophages and degeneration of myenteric neurons. Microbiol Res 2023; 276:127470. [PMID: 37574627 DOI: 10.1016/j.micres.2023.127470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
OBJECTIVE The gut microbiota plays a critical role in the appropriate development and maintenance of the enteric nervous system (ENS). Esophageal achalasia (EA) is a rare motility disorder characterized by the selective degeneration of inhibitory neurons in the esophageal myenteric plexus. This study aimed to evaluate the composition of the esophageal microbiota in achalasia and explore the potential microbial mechanisms involved in its pathogenesis. DESIGN The lower esophageal mucosal microbiota was analyzed in patients with achalasia and control participants using 16 S rRNA sequencing. The association between the esophageal microbiota and achalasia was validated by inducing esophageal dysbiosis in C57BL/10 J and C57BL/10ScNJ (TLR4KO) mice via chronic exposure to ampicillin sodium in their drinking water. RESULTS The esophageal microbiota in EA patients had lower diversity and a predominance of Gram-negative bacteria (Type II microbiota) compared to that in the healthy controls. Additionally, the relative abundance of Rhodobacter decreased significantly in patients with achalasia, which correlated with an enrichment of lipopolysaccharide (LPS) biosynthesis based on the COG database. Antibiotic-treated mice showed an esophageal microbiota characterized by increased abundance of Gram-negative bacteria (Type II microbiome), decreased abundance of Rhodobacter, and enriched LPS biosynthesis. Compared to the control and TLR4KO mice, the antibiotic-treated wild-type mice had higher LES resting pressure, increased LES contraction rate after carbachol stimulation, and decreased relaxation response to L-arginine. Moreover, the number of myenteric neurons decreased, while the number of lamina propria macrophages (LpMs) increased after antibiotic exposure. Furthermore, the TLR4-MYD88-NF-κB pathway was up-regulated, and the production of TNF-α, IL-1β, and IL-6 increased in the antibiotic-treated mice. CONCLUSIONS Patients with achalasia exhibit esophageal dysbiosis, which may induce aberrant esophageal motility.
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Affiliation(s)
- Zi-Han Geng
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
| | - Yan Zhu
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
| | - Wei-Feng Chen
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
| | - Pei-Yao Fu
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
| | - Jia-Qi Xu
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
| | - Tong-Yao Wang
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences & National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Lu Yao
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
| | - Zu-Qiang Liu
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
| | - Xiao-Qing Li
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
| | - Zhao-Chao Zhang
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
| | - Yun Wang
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
| | - Li-Yun Ma
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
| | - Sheng-Li Lin
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
| | - Meng-Jiang He
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
| | - Chao Zhao
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences & National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.
| | - Quan-Lin Li
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China.
| | - Ping-Hong Zhou
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China.
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Crichton M, Marshall S, Marx W, Isenring E, Vázquez-Campos X, Dawson SL, Lohning A. Effect of Ginger Root Powder on Gastrointestinal Bacteria Composition, Gastrointestinal Symptoms, Mental Health, Fatigue, and Quality of Life: A Double-Blind Placebo-Controlled Trial. J Nutr 2023; 153:3193-3206. [PMID: 37690779 DOI: 10.1016/j.tjnut.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 08/02/2023] [Accepted: 09/01/2023] [Indexed: 09/12/2023] Open
Abstract
BACKGROUND Despite compositional alterations in gastrointestinal microbiota being purported to underpin some of the therapeutic effects of ginger, the effect of a standardized ginger supplement on gut microbiota has not been tested in humans. OBJECTIVES To determine the effect of a standardized ginger (Zingiber officinale) root powder, compared to placebo, on gastrointestinal bacteria and associated outcomes in healthy adults. METHODS A randomized double-blind placebo-controlled trial allocated participants aged 18 to 30 y to ginger or microcrystalline cellulose (MCC) placebo. The intervention comprised 1.2 g/d of ginger (4 capsules per day totaling 84 mg/d of active gingerols/shogaols) for 14 d following a 1-wk run-in period. Primary outcomes were gastrointestinal community composition, alpha and beta diversity, and differential abundance, measured using 16S rRNA gene sequencing of fecal samples. Secondary outcomes were gastrointestinal symptoms, bowel function, depression, anxiety, stress, fatigue, quality of life, and adverse events. RESULTS Fifty-one participants were enrolled and analyzed (71% female; mean age 25 ± 3 y; ginger: n = 29, placebo: n = 22). There was a greater increase in relative abundance of phylum, Actinobacteria, observed following ginger supplementation compared to placebo (U: 145.0; z: -2.1; P = 0.033). Ginger was associated with a greater abundance of the genera Parabacteroides, Bacillus, Ruminococcaceae incertae sedis, unclassified Bacilli, families Defluviitaleaceae, Morganellaceae, and Bacillaceae as well as lower abundance of the genus Blautia and family Sphingomonadaceae (P < 0.05). An improvement in indigestion symptoms was observed with ginger supplementation (U: 196.0; z: -2.4; P = 0.015). No differences between ginger and placebo groups were found for alpha and beta diversity or other secondary outcomes. No moderate or severe adverse events were reported. CONCLUSIONS Supplementation with ginger root powder was safe and altered aspects of gastrointestinal bacteria composition; however, it did not change alpha- or beta diversity, bowel function, gastrointestinal symptoms, mood, or quality of life in healthy adults. These results provide further understanding regarding the mechanisms of action of ginger supplementation. This trial was registered in the Australia New Zealand Clinical Trials Registry as ACTRN12620000302954p and the Therapeutic Goods Administration as CT-2020-CTN-00380-1.
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Affiliation(s)
- Megan Crichton
- Bond University Nutrition and Dietetics Research Group, Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Queensland, Australia; Cancer and Palliative Care Outcomes Centre, Centre for Healthcare Transformation, School of Nursing, Faculty of Health, Kelvin Grove, Queensland, Australia.
| | - Skye Marshall
- Bond University Nutrition and Dietetics Research Group, Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Queensland, Australia; Research Institute for Future Health, Gold Coast, Queensland, Australia
| | - Wolfgang Marx
- Bond University Nutrition and Dietetics Research Group, Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Queensland, Australia; Deakin University, Food & Mood Centre, IMPACT Strategic Research Centre, School of Medicine, Barwon Health, Geelong, Victoria, Australia
| | - Elizabeth Isenring
- Bond University Nutrition and Dietetics Research Group, Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Queensland, Australia
| | - Xabier Vázquez-Campos
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, New South Wales, Australia
| | - Samantha L Dawson
- Deakin University, Food & Mood Centre, IMPACT Strategic Research Centre, School of Medicine, Barwon Health, Geelong, Victoria, Australia
| | - Anna Lohning
- Bond University Nutrition and Dietetics Research Group, Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Queensland, Australia
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10
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Ni Z, Li J, Qian X, Yong Y, Wu M, Wang Y, Lv W, Zhang S, Zhang Y, Shao Y, Chen A. Phellinus igniarius Polysaccharides Ameliorate Hyperglycemia by Modulating the Composition of the Gut Microbiota and Their Metabolites in Diabetic Mice. Molecules 2023; 28:7136. [PMID: 37894615 PMCID: PMC10609020 DOI: 10.3390/molecules28207136] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/11/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
Gut microbiota dysbiosis has been reported as a risk factor in the development of type 2 diabetes mellitus (T2DM). Polysaccharides from Phellinus igniarius (P. igniarius) possess various properties that help manage metabolic diseases; however, their underlying mechanism of action remains unclear. Therefore, in this study, we aimed to evaluate the effect of P. igniarius polysaccharides (SH-P) on improving hyperglycemia in mice with T2DM and clarified its association with the modulation of gut microbiota and their metabolites using 16S rDNA sequencing and liquid chromatography-mass spectrometry. Fecal microbiota transplantation (FMT) was used to verify the therapeutic effects of microbial remodeling. SH-P supplementation alleviated hyperglycemia symptoms in T2DM mice, ameliorated gut dysbiosis, and significantly increased the abundance of Lactobacillus in the gut. Pathway enrichment analysis indicated that SH-P treatment altered metabolic pathways associated with the occurrence and development of diabetes. Spearman's correlation analysis revealed that changes in the dominant bacterial genera were significantly correlated with metabolite levels closely associated with hyperglycemia. Additionally, FMT significantly improved insulin sensitivity and antioxidative capacity and reduced inflammation and tissue injuries, indicating improved glucose homeostasis. These results indicate that the ameliorative effects of SH-P on hyperglycemia are associated with the modulation of gut microbiota composition and its metabolites.
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Affiliation(s)
- Zaizhong Ni
- College of Food and Bioengineering, Xuzhou University of Technology, Xuzhou 221018, China
| | - Jinting Li
- College of Food and Bioengineering, Xuzhou University of Technology, Xuzhou 221018, China
| | - Xinyi Qian
- College of Food and Bioengineering, Xuzhou University of Technology, Xuzhou 221018, China
| | - Yidan Yong
- College of Food and Bioengineering, Xuzhou University of Technology, Xuzhou 221018, China
| | - Mengmeng Wu
- College of Food and Bioengineering, Xuzhou University of Technology, Xuzhou 221018, China
| | - Yanan Wang
- College of Food and Bioengineering, Xuzhou University of Technology, Xuzhou 221018, China
| | - Wendi Lv
- College of Food and Bioengineering, Xuzhou University of Technology, Xuzhou 221018, China
| | - Simeng Zhang
- College of Food and Bioengineering, Xuzhou University of Technology, Xuzhou 221018, China
| | - Yifei Zhang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ying Shao
- College of Food and Bioengineering, Xuzhou University of Technology, Xuzhou 221018, China
| | - Anhui Chen
- College of Food and Bioengineering, Xuzhou University of Technology, Xuzhou 221018, China
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11
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Igudesman D, Abbaspour A, Reed KK, Flatt RE, Becken B, Thornton LM, Bulik CM, Carroll IM. Laxative Abuse Is Associated With a Depleted Gut Microbial Community Structure Among Women and Men With Binge-Eating Disorder or Bulimia Nervosa: The Binge Eating Genetics Initiative. Psychosom Med 2023; 85:727-735. [PMID: 37363967 PMCID: PMC10543565 DOI: 10.1097/psy.0000000000001226] [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] [Indexed: 06/28/2023]
Abstract
OBJECTIVE This study assessed the associations of binge eating, compensatory behaviors, and dietary restraint with the composition and diversity of the intestinal microbiota among participants with binge-eating disorder or bulimia nervosa. METHODS We analyzed data from 265 participants aged 18 to 45 years with current binge-eating disorder or bulimia nervosa enrolled in the Binge Eating Genetics Initiative study. We evaluated the associations of binge-eating frequency; presence/absence and frequency of vomiting, laxative use, and compulsive exercise; and dietary restraint with abundances of gut microbial genera, species, and diversity (Shannon diversity, Faith phylogenetic diversity, and Peilou's evenness) from 16S rRNA gene sequencing. General linear regression models adjusted for potential confounders, including age and current body mass index, were used to test associations; p values were corrected for the false discovery rate. RESULTS The normalized abundance of four genus- and species-level gut microbes and three diversity indices were lower among Binge Eating Genetics Initiative participants who reported any laxative use compared with those who reported no laxative use. Vomiting frequency was positively associated with the normalized abundance of the genus Escherichia-Shigella , a potential pathobiont, although the association was attenuated to nonsignificance after adjustment for age, body mass index, and binge-eating episodes. CONCLUSIONS Laxative use was highly and uniformly predictive of a reduced gut microbial diversity including potential commensals and pathobionts, and should be assessed and accounted for in all future studies of eating disorders and the gut microbiota. Future studies should collect data on specific medications-particularly laxatives-and dietary intake to obtain unbiased estimates of the effect of eating disorders on the gut microbiota and identify potential downstream clinical implications.Trial Registration:ClinicalTrials.gov identifier: NCT04162574 .
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Affiliation(s)
- Daria Igudesman
- From the Department of Nutrition (Igudesman, Reed, Bulik, Carroll), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Medical Epidemiology and Biostatistics (Abbaspour, Bulik) Karolinska Institutet, Stockholm, Sweden; Department of Psychology and Neuroscience (Flatt), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Division of Pediatric Infectious Diseases (Becken), University of Nebraska Medical Center, Omaha, Nebraska; and Department of Psychiatry, University of North Carolina at Chapel Hill (Thornton, Bulik), Chapel Hill, North Carolina
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12
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Huynh U, Nguyen HN, Trinh BK, Elhaj J, Zastrow ML. A bioinformatic analysis of zinc transporters in intestinal Lactobacillaceae. Metallomics 2023; 15:mfad044. [PMID: 37463796 PMCID: PMC10391621 DOI: 10.1093/mtomcs/mfad044] [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: 05/04/2023] [Accepted: 07/17/2023] [Indexed: 07/20/2023]
Abstract
As the second most abundant transition element and a crucial cofactor for many proteins, zinc is essential for the survival of all living organisms. To maintain required zinc levels and prevent toxic overload, cells and organisms have a collection of metal transport proteins for uptake and efflux of zinc. In bacteria, metal transport proteins are well defined for model organisms and many pathogens, but fewer studies have explored metal transport proteins, including those for zinc, in commensal bacteria from the gut microbiota. The healthy human gut microbiota comprises hundreds of species and among these, bacteria from the Lactobacillaceae family are well documented to have various beneficial effects on health. Furthermore, changes in dietary metal intake, such as for zinc and iron, are frequently correlated with changes in abundance of Lactobacillaceae. Few studies have explored zinc requirements and zinc homeostasis mechanisms in Lactobacillaceae, however. Here we applied a bioinformatics approach to identify and compare predicted zinc uptake and efflux proteins in several Lactobacillaceae genera of intestinal relevance. Few Lactobacillaceae had zinc transporters currently annotated in proteomes retrieved from the UniProt database, but protein sequence-based homology searches revealed that high-affinity ABC transporter genes are likely common, albeit with genus-specific domain features. P-type ATPase transporters are probably also common and some Lactobacillaceae genera code for predicted zinc efflux cation diffusion facilitators. This analysis confirms that Lactobacillaceae harbor genes for various zinc transporter homologs, and provides a foundation for systematic experimental studies to elucidate zinc homeostasis mechanisms in these bacteria.
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Affiliation(s)
- Uyen Huynh
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Hazel N Nguyen
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Brittany K Trinh
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Joanna Elhaj
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
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13
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Lu Y, Yang J, Zhang L, Chen F, Han P, Fu Y. Characteristics of bacterial community and ARG profiles in the surface and air environments in a spacecraft assembly cleanroom. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121613. [PMID: 37087089 DOI: 10.1016/j.envpol.2023.121613] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/13/2023] [Accepted: 04/09/2023] [Indexed: 05/03/2023]
Abstract
Understanding the microbial communities and antibiotic resistance genes (ARGs) in spacecraft assembly cleanrooms is crucial for spacecraft microbial control and astronaut safety. However, there have been few reports of ARG profiles and their relationship with microbiomes in such environments. In the present study, we assessed the bacterial community and ARGs in the air dust and surface environments of a typical spacecraft assembly cleanroom. Our results show a significant difference in bacterial composition between surfaces and air dust, as they belong to two distinct ecostates. Bacillus and Acinetobacter were significantly enriched in the air samples. Bacterial community network analysis revealed lower topological parameters and robustness of bacterial networks in the air samples. We also observed different distribution patterns of some typical ARGs between surface and air dust samples. Notably, the ermB gene exhibited a relatively high copy number and was enriched in the surface environment, compared to that in the air. Overall, our study provides insight into the complex microbial community and the distribution and transfer of ARGs in spacecraft assembly cleanrooms, and offers important input for developing control strategies against ARGs.
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Affiliation(s)
- Yueying Lu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100083, China.
| | - Jianlou Yang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100083, China.
| | - Lantao Zhang
- Institute of Manned Space System and Engineering, China Academy of Space Technology, Beijing, 100094, China.
| | - Fangqi Chen
- Shen Yuan Honors College, Beihang University, Beijing, 100191, China.
| | - Pei Han
- Laboratory of Space Utilization, Technology and Engineering Center for Space Utilization, Chinese Academy of Sciences, Beijing, 100094, China.
| | - Yuming Fu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China; State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing, 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100083, China.
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14
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Toro-Ascuy D, Cárdenas JP, Zorondo-Rodríguez F, González D, Silva-Moreno E, Puebla C, Nunez-Parra A, Reyes-Cerpa S, Fuenzalida LF. Microbiota Profile of the Nasal Cavity According to Lifestyles in Healthy Adults in Santiago, Chile. Microorganisms 2023; 11:1635. [PMID: 37512807 PMCID: PMC10384449 DOI: 10.3390/microorganisms11071635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND The respiratory microbiome is dynamic, varying between anatomical niches, and it is affected by various host and environmental factors, one of which is lifestyle. Few studies have characterized the upper respiratory tract microbiome profile according to lifestyle. We explored the association between lifestyles and microbiota profiles in the upper respiratory tract of healthy adults. METHODS We analyzed nasal samples from 110 healthy adults who were living in Santiago, Chile, using 16S ribosomal RNA gene-sequencing methods. Volunteers completed a structured questionnaire about lifestyle. RESULTS The composition and abundance of taxonomic groups varied across lifestyle attributes. Additionally, multivariate models suggested that alpha diversity varied in the function of physical activity, nutritional status, smoking, and the interaction between nutritional status and smoking, although the significant impact of those variables varied between women and men. Although physical activity and nutritional status were significantly associated with all indexes of alpha diversity among women, the diversity of microbiota among men was associated with smoking and the interaction between nutritional status and smoking. CONCLUSIONS The alpha diversity of nasal microbiota is associated with lifestyle attributes, but these associations depend on sex and nutritional status. Our results suggest that future studies of the airway microbiome may provide a better resolution if data are stratified for differences in sex and nutritional status.
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Affiliation(s)
- Daniela Toro-Ascuy
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8910060, Chile
| | - Juan P Cárdenas
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
| | - Francisco Zorondo-Rodríguez
- Departamento de Gestión Agraria, Facultad Tecnológica, Universidad de Santiago de Chile, Santiago 8910060, Chile
| | - Damariz González
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
| | - Evelyn Silva-Moreno
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8910060, Chile
| | - Carlos Puebla
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8910060, Chile
| | - Alexia Nunez-Parra
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8910060, Chile
| | - Sebastián Reyes-Cerpa
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
| | - Loreto F Fuenzalida
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8910060, Chile
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15
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Hradicka P, Adamkova P, Lenhardt L, Gancarcikova S, Iannaccone SF, Demeckova V. Addressing safety concerns of long-term probiotic use: In vivo evidence from a rat model. J Funct Foods 2023. [DOI: 10.1016/j.jff.2023.105521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
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16
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Pezzino S, Sofia M, Mazzone C, Castorina S, Puleo S, Barchitta M, Agodi A, Gallo L, La Greca G, Latteri S. Gut Microbiome in the Progression of NAFLD, NASH and Cirrhosis, and Its Connection with Biotics: A Bibliometric Study Using Dimensions Scientific Research Database. BIOLOGY 2023; 12:biology12050662. [PMID: 37237476 DOI: 10.3390/biology12050662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/30/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023]
Abstract
There is growing evidence that gut microbiota dysbiosis is linked to the etiopathogenesis of nonalcoholic fatty liver disease (NAFLD), from the initial stage of disease until the progressive stage of nonalcoholic steatohepatitis (NASH) and the final stage of cirrhosis. Conversely, probiotics, prebiotics, and synbiotics have shown promise in restoring dysbiosis and lowering clinical indicators of disease in a number of both preclinical and clinical studies. Additionally, postbiotics and parabiotics have recently garnered some attention. The purpose of this bibliometric analysis is to assess recent publishing trends concerning the role of the gut microbiome in the progression of NAFLD, NASH and cirrhosis and its connection with biotics. The free access version of the Dimensions scientific research database was used to find publications in this field from 2002 to 2022. VOSviewer and Dimensions' integrated tools were used to analyze current research trends. Research into the following topics is expected to emerge in this field: (1) evaluation of risk factors which are correlated with the progression of NAFLD, such as obesity and metabolic syndrome; (2) pathogenic mechanisms, such as liver inflammation through toll-like receptors activation, or alteration of short-chain fatty acids metabolisms, which contribute to NAFLD development and its progression in more severe forms, such as cirrhosis; (3) therapy for cirrhosis through dysbiosis reduction, and research on hepatic encephalopathy a common consequence of cirrhosis; (4) evaluation of diversity, and composition of gut microbiome under NAFLD, and as it varies under NASH and cirrhosis by rRNA gene sequencing, a tool which can also be used for the development of new probiotics and explore into the impact of biotics on the gut microbiome; (5) treatments to reduce dysbiosis with new probiotics, such as Akkermansia, or with fecal microbiome transplantation.
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Affiliation(s)
- Salvatore Pezzino
- Department of Surgical Sciences and Advanced Technologies "G. F. Ingrassia", Cannizzaro Hospital, University of Catania, 95123 Catania, Italy
| | - Maria Sofia
- Department of Surgical Sciences and Advanced Technologies "G. F. Ingrassia", Cannizzaro Hospital, University of Catania, 95123 Catania, Italy
| | - Chiara Mazzone
- Department of Surgical Sciences and Advanced Technologies "G. F. Ingrassia", Cannizzaro Hospital, University of Catania, 95123 Catania, Italy
| | - Sergio Castorina
- Department of Surgical Sciences and Advanced Technologies "G. F. Ingrassia", Cannizzaro Hospital, University of Catania, 95123 Catania, Italy
| | - Stefano Puleo
- Department of Surgical Sciences and Advanced Technologies "G. F. Ingrassia", Cannizzaro Hospital, University of Catania, 95123 Catania, Italy
| | - Martina Barchitta
- Department of Surgical Sciences and Advanced Technologies "G. F. Ingrassia", Cannizzaro Hospital, University of Catania, 95123 Catania, Italy
| | - Antonella Agodi
- Department of Surgical Sciences and Advanced Technologies "G. F. Ingrassia", Cannizzaro Hospital, University of Catania, 95123 Catania, Italy
| | - Luisa Gallo
- Department of Surgical Sciences and Advanced Technologies "G. F. Ingrassia", Cannizzaro Hospital, University of Catania, 95123 Catania, Italy
| | - Gaetano La Greca
- Department of Surgical Sciences and Advanced Technologies "G. F. Ingrassia", Cannizzaro Hospital, University of Catania, 95123 Catania, Italy
| | - Saverio Latteri
- Department of Surgical Sciences and Advanced Technologies "G. F. Ingrassia", Cannizzaro Hospital, University of Catania, 95123 Catania, Italy
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Zeng J, Yang K, Nie H, Yuan L, Wang S, Zeng L, Ge A, Ge J. The mechanism of intestinal microbiota regulating immunity and inflammation in ischemic stroke and the role of natural botanical active ingredients in regulating intestinal microbiota: A review. Biomed Pharmacother 2023; 157:114026. [PMID: 36436491 DOI: 10.1016/j.biopha.2022.114026] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/07/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022] Open
Abstract
Intestinal microbiota is a unique ecosystem, known as the "second genome" of human beings. With the widespread application of next generation sequencing (NGS), especially 16 S rRNA and shotgun sequencing, numerous studies have shown that dysregulation of intestinal microbiota is associated with many central nervous system diseases. Ischemic stroke (IS) is a cerebrovascular disease with high morbidity and mortality. Brain damage in IS affects intestinal function, and intestinal dysfunction further aggravates brain damage, forming a vicious circle of mutual interference in pathology. The microbiota-gut-brain axis study based on the intestinal microbiota has opened up broader ideas for exploring its pathogenesis and risk factors, and also provided more possibilities for the selection of therapeutic targets for this type of drug. This review discussed the application of NGS technology in the study of intestinal microbiota and the research progress of microbiota-gut-brain axis in recent years, and systematically sorts out the literature on the relationship between ischemic stroke and intestinal microbiota. It starts with the characteristics of microbiota-gut-brain axis' bidirectional regulation, respectively discusses the high risk factors of IS under intestinal microbiota imbalance and the physiological and pathological changes of intestinal microbiota after IS, and summarizes the related targets, in order to provide reliable reference for the treatment of IS from intestinal microbiota. In addition, natural botanical active ingredients have achieved good results in the treatment of IS based on regulating the homeostasis of gut microbiota, providing new evidence for studying the potential targets and therapies of IS based on the microbiota-gut-brain axis.
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Affiliation(s)
- Jinsong Zeng
- The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan Province, China
| | - Kailin Yang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha City, China..
| | - Huifang Nie
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha City, China
| | - Le Yuan
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha City, China
| | - Shanshan Wang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha City, China
| | - Liuting Zeng
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha City, China..
| | - Anqi Ge
- The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan Province, China
| | - Jinwen Ge
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha City, China.; Hunan Academy of Chinese Medicine, Changsha, China..
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18
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Moutinho TJ, Powers DA, Hanson GF, Levy S, Baveja R, Hefner I, Mohamed M, Abdelghani A, Baker RL, Papin JA, Moore SR, Hourigan SK. Fecal sphingolipids predict parenteral nutrition-associated cholestasis in the neonatal intensive care unit. JPEN J Parenter Enteral Nutr 2022; 46:1903-1913. [PMID: 35285019 PMCID: PMC9468188 DOI: 10.1002/jpen.2374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/23/2022] [Accepted: 03/06/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND Parenteral nutrition-associated cholestasis (PNAC) in the neonatal intensive care unit (NICU) causes significant morbidity and associated healthcare costs. Laboratory detection of PNAC currently relies on elevated serum conjugated bilirubin levels in the aftermath of impaired bile flow. Here, we sought to identify fecal biomarkers, which when integrated with clinical data, would better predict risk for developing PNAC. METHODS Using untargeted metabolomics in 200 serial stool samples from 60 infants, we applied statistical and machine learning approaches to identify clinical features and metabolic biomarkers with the greatest associative potential for risk of developing PNAC. Stools were collected prospectively from infants receiving PN with soybean oil-based lipid emulsion at a level IV NICU. RESULTS Low birth weight, extreme prematurity, longer duration of PN, and greater number of antibiotic courses were all risk factors for PNAC (P < 0.05). We identified 78 stool biomarkers with early predictive potential (P < 0.05). From these 78 biomarkers, we further identified 12 sphingomyelin lipids with high association for the development of PNAC in precholestasis stool samples when combined with birth anthropometry. CONCLUSION We demonstrate the potential for stool metabolomics to enhance early identification of PNAC risk. Earlier detection of high-risk infants would empower proactive mitigation with alterations to PN for at-risk infants and optimization of energy nutrition with PN for infants at lower risk.
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Affiliation(s)
- Thomas J. Moutinho
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Deborah A. Powers
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Gabriel F. Hanson
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Shira Levy
- Inova Children's HospitalFalls ChurchVirginiaUSA
| | - Rajiv Baveja
- Fairfax Neonatal AssociatesFalls ChurchVirginiaUSA
| | | | | | | | | | - Jason A. Papin
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Sean R. Moore
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of PediatricsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Suchitra K. Hourigan
- Inova Children's HospitalFalls ChurchVirginiaUSA,Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of PediatricsUniversity of VirginiaCharlottesvilleVirginiaUSA,Division of Pediatric GastroenterologyPediatric Specialists of VirginiaFairfaxVirginiaUSA,Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMarylandUSA
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19
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Expression of Concern: 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome. PLoS One 2022; 17:e0276752. [PMID: 36264907 PMCID: PMC9584445 DOI: 10.1371/journal.pone.0276752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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20
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Abduweli Uyghurturk D, Lu Y, Urata J, C. Dvorak C, Den Besten P. Dental caries as a risk factor for bacterial blood stream infection (BSI) in children undergoing hematopoietic cell transplantation (HCT). PeerJ 2022; 10:e14040. [PMID: 36172496 PMCID: PMC9511999 DOI: 10.7717/peerj.14040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/19/2022] [Indexed: 01/19/2023] Open
Abstract
Background Hematopoietic cell transplantation (HCT) is a potentially curative therapy for a wide range of pediatric malignant and nonmalignant diseases. However, complications, including blood stream infection (BSI) remain a major cause of morbidity and mortality. While certain bacteria that are abundant in the oral microbiome, such as S. mitis, can cause BSI, the role of the oral microbial community in the etiology of BSI is not well understood. The finding that the use of xylitol wipes, which specifically targets the cariogenic bacteria S. mutans is associated with reduced BSI in pediatric patients, lead us to investigate dental caries as a risk factor for BSI. Methods A total of 41 pediatric patients admitted for allogenic or autologous HCT, age 8 months to 25 years, were enrolled. Subjects with high dental caries risk were identified as those who had dental restorations completed within 2 months of admission for transplant, or who had untreated decay. Fisher's exact test was used to determine if there was a significant association between caries risk and BSI. Dental plaque and saliva were collected on a cotton swab from a subset of four high caries risk (HCR) and four low caries risk (LCR) children following pretransplant conditioning. 16SrRNA sequencing was used to compare the microbiome of HCR and LCR subjects and to identify microbes that were significantly different between the two groups. Results There was a statistically significant association between caries risk and BSI (p < 0.035) (Fisher's exact test). Multivariate logistic regression analysis showed children in the high dental caries risk group were 21 times more likely to have BSI, with no significant effect of age or mucositis severity. HCR subjects showed significantly reduced microbial alpha diversity as compared to LCR subjects. LEfse metagenomic analyses, showed the oral microbiome in HCR children enriched in order Lactobacillales. This order includes Streptococcus and Lactobacillus, both which contain bacteria primarily associated with dental caries. Discussion These findings support the possibility that the cariogenic microbiome can enhance the risk of BSI in pediatric populations. Future metagenomic analyses to measure microbial differences at, before, and after conditioning related to caries risk, may further unravel the complex relationship between the oral microbiome, and whether it affects health outcomes such as BSI.
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Affiliation(s)
- Dawud Abduweli Uyghurturk
- Orofacial Science, University of California, San Francisco, San Francisco, CA, United States
- Center for Children’s Oral Health Research, School of Dentistry, University of California, San Francisco, San Francisco, California, United States
| | - Ying Lu
- Division of Pediatric Allergy, Immunology and Bone Marrow Transplant, University of California, San Francisco, San Francisco, California, United States
| | - Janelle Urata
- Orofacial Science, University of California, San Francisco, San Francisco, CA, United States
- Center for Children’s Oral Health Research, School of Dentistry, University of California, San Francisco, San Francisco, California, United States
| | - Christopher C. Dvorak
- Division of Pediatric Allergy, Immunology and Bone Marrow Transplant, University of California, San Francisco, San Francisco, California, United States
| | - Pamela Den Besten
- Orofacial Science, University of California, San Francisco, San Francisco, CA, United States
- Center for Children’s Oral Health Research, School of Dentistry, University of California, San Francisco, San Francisco, California, United States
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21
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Petrillo F, Petrillo A, Marrapodi M, Capristo C, Gicchino MF, Montaldo P, Caredda E, Reibaldi M, Boatti LMV, Dell’Annunziata F, Folliero V, Galdiero M. Characterization and Comparison of Ocular Surface Microbiome in Newborns. Microorganisms 2022; 10:microorganisms10071390. [PMID: 35889110 PMCID: PMC9320102 DOI: 10.3390/microorganisms10071390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 12/10/2022] Open
Abstract
The ocular microbiome is of fundamental importance for immune eye homeostasis, and its alteration would lead to an impairment of ocular functionality. Little evidence is reported on the composition of the ocular microbiota of term infants and on the impact of antibiotic prophylaxis. Methods: A total of 20 conjunctival swabs were collected from newborns at birth and after antibiotic treatment. Samples were subjected to 16S rRNA sequencing via system MiSeq Illumina. The data were processed with the MicrobAT software and statistical analysis were performed using two-way ANOVA. Results: Antibiotic prophylaxis with gentamicin altered the composition of the microbiota. In detail, a 1.5- and 2.01-fold reduction was recorded for Cutibacterium acnes (C. acnes) and Massilia timonae (M. timonae), respectively, whereas an increase in Staphylococcus spp. of 6.5 times occurred after antibiotic exposure. Conclusions: Antibiotic prophylaxis altered the ocular microbiota whose understanding could avoid adverse effects on eye health.
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Affiliation(s)
- Francesco Petrillo
- Department of Surgical Sciences, Eye Clinic Section, University of Turin, 10124 Turin, Italy; (F.P.); (M.R.)
| | - Arianna Petrillo
- Pediatric Unit, Fondazione IRCCS “Ca’ Granda-Ospedale Maggiore-Policlinico”, 20122 Milan, Italy;
| | - Maddalena Marrapodi
- Department of Woman, Child and General and Specialist Surgery, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy; (M.M.); (M.F.G.)
| | - Carlo Capristo
- Department of Neonatology, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.C.); (P.M.); (E.C.)
| | - Maria Francesca Gicchino
- Department of Woman, Child and General and Specialist Surgery, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy; (M.M.); (M.F.G.)
| | - Paolo Montaldo
- Department of Neonatology, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.C.); (P.M.); (E.C.)
| | - Elisabetta Caredda
- Department of Neonatology, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.C.); (P.M.); (E.C.)
| | - Michele Reibaldi
- Department of Surgical Sciences, Eye Clinic Section, University of Turin, 10124 Turin, Italy; (F.P.); (M.R.)
| | | | - Federica Dell’Annunziata
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (F.D.); (V.F.)
| | - Veronica Folliero
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (F.D.); (V.F.)
| | - Marilena Galdiero
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (F.D.); (V.F.)
- Correspondence:
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22
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Yeo LF, Lee SC, Palanisamy UD, Khalid BAK, Ayub Q, Lim SY, Lim YAL, Phipps ME. The Oral, Gut Microbiota and Cardiometabolic Health of Indigenous Orang Asli Communities. Front Cell Infect Microbiol 2022; 12:812345. [PMID: 35531342 PMCID: PMC9074829 DOI: 10.3389/fcimb.2022.812345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
The Orang Asli (OA) of Malaysia have been relatively understudied where little is known about their oral and gut microbiomes. As human health is closely intertwined with the human microbiome, this study first assessed the cardiometabolic health in four OA communities ranging from urban, rural to semi-nomadic hunter-gatherers. The urban Temuan suffered from poorer cardiometabolic health while rural OA communities were undergoing epidemiological transition. The oral microbiota of the OA were characterised by sequencing the V4 region of the 16S rRNA gene. The OA oral microbiota were unexpectedly homogenous, with comparably low alpha diversity across all four communities. The rural Jehai and Temiar PP oral microbiota were enriched for uncharacterised bacteria, exhibiting potential for discoveries. This finding also highlights the importance of including under-represented populations in large cohort studies. The Temuan oral microbiota were also elevated in opportunistic pathogens such as Corynebacterium, Prevotella, and Mogibacterium, suggesting possible oral dysbiosis in these urban settlers. The semi-nomadic Jehai gut microbiota had the highest alpha diversity, while urban Temuan exhibited the lowest. Rural OA gut microbiota were distinct from urban-like microbiota and were elevated in bacteria genera such as Prevotella 2, Prevotella 9, Lachnospiraceae ND3007, and Solobacterium. Urban Temuan microbiota were enriched in Odoribacter, Blautia, Parabacetroides, Bacteroides and Ruminococcacecae UCG-013. This study brings to light the current health trend of these indigenous people who have minimal access to healthcare and lays the groundwork for future, in-depth studies in these populations.
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Affiliation(s)
- Li-Fang Yeo
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
- *Correspondence: Maude Elvira Phipps, ; Li-Fang Yeo,
| | - Soo Ching Lee
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Uma Devi Palanisamy
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
| | - BAK. Khalid
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Qasim Ayub
- Tropical Medicine and Biology Multidisciplinary Platform, School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
- Monash University Malaysia Genomics Facility, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Shu Yong Lim
- Monash University Malaysia Genomics Facility, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Yvonne AL. Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Maude Elvira Phipps
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
- *Correspondence: Maude Elvira Phipps, ; Li-Fang Yeo,
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Huang R, Wu F, Zhou Q, Wei W, Yue J, Xiao B, Luo Z. Lactobacillus and intestinal diseases: mechanisms of action and clinical applications. Microbiol Res 2022; 260:127019. [DOI: 10.1016/j.micres.2022.127019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 12/12/2022]
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Price CA, Jospin G, Brownell K, Eisen JA, Laraia B, Epel ES. Differences in gut microbiome by insulin sensitivity status in Black and White women of the National Growth and Health Study (NGHS): A pilot study. PLoS One 2022; 17:e0259889. [PMID: 35045086 PMCID: PMC8769296 DOI: 10.1371/journal.pone.0259889] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 10/28/2021] [Indexed: 12/22/2022] Open
Abstract
The prevalence of overweight and obesity is greatest amongst Black women in the U.S., contributing to disproportionately higher type 2 diabetes prevalence compared to White women. Insulin resistance, independent of body mass index, tends to be greater in Black compared to White women, yet the mechanisms to explain these differences are not completely understood. The gut microbiome is implicated in the pathophysiology of obesity, insulin resistance and cardiometabolic disease. Only two studies have examined race differences in Black and White women, however none characterizing the gut microbiome based on insulin sensitivity by race and sex. Our objective was to determine if gut microbiome profiles differ between Black and White women and if so, determine if these race differences persisted when accounting for insulin sensitivity status. In a pilot cross-sectional analysis, we measured the relative abundance of bacteria in fecal samples collected from a subset of 168 Black (n = 94) and White (n = 74) women of the National Growth and Health Study (NGHS). We conducted analyses by self-identified race and by race plus insulin sensitivity status (e.g. insulin sensitive versus insulin resistant as determined by HOMA-IR). A greater proportion of Black women were classified as IR (50%) compared to White women (30%). Alpha diversity did not differ by race nor by race and insulin sensitivity status. Beta diversity at the family level was significantly different by race (p = 0.033) and by the combination of race plus insulin sensitivity (p = 0.038). Black women, regardless of insulin sensitivity, had a greater relative abundance of the phylum Actinobacteria (p = 0.003), compared to White women. There was an interaction between race and insulin sensitivity for Verrucomicrobia (p = 0.008), where among those with insulin resistance, Black women had four fold higher abundance than White women. At the family level, we observed significant interactions between race and insulin sensitivity for Lachnospiraceae (p = 0.007) and Clostridiales Family XIII (p = 0.01). Our findings suggest that the gut microbiome, particularly lower beta diversity and greater Actinobacteria, one of the most abundant species, may play an important role in driving cardiometabolic health disparities of Black women, indicating an influence of social and environmental factors on the gut microbiome.
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Affiliation(s)
- Candice A. Price
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Guillaume Jospin
- Genome Center, University of California Davis, Davis, CA, United States of America
| | - Kristy Brownell
- Center for Obesity Assessment, Study and Treatment, University of California, San Francisco, California, United States of America
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Jonathan A. Eisen
- Genome Center, University of California Davis, Davis, CA, United States of America
- Department of Evolution and Ecology, University of California, Davis, CA, United States of America
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, United States of America
| | - Barbara Laraia
- Center for Obesity Assessment, Study and Treatment, University of California, San Francisco, California, United States of America
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Elissa S. Epel
- Department of Psychiatry, University of California, San Francisco, CA, United States of America
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25
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Tian R, Imanian B. ASAP 2: a pipeline and web server to analyze marker gene amplicon sequencing data automatically and consistently. BMC Bioinformatics 2022; 23:27. [PMID: 34991446 PMCID: PMC8740450 DOI: 10.1186/s12859-021-04555-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/30/2021] [Indexed: 01/04/2023] Open
Abstract
Background Amplicon sequencing of marker genes such as 16S rDNA have been widely used to survey and characterize microbial community. However, the complex data analyses have required many interfering manual steps often leading to inconsistencies in results. Results Here, we have developed a pipeline, amplicon sequence analysis pipeline 2 (ASAP 2), to automate and glide through the processes without the usual manual inspections and user’s interference, for instance, in the detection of barcode orientation, selection of high-quality region of reads, and determination of resampling depth and many more. The pipeline integrates all the analytical processes such as importing data, demultiplexing, summarizing read profiles, trimming quality, denoising, removing chimeric sequences and making the feature table among others. The pipeline accepts multiple file formats as input including multiplexed or demultiplexed, paired-end or single-end, barcode inside or outside and raw or intermediate data (e.g. feature table). The outputs include taxonomic classification, alpha/beta diversity, community composition, ordination analysis and statistical tests. ASAP 2 supports merging multiple sequencing runs which helps integrate and compare data from different sources (public databases and collaborators). Conclusions Our pipeline minimizes hands-on interference and runs amplicon sequence variant (ASV)-based amplicon sequencing analysis automatically and consistently. Our web server assists researchers that have no access to high performance computer (HPC) or have limited bioinformatics skills. The pipeline and web server can be accessed at https://github.com/tianrenmaogithub/asap2 and https://hts.iit.edu/asap2, respectively. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04555-0.
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Affiliation(s)
- Renmao Tian
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, 60501, USA
| | - Behzad Imanian
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, 60501, USA. .,Department of Food Science and Nutrition, Illinois Institute of Technology, Bedford Park, IL, 60501, USA.
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26
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Moreno I, Garcia-Grau I, Perez-Villaroya D, Gonzalez-Monfort M, Bahçeci M, Barrionuevo MJ, Taguchi S, Puente E, Dimattina M, Lim MW, Meneghini G, Aubuchon M, Leondires M, Izquierdo A, Perez-Olgiati M, Chavez A, Seethram K, Bau D, Gomez C, Valbuena D, Vilella F, Simon C. Endometrial microbiota composition is associated with reproductive outcome in infertile patients. MICROBIOME 2022; 10:1. [PMID: 34980280 PMCID: PMC8725275 DOI: 10.1186/s40168-021-01184-w] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 11/01/2021] [Indexed: 05/15/2023]
Abstract
BACKGROUND Previous evidence indicates associations between the female reproductive tract microbiome composition and reproductive outcome in infertile patients undergoing assisted reproduction. We aimed to determine whether the endometrial microbiota composition is associated with reproductive outcomes of live birth, biochemical pregnancy, clinical miscarriage or no pregnancy. METHODS Here, we present a multicentre prospective observational study using 16S rRNA gene sequencing to analyse endometrial fluid and biopsy samples before embryo transfer in a cohort of 342 infertile patients asymptomatic for infection undergoing assisted reproductive treatments. RESULTS A dysbiotic endometrial microbiota profile composed of Atopobium, Bifidobacterium, Chryseobacterium, Gardnerella, Haemophilus, Klebsiella, Neisseria, Staphylococcus and Streptococcus was associated with unsuccessful outcomes. In contrast, Lactobacillus was consistently enriched in patients with live birth outcomes. CONCLUSIONS Our findings indicate that endometrial microbiota composition before embryo transfer is a useful biomarker to predict reproductive outcome, offering an opportunity to further improve diagnosis and treatment strategies. Video Abstract.
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Affiliation(s)
- Inmaculada Moreno
- Igenomix Foundation, INCLIVA Health Research Institute, Valencia, Spain
- Igenomix R&D, Valencia, Spain
| | - Iolanda Garcia-Grau
- Igenomix Foundation, INCLIVA Health Research Institute, Valencia, Spain
- Department of Obstetrics and Gynecology, University of Valencia, Valencia, Spain
| | | | - Marta Gonzalez-Monfort
- Igenomix Foundation, INCLIVA Health Research Institute, Valencia, Spain
- Igenomix R&D, Valencia, Spain
| | | | | | | | | | | | - Mei Wei Lim
- Alpha IVF and Women's Specialists Centre, Petaling Jaya, Selangor, Malaysia
| | | | - Mira Aubuchon
- Missouri Center for Reproductive Medicine, Chesterfield, MO, USA
| | | | - Alexandra Izquierdo
- ProcreaTec, Madrid, Spain
- Present Address: Médipôle Lyon-Villeurbanne, Villeurbanne, France
| | | | | | - Ken Seethram
- Pacific Centre for Reproductive Medicine, Burnaby, British Columbia, Canada
| | | | | | | | - Felipe Vilella
- Igenomix Foundation, INCLIVA Health Research Institute, Valencia, Spain
| | - Carlos Simon
- Igenomix Foundation, INCLIVA Health Research Institute, Valencia, Spain.
- Igenomix R&D, Valencia, Spain.
- Department of Obstetrics and Gynecology, University of Valencia, Valencia, Spain.
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA.
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Abstract
OPINION STATEMENT Immunotherapy is revolutionizing tumor treatment by activating the immune response to tumors. Among them, immunotherapy represented by immune checkpoint inhibitors is considered to be a milestone in tumor treatment. It has revolutionized the management of advanced malignant tumors by activating T cells, promoting cytotoxic signaling pathways, and killing tumor cells, effectively improving the overall survival of patients. However, resistance to immunotherapy and immune-related adverse events remain challenges for immunotherapy. It has been demonstrated in previous studies that modulating intestinal microbiota can enhance immunotherapy response and reduce complications. Currently, the more mature method for microbiota regulation is fecal microbiota transplantation, which involves transfering a donor's microbiome to the recipient in the form of capsules or fecal microbiota suspension to restore the richness of the recipient's intestinal microbiota. In terms of cancer immunotherapy, fecal microbiota transplantation in patients who fail to respond to immune checkpoint inhibitors is expected to produce better prognosis for patients.
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28
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The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host. Sci Rep 2021; 11:24017. [PMID: 34911987 PMCID: PMC8674285 DOI: 10.1038/s41598-021-03334-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 11/24/2021] [Indexed: 12/15/2022] Open
Abstract
Plant microbiomes have been extensively studied for their agricultural relevance on growth promotion and pathogenesis, but little is known about their role as part of the diet when fresh fruits and vegetables are consumed raw. Most studies describing these communities are based on 16S rRNA gene amplicon surveys, limiting our understanding of the taxonomic resolution at the species level and functional capabilities. In this study, we characterized microbes colonizing tomatoes, spinach, brined olives, and dried figs using shotgun metagenomics. We recovered metagenome-assembled genomes of novel lactic acid bacteria from green olives and identified high intra- and inter-specific diversity of Pseudomonas in tomatoes. All samples were colonized by Pseudomonas, consistent with other reports with distinct community structure. Functional characterization showed the presence of enzymes involved in vitamin and short chain fatty acid metabolism and degradation of diverse carbohydrate substrates including plant fibers. The dominant bacterial members were isolated, sequenced, and mapped to its metagenome confirming their identity and indicating the microbiota is culturable. Our results reveal high genetic diversity, previously uncultured genera, and specific functions reflecting a likely plant host association. This study highlights the potential that plant microbes can play when consumed as part of our diet and proposes these as transient contributors to the gut microbiome.
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Okwelogu SI, Ikechebelu JI, Agbakoba NR, Anukam KC. Microbiome Compositions From Infertile Couples Seeking In Vitro Fertilization, Using 16S rRNA Gene Sequencing Methods: Any Correlation to Clinical Outcomes? Front Cell Infect Microbiol 2021; 11:709372. [PMID: 34660337 PMCID: PMC8517523 DOI: 10.3389/fcimb.2021.709372] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 09/08/2021] [Indexed: 01/22/2023] Open
Abstract
Background Bacterial infections are usually suspected in infertile couples seeking IVF with no clear understanding of the microbial compositions present in the seminal fluids and vaginal niche of the patients. We used next-generation sequencing technology to correlate microbiota compositions with IVF clinical outcomes. Methods Thirty-six couples were recruited to provide seminal fluids and vaginal swabs. Bacterial DNA was extracted, and V4 region of the 16S rRNA was amplified and sequenced in a pair-end configuration on the Illumina MiSeq platform rendering 2 × 150 bp sequences. Microbial taxonomy to species level was generated using the Greengenes database. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biologically and statistically significant differences in relative abundance. Results Seminal fluid microbiota compositions had lower bacterial concentrations compared with the vagina, but species diversity was significantly higher in seminal fluid samples. Azoospermic subjects had more relative abundance of Mycoplasma and Ureaplasma. In Normospermic semen, Lactobacillus (43.86%) was the most abundant, followed by Gardnerella (25.45%), while the corresponding vaginal samples, Lactobacillus (61.74%) was the most abundant, followed by Prevotella (6.07%) and Gardnerella (5.86%). Conclusions Semen samples with positive IVF were significantly colonized by Lactobacillus jensenii (P=0.002), Faecalibacterium (P=0.042) and significantly less colonized by Proteobacteria, Prevotella, Bacteroides, and lower Firmicutes/Bacteroidetes ratio compared with semen samples with negative IVF. Vaginal samples with positive IVF clinical outcome were significantly colonized by Lactobacillus gasseri, less colonized by Bacteroides and Lactobacillus iners. This study has opened a window of possibility for Lactobacillus replenishments in men and women before IVF treatment.
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Affiliation(s)
- Somadina I Okwelogu
- Department of Medical Laboratory Science, Faculty of Health Sciences & Technology, Nnamdi Azikiwe University, Nnewi, Nigeria
| | - Joseph I Ikechebelu
- Department of Obstetrics and Gynaecology, Nnamdi Azikiwe University Teaching Hospital, Nnewi, Nigeria
| | - Nneka R Agbakoba
- Department of Medical Laboratory Science, Faculty of Health Sciences & Technology, Nnamdi Azikiwe University, Nnewi, Nigeria
| | - Kingsley C Anukam
- Department of Medical Laboratory Science, Faculty of Health Sciences & Technology, Nnamdi Azikiwe University, Nnewi, Nigeria.,Department of Pharmaceutical Microbiology, Faculty of Pharmaceutical Sciences, Nnamdi Azikiwe University, Awka, Nigeria.,Department of Research and Development, Uzobiogene Genomics, London, ON, Canada
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30
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Abstract
Microbes in the 21st century are understood as symbionts ‘completing’ the human ‘superorganism’ (Homo sapiens plus microbial partners-in-health). This paper addresses a significant paradox: despite the vast majority of our genes being microbial, the lack of routine safety testing for the microbiome has led to unintended collateral side effects from pharmaceuticals that can damage the microbiome and inhibit innate ‘colonization resistance’ against pathobionts. Examples are discussed in which a Microbiome First Medicine approach provides opportunities to ‘manage our microbes’ holistically, repair dysbiotic superorganisms, and restore health and resilience in the gut and throughout the body: namely, managing nosocomial infections for Clostridioides difficile and Staphylococcus aureus and managing the gut and neural systems (gut–brain axis) in autism spectrum disorder. We then introduce a risk analysis tool: the evidence map. This ‘mapping’ tool was recently applied by us to evaluate evidence for benefits, risks, and uncertainties pertaining to the breastmilk ecosystem. Here, we discuss the potential role of the evidence map as a risk analysis methodology to guide scientific and societal efforts to: (1) enhance ecosystem resilience, (2) ‘manage our microbes’, and (3) minimize the adverse effects of both acute and chronic diseases.
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Hillman AR, Chrismas BCR. Thirty Days of Montmorency Tart Cherry Supplementation Has No Effect on Gut Microbiome Composition, Inflammation, or Glycemic Control in Healthy Adults. Front Nutr 2021; 8:733057. [PMID: 34604282 PMCID: PMC8481367 DOI: 10.3389/fnut.2021.733057] [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: 06/29/2021] [Accepted: 08/19/2021] [Indexed: 01/14/2023] Open
Abstract
Tart cherries possess properties that may reduce inflammation and improve glycemic control, however human data on supplementation and the gut microbiota is equivocal. Processing (i.e., juice concentrate, dried, frozen) may affect the properties of tart cherries, and therefore alter their efficacious health benefits. Therefore, the purpose of this study was to investigate the effect of 30 days of supplementation with Montmorency tart cherry (MTC) in concentrate or freeze-dried form on the gut microbiome and markers of inflammation and glycemic control. Healthy participants with no known disease (n = 58, age: 28 ± 10 y, height: 169.76 ± 8.55 cm, body mass: 72.2 ± 12.9 kg) were randomly allocated to four groups and consumed either concentrate or freeze-dried capsules or their corresponding placebos for 30 days. Venous blood samples were drawn at baseline, day 7, 14, and 30 and analyzed for inflammatory markers TNF-alpha, uric acid, C-reactive protein, and erythrocyte sedimentation rate and glycemic control markers glycated albumin, glucose and insulin. A fecal sample was provided at baseline, day 14 and 30 for microbiome analysis. TNF-alpha was significantly lower at 30 vs. 14 days (p = 0.01), however there was no other significant change in the inflammatory markers. Insulin was not changed over time (p = 0.16) or between groups (p = 0.24), nor was glycated albumin different over time (p = 0.08) or between groups (p = 0.56), however glucose levels increased (p < 0.001) from baseline (4.79 ± 1.00 mmol·L-1) to 14 days (5.21 ± 1.02 mmol·L-1) and 30 days (5.61 ± 1.22 mmol·L-1) but this was no different between groups (p = 0.33). There was no significant change in composition of bacterial phyla, families, or subfamilies for the duration of this study nor was there a change in species richness. These data suggest that 30 days of MTC supplementation does not modulate the gut microbiome, inflammation, or improve glycemic control in a healthy, diverse group of adults. Clinical Trail Registration:https://clinicaltrials.gov/ct2/show/NCT04467372, identifier: NCT04467372.
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Affiliation(s)
- Angela R Hillman
- School of Applied Health Sciences and Wellness, Division of Exercise Physiology, Ohio University, Athens, OH, United States
| | - Bryna C R Chrismas
- College of Education, Department of Physical Education, Qatar University, Doha, Qatar
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Mindus C, van Staaveren N, Fuchs D, Gostner JM, Kjaer JB, Kunze W, Mian MF, Shoveller AK, Forsythe P, Harlander-Matauschek A. L. rhamnosus improves the immune response and tryptophan catabolism in laying hen pullets. Sci Rep 2021; 11:19538. [PMID: 34599202 PMCID: PMC8486881 DOI: 10.1038/s41598-021-98459-x] [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: 06/09/2021] [Accepted: 08/30/2021] [Indexed: 02/08/2023] Open
Abstract
In mammals, early-life probiotic supplementation is a promising tool for preventing unfavourable, gut microbiome-related behavioural, immunological, and aromatic amino acid alterations later in life. In laying hens, feather-pecking behaviour is proposed to be a consequence of gut-brain axis dysregulation. Lactobacillus rhamnosus decreases stress-induced severe feather pecking in adult hens, but whether its effect in pullets is more robust is unknown. Consequently, we investigated whether early-life, oral supplementation with a single Lactobacillus rhamnosus strain can prevent stress-induced feather-pecking behaviour in chickens. To this end, we monitored both the short- and long-term effects of the probiotic supplement on behaviour and related physiological parameters. We hypothesized that L. rhamnosus would reduce pecking behaviour by modulating the biological pathways associated with this detrimental behaviour, namely aromatic amino acid turnover linked to neurotransmitter production and stress-related immune responses. We report that stress decreased the proportion of cytotoxic T cells in the tonsils (P = 0.047). Counteracting this T cell depression, birds receiving the L. rhamnosus supplementation significantly increased all T lymphocyte subset proportions (P < 0.05). Both phenotypic and genotypic feather peckers had lower plasma tryptophan concentrations compared to their non-pecking counterparts. The probiotic supplement caused a short-term increase in plasma tryptophan (P < 0.001) and the TRP:(PHE + TYR) ratio (P < 0.001). The administration of stressors did not significantly increase feather pecking in pullets, an observation consistent with the age-dependent onset of pecking behaviour. Despite minimal changes to behaviour, our data demonstrate the impact of L. rhamnosus supplementation on the immune system and the turnover of the serotonin precursor tryptophan. Our findings indicate that L. rhamnosus exerts a transient, beneficial effect on the immune response and tryptophan catabolism in pullets.
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Affiliation(s)
- Claire Mindus
- grid.34429.380000 0004 1936 8198Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1 Canada
| | - Nienke van Staaveren
- grid.34429.380000 0004 1936 8198Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1 Canada
| | - Dietmar Fuchs
- grid.5361.10000 0000 8853 2677Institute of Biological Chemistry, Biocenter, Center for Chemistry and Biomedicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Johanna M. Gostner
- grid.5361.10000 0000 8853 2677Institute of Medical Biochemistry, Biocenter, Center for Chemistry and Biomedicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Joergen B. Kjaer
- grid.417834.dInstitute of Animal Welfare and Animal Husbandry, Friedrich-Loeffler-Institut, Celle, Germany
| | - Wolfgang Kunze
- grid.25073.330000 0004 1936 8227Brain-Body Institute, St. Joseph’s Healthcare, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1 Canada
| | - M. Firoz Mian
- grid.25073.330000 0004 1936 8227Division of Respirology, Department of Medicine, McMaster University, 50 Charlton Avenue East, Hamilton, ON L8N 4A6 Canada
| | - Anna K. Shoveller
- grid.34429.380000 0004 1936 8198Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1 Canada
| | - Paul Forsythe
- grid.25073.330000 0004 1936 8227Division of Respirology, Department of Medicine, McMaster University, 50 Charlton Avenue East, Hamilton, ON L8N 4A6 Canada
| | - Alexandra Harlander-Matauschek
- grid.34429.380000 0004 1936 8198Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1 Canada
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Nogal B, Blumberg JB, Blander G, Jorge M. Gut Microbiota-Informed Precision Nutrition in the Generally Healthy Individual: Are We There Yet? Curr Dev Nutr 2021; 5:nzab107. [PMID: 34514287 PMCID: PMC8421235 DOI: 10.1093/cdn/nzab107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 02/07/2023] Open
Abstract
Since next generation sequencing facilitated high-throughput and cost-efficient genomics analyses, the human gut metagenome has become an emerging frontier to explore toward precision nutrition. Significant progress has been made in identifying gut microbial features associated with a wide spectrum of human disease. However, other than a few microbiome-disease relations, there is a dearth of confirmed causal inferences, particularly in generally healthy populations. The relatively high unexplained variability in microbiome compositions in this group warrants caution in applying this complex biomarker toward precision nutrition, because our understanding of what constitutes a healthy microbiome is still rudimentary. Although gut microbiota harbor integrated environmental and host-specific information with the potential to facilitate personalized nutritional and lifestyle advice, these data cannot yet be confidently interpreted toward precise recommendations. Thus, nutritional advice for generally healthy individuals based on personal microbiome composition analysis might not yet be appropriate unless accompanied by established blood and physiological biomarkers.
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Affiliation(s)
| | - Jeffrey B Blumberg
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
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Zhang F, Xu N, Wang W, Yu Y, Wu S. The gut microbiome of the Sunda pangolin ( Manis javanica) reveals its adaptation to specialized myrmecophagy. PeerJ 2021; 9:e11490. [PMID: 34141474 PMCID: PMC8179220 DOI: 10.7717/peerj.11490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/28/2021] [Indexed: 12/24/2022] Open
Abstract
Background The gut microbiomes of mammals are closely related to the diets of their hosts. The Sunda pangolin (Manis javanica) is a specialized myrmecophage, but its gut microbiome has rarely been studied. Methods Using high-throughput Illumina barcoded 16S rRNA amplicons of nine fecal samples from nine captive Sunda pangolins, we investigated their gut microbiomes. Results The detected bacteria were classified into 14 phyla, 24 classes, 48 orders, 97 families, and 271 genera. The main bacterial phyla were Firmicutes (73.71%), Proteobacteria (18.42%), Actinobacteria (3.44%), and Bacteroidetes (0.51%). In the PCoA and neighbor-net network (PERMANOVA: pangolins vs. other diets, weighted UniFrac distance p < 0.01, unweighted UniFrac distance p < 0.001), the gut microbiomes of the Sunda pangolins were distinct from those of mammals with different diets, but were much closer to other myrmecophages, and to carnivores, while distant from herbivores. We identified some gut microbiomes related to the digestion of chitin, including Lactococcus, Bacteroides, Bacillus, and Staphylococcus species, which confirms that the gut microbiome of pangolins may help them to digest chitin. Significance The results will aid studies of extreme dietary adaption and the mechanisms of diet differentiation in mammals, as well as metagenomic studies, captive breeding, and ex situ conservation of pangolins.
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Affiliation(s)
- Fuhua Zhang
- School of Life Science, South China Normal University, Guangzhou, Guangdong Province, China
| | - Na Xu
- School of Life Science, South China Normal University, Guangzhou, Guangdong Province, China
| | - Wenhua Wang
- School of Life Science, South China Normal University, Guangzhou, Guangdong Province, China
| | - Yishuang Yu
- School of Life Science, South China Normal University, Guangzhou, Guangdong Province, China
| | - Shibao Wu
- School of Life Science, South China Normal University, Guangzhou, Guangdong Province, China
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Mindus C, Ellis J, van Staaveren N, Harlander-Matauschek A. Lactobacillus-Based Probiotics Reduce the Adverse Effects of Stress in Rodents: A Meta-analysis. Front Behav Neurosci 2021; 15:642757. [PMID: 34220459 PMCID: PMC8241911 DOI: 10.3389/fnbeh.2021.642757] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/19/2021] [Indexed: 12/27/2022] Open
Abstract
Lactobacillus species play a critical role in the bidirectional communication between the gut and the brain. Consequently, they have the potential to aid in the treatment of psychological disorders. The impact of Lactobacillus supplementation on the stress responses triggering psychological disorders has not been systematically reviewed. Therefore, the aim of this meta-analysis is to summarize the body of research assessing the effects of Lactobacillus-based probiotics in rodents that underwent an experimental stress treatment or not. The duration of immobility in a Forced Swim Test (FST) was the outcome used to measure changes induced by various treatments. Four online databases were systematically searched for relevant studies published in English. Fourteen studies meeting the criteria were included in the meta-analysis. The effects of probiotic supplementation and stress treatment on the duration of immobility in the FST were analyzed using a generalized linear mixed model. Publication bias was evaluated by funnel plots. Our analysis shows that Lactobacillus-based probiotic supplements significantly reduce immobility in the FST (P < 0.001) in stressed rodents. However, probiotics did not affect the rodents that did not undergo the stress treatment (P = 0.168). These findings provide a better understanding of the potential of Lactobacillus-based probiotics for the management of stress-induced behavior.
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Affiliation(s)
- Claire Mindus
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Jennifer Ellis
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
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Majumdar R, Kandel SL, Cary JW, Rajasekaran K. Changes in Bacterial Endophyte Community Following Aspergillus flavus Infection in Resistant and Susceptible Maize Kernels. Int J Mol Sci 2021; 22:ijms22073747. [PMID: 33916873 PMCID: PMC8038446 DOI: 10.3390/ijms22073747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 01/10/2023] Open
Abstract
Aspergillus flavus (A. flavus)-mediated aflatoxin contamination in maize is a major global economic and health concern. As A. flavus is an opportunistic seed pathogen, the identification of factors contributing to kernel resistance will be of great importance in the development of novel mitigation strategies. Using V3–V4 bacterial rRNA sequencing and seeds of A. flavus-resistant maize breeding lines TZAR102 and MI82 and a susceptible line, SC212, we investigated kernel-specific changes in bacterial endophytes during infection. A total of 81 bacterial genera belonging to 10 phyla were detected. Bacteria belonging to the phylum Tenericutes comprised 86–99% of the detected phyla, followed by Proteobacteria (14%) and others (<5%) that changed with treatments and/or genotypes. Higher basal levels (without infection) of Streptomyces and Microbacterium in TZAR102 and increases in the abundance of Stenotrophomonas and Sphingomonas in MI82 following infection may suggest their role in resistance. Functional profiling of bacteria using 16S rRNA sequencing data revealed the presence of bacteria associated with the production of putative type II polyketides and sesquiterpenoids in the resistant vs. susceptible lines. Future characterization of endophytes predicted to possess antifungal/ anti-aflatoxigenic properties will aid in their development as effective biocontrol agents or microbiome markers for maize aflatoxin resistance.
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Kiecolt-Glaser JK, Wilson SJ, Shrout MR, Madison AA, Andridge R, Peng J, Malarkey WB, Bailey MT. The gut reaction to couples' relationship troubles: A route to gut dysbiosis through changes in depressive symptoms. Psychoneuroendocrinology 2021; 125:105132. [PMID: 33486306 PMCID: PMC7904664 DOI: 10.1016/j.psyneuen.2021.105132] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 12/16/2022]
Abstract
The gut microbiota plays a role in a wide range of diseases and disorders, with low microbial diversity and richness emerging as notable risk factors. This longitudinal study addressed the impact of marital quality (assessed by the Couples Satisfaction Index) on changes in depressive symptoms, and gut diversity, richness, and permeability. On two occasions an average of 90 days apart, 162 people provided stool and blood samples, and completed questionnaires. Depressive symptoms, assessed by the Center for Epidemiological Studies Depression Scale (CES-D), increased from visit 1 to visit 2 in those with clinically significant relationship problems, in contrast to the lack of change among their more satisfied counterparts. These changes in depression were consequential: the gut microbiota's diversity and richness decreased in tandem with the increase in depressive symptoms. Lower relationship satisfaction also foreshadowed increases in lipopolysaccharide binding protein from visit 1 to visit 2, reflecting greater translocation of bacterial endotoxin from the gut to blood circulation, a process that fuels inflammation. Lower diversity and richness provide a pathway from depressive symptoms and marital distress to subsequent health risk.
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Affiliation(s)
- Janice K Kiecolt-Glaser
- Institute for Behavioral Medicine Research, The Ohio State University College of Medicine, Columbus, OH, USA; Department of Psychiatry and Behavioral Health, The Ohio State University College of Medicine, Columbus, OH, USA.
| | - Stephanie J Wilson
- Department of Psychology, Southern Methodist University, Dallas, TX, USA
| | - M Rosie Shrout
- Institute for Behavioral Medicine Research, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Annelise A Madison
- Institute for Behavioral Medicine Research, The Ohio State University College of Medicine, Columbus, OH, USA; Department of Psychology, The Ohio State University, Columbus, OH, USA
| | - Rebecca Andridge
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Juan Peng
- Center for Biostatistics, The Ohio State University, Columbus, OH, USA
| | - William B Malarkey
- Institute for Behavioral Medicine Research, The Ohio State University College of Medicine, Columbus, OH, USA; Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Michael T Bailey
- Institute for Behavioral Medicine Research, The Ohio State University College of Medicine, Columbus, OH, USA; Department of Pediatrics, The Ohio State College of Medicine and Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
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Cleary DW, Morris DE, Anderson RA, Jones J, Alattraqchi AG, A Rahman NI, Ismail S, Razali MS, Mohd Amin R, Abd Aziz A, Esa NK, Amiruddin S, Chew CH, Simin H, Abdullah R, Yeo CC, Clarke SC. The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia. NPJ Biofilms Microbiomes 2021; 7:1. [PMID: 33402693 PMCID: PMC7785749 DOI: 10.1038/s41522-020-00173-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022] Open
Abstract
Much microbiome research has focused on populations that are predominantly of European descent, and from narrow demographics that do not capture the socio-economic and lifestyle differences which impact human health. Here we examined the airway microbiomes of the Orang Asli, the indigenous peoples of Malaysia. A total of 130 participants were recruited from two sites in the north-eastern state of Terengganu in Peninsular Malaysia. Using 16S rRNA sequencing, the nasal microbiome was significantly more diverse in those aged 5-17 years compared to 50+ years (p = 0.023) and clustered by age (PERMANOVA analysis of the Bray-Curtis distance, p = 0.001). Hierarchical clustering of Bray-Curtis dissimilarity scores revealed six microbiome clusters. The largest cluster (n = 28; 35.4%) had a marked abundance of Corynebacterium. In the oral microbiomes Streptococcus, Neisseria and Haemophilus were dominant. Using conventional microbiology, high levels of Staphylococcus aureus carriage were observed, particularly in the 18-65 age group (n = 17/36; 47.2% 95% CI: 30.9-63.5). The highest carriage of pneumococci was in the <5 and 5 to 17 year olds, with 57.1% (4/7) and 49.2% (30/61), respectively. Sixteen pneumococcal serotypes were identified, the most common being the nonvaccine-type 23A (14.6%) and the vaccine-type 6B (9.8%). The prevalence of pneumococcal serotypes covered by pneumococcal conjugate vaccines support introduction into a Malaysian national immunisation schedule. In addition, the dominance of Corynebacterium in the airway microbiomes is intriguing given their role as a potentially protective commensal with respect to acute infection and respiratory health.
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Affiliation(s)
- David W Cleary
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Trust, Southampton, UK.
| | - Denise E Morris
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Rebecca A Anderson
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Jessica Jones
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Ahmed Ghazi Alattraqchi
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Nor Iza A Rahman
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Salwani Ismail
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Mohd Sayuti Razali
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Rahmah Mohd Amin
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Aniza Abd Aziz
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Nor Kamaruzaman Esa
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Salman Amiruddin
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Ching Hoong Chew
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Gong Badak Campus, 21300, Kuala Nerus, Terengganu, Malaysia
| | - Hafis Simin
- Faculty of Applied Social Sciences, Universiti Sultan Zainal Abidin, Gong Badak Campus, 21300, Kuala Nerus, Terengganu, Malaysia
- Akademi Seni Budaya dan Warisan Kebangsaan, (ASWARA), Jalan Tun Ismail, Kuala Lumpur, Malaysia
| | - Ramle Abdullah
- Faculty of Applied Social Sciences, Universiti Sultan Zainal Abidin, Gong Badak Campus, 21300, Kuala Nerus, Terengganu, Malaysia
| | - Chew Chieng Yeo
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Stuart C Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Trust, Southampton, UK
- Global Health Research Institute, University of Southampton, Southampton, UK
- School of Postgraduate Studies, International Medical University, Kuala Lumpur, Malaysia
- Centre for Translational Research, IMU Institute for Research, Development and Innovation (IRDI), Kuala Lumpur, Malaysia
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Wu D, Sun Z, Li T, Tan Q, Sun Y, Chen T, Liu Y, Li J, Jiang H, Yuan Z, Zhao Y, Chen W. Efficacy of quadruple regimen with polaprezinc for gastric Helicobacter pylori infection eradication: protocol for a single-centre, single-blind, non-inferiority, randomised clinical trial. BMJ Open 2020; 10:e037182. [PMID: 33203625 PMCID: PMC7674085 DOI: 10.1136/bmjopen-2020-037182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Helicobacter pylori (H. pylori) is the most well-known risk factor for gastric cancer. At present, H. pylori shows varying levels of resistance to different treatments, leading to a lower rate of H. pylori eradication. The aim of this study is to evaluate the efficacy of polaprezinc-containing quadruple therapy (PQT) for the eradication of H. pylori infection and, thus, to provide more evidence to inform the clinical treatment of H. pylori infection in China. METHODS AND ANALYSIS This is a single-centre, single-blind, non-inferiority, randomised controlled trial, enrolling 158 patients with H. pylori infection. Patients are randomised (1:1) to the two groups for a 14-day therapy. Treatment group: PQT (esomeprazole 20 mg, amoxicillin 1 g, clarithromycin 500 mg, polaprezinc 75 mg) two times per day; control group: bismuth-containing quadruple therapy (esomeprazole 20 mg, amoxicillin 1 g, clarithromycin 500 mg, bismuth potassium citrate 220 mg) two times per day. The primary outcome is the rate of H. pylori eradication. Secondary outcomes are the incidence of adverse events and the gastrointestinal microbiota distribution. The 16S ribosomal RNA (16S rRNA) next-generation sequencing (NGS) is used to evaluate the effect of two different therapies on the distribution of the gastrointestinal microbiota. ETHICS AND DISSEMINATION This study was approved by the Ethics Committee of Sichuan Cancer Center & Hospital (No. SCCHEC-02-2019-015). Any amendment to the research protocol will be submitted for ethical approval. All participants must provide informed consent. On completion, the results of the study will be published in the appropriate peer-reviewed journal. TRIAL REGISTRATION NUMBER ChiCTR1900025800; preresults.
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Affiliation(s)
- Dingkun Wu
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Center for Cancer Prevention Research, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhen Sun
- Department of Gastroenterology, Jilin People's Hospital, Jilin, China
| | - Tingyuan Li
- Center for Cancer Prevention Research, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Qinwen Tan
- Center for Cancer Prevention Research, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Chongqing Medical University, Chongqing, China
| | - Yue Sun
- Center for Cancer Prevention Research, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Tingting Chen
- West China School of Public Health/West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yujing Liu
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jun Li
- Cancer Prevention and Treatment Office, Yanting Cancer Hospital, Mianyang, China
| | - Haidong Jiang
- Cancer Prevention and Treatment Office, Yanting Cancer Hospital, Mianyang, China
| | - Zhiqiang Yuan
- Cancer Prevention and Treatment Office, Yanting Cancer Hospital, Mianyang, China
| | - Yuqian Zhao
- Center for Cancer Prevention Research, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Wen Chen
- Center for Cancer Prevention Research, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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40
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Arreguin-Nava MA, Graham BD, Adhikari B, Agnello M, Selby CM, Hernandez-Velasco X, Vuong CN, Solis-Cruz B, Hernandez-Patlan D, Latorre JD, Tellez G, Hargis BM, Tellez-Isaias G. In ovo Administration of Defined Lactic Acid Bacteria Previously Isolated From Adult Hens Induced Variations in the Cecae Microbiota Structure and Enterobacteriaceae Colonization on a Virulent Escherichia coli Horizontal Infection Model in Broiler Chickens. Front Vet Sci 2020; 7:489. [PMID: 32974395 PMCID: PMC7472437 DOI: 10.3389/fvets.2020.00489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/30/2020] [Indexed: 12/14/2022] Open
Abstract
The effects of in ovo administration of a defined lactic acid microbiota (LAM), previously isolated from adult hens, in the cecae microbiota structure and Enterobacteriaceae colonization after exposure to virulent Escherichia coli during the hatching phase of broiler chickens were evaluated. Embryos inoculated with LAM showed a significant (P < 0.05) reduction of Enterobacteriaceae colonization at day-of-hatch (DOH) and day (d) 7. Furthermore, there was a significant increase in total lactic acid bacteria on DOH, body weight (BW) DOH, BW d7, and d0–d7 BW gain and reduced mortality d0–d7 was observed in the LAM group compared with that in phosphate-buffered saline (PBS) control. The bacterial composition at the family level revealed that the Enterobacteriaceae was numerically reduced, whereas the Ruminococcaceae was significantly increased in the LAM group when compared with that in the PBS control. Moreover, the bacterial genera Proteus and Butyricicoccus and unidentified bacterial genera of family Lachnospiraceae and Erysipelotrichaceae were significantly enriched in the LAM group. In contrast, the Clostridium of the family Peptostreptococcaceae and unidentified genus of family Enterobacteriaceae were significantly abundant in the PBS control group. In summary, in ovo administration of a defined LAM isolated from adult hens did not affect hatchability, improved body weight gain and reduced mortality at d7, induced variations in the cecae microbiota structure and reduced Enterobacteriaceae colonization on a virulent E. coli horizontal infection model in broiler chickens.
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Affiliation(s)
| | - Brittany D Graham
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Bishnu Adhikari
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | | | - Callie M Selby
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Xochitl Hernandez-Velasco
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autonoma de Mexico (UNAM), Mexico City, Mexico
| | - Christine N Vuong
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Bruno Solis-Cruz
- Laboratorio 5: LEDEFAR, Unidad de Investigación Multidisciplinaria, FES Cuautitlán, UNAM, Cuautitlán Izcalli, Mexico
| | - Daniel Hernandez-Patlan
- Laboratorio 5: LEDEFAR, Unidad de Investigación Multidisciplinaria, FES Cuautitlán, UNAM, Cuautitlán Izcalli, Mexico
| | - Juan D Latorre
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Guillermo Tellez
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Billy M Hargis
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
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41
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Kahleova H, Rembert E, Alwarith J, Yonas WN, Tura A, Holubkov R, Agnello M, Chutkan R, Barnard ND. Effects of a Low-Fat Vegan Diet on Gut Microbiota in Overweight Individuals and Relationships with Body Weight, Body Composition, and Insulin Sensitivity. A Randomized Clinical Trial. Nutrients 2020; 12:E2917. [PMID: 32987642 PMCID: PMC7598634 DOI: 10.3390/nu12102917] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/18/2020] [Accepted: 09/20/2020] [Indexed: 12/21/2022] Open
Abstract
Diet modulates gut microbiota and plays an important role in human health. The aim of this study was to test the effect of a low-fat vegan diet on gut microbiota and its association with weight, body composition, and insulin resistance in overweight men and women. We enrolled 168 participants and randomly assigned them to a vegan (n = 84) or a control group (n = 84) for 16 weeks. Of these, 115 returned all gut microbiome samples. Gut microbiota composition was assessed using uBiome Explorer™ kits. Body composition was measured using dual energy X-ray absorptiometry. Insulin sensitivity was quantified with the predicted clamp-derived insulin sensitivity index from a standard meal test. Repeated measure ANOVA was used for statistical analysis. Body weight decreased in the vegan group (treatment effect -5.9 kg [95% CI, -7.0 to -4.9 kg]; p < 0.001), mainly due to a reduction in fat mass (-3.9 kg [95% CI, -4.6 to -3.1 kg]; p < 0.001) and in visceral fat (-240 cm3 [95% CI, -345 to -135 kg]; p < 0.001). PREDIcted M, insulin sensitivity index (PREDIM) increased in the vegan group (treatment effect +0.83 [95% CI, +0.48 to +1.2]; p < 0.001). The relative abundance of Faecalibacterium prausnitzii increased in the vegan group (+5.1% [95% CI, +2.4 to +7.9%]; p < 0.001) and correlated negatively with changes in weight (r = -0.24; p = 0.01), fat mass (r = -0.22; p = 0.02), and visceral fat (r = -0.20; p = 0.03). The relative abundance of Bacteroides fragilis decreased in both groups, but less in the vegan group, making the treatment effect positive (+18.9% [95% CI, +14.2 to +23.7%]; p < 0.001), which correlated negatively with changes in weight (r = -0.44; p < 0.001), fat mass (r = -0.43; p < 0.001), and visceral fat (r = -0.28; p = 0.003) and positively with PREDIM (r = 0.36; p < 0.001), so a smaller reduction in Bacteroides fragilis was associated with a greater loss of body weight, fat mass, visceral fat, and a greater increase in insulin sensitivity. A low-fat vegan diet induced significant changes in gut microbiota, which were related to changes in weight, body composition, and insulin sensitivity in overweight adults, suggesting a potential use in clinical practice.
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Affiliation(s)
- Hana Kahleova
- Physicians Committee for Responsible Medicine, Washington, DC 20016, USA; (E.R.); (J.A.); (W.N.Y.); (N.D.B.)
| | - Emilie Rembert
- Physicians Committee for Responsible Medicine, Washington, DC 20016, USA; (E.R.); (J.A.); (W.N.Y.); (N.D.B.)
| | - Jihad Alwarith
- Physicians Committee for Responsible Medicine, Washington, DC 20016, USA; (E.R.); (J.A.); (W.N.Y.); (N.D.B.)
| | - Willy N. Yonas
- Physicians Committee for Responsible Medicine, Washington, DC 20016, USA; (E.R.); (J.A.); (W.N.Y.); (N.D.B.)
| | - Andrea Tura
- Metabolic Unit, CNR Institute of Neuroscience, 35127 Padua, Italy;
| | - Richard Holubkov
- School of Medicine, University of Utah, Salt Lake City, UT 84132, USA;
| | | | - Robynne Chutkan
- Department of Gastroenterology, Georgetown MedStar Hospital, Washington, DC 20007, USA;
| | - Neal D. Barnard
- Physicians Committee for Responsible Medicine, Washington, DC 20016, USA; (E.R.); (J.A.); (W.N.Y.); (N.D.B.)
- Adjunct Faculty, George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
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42
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Batool M, Ali SB, Jaan A, Khalid K, Ali SA, Kamal K, Raja AA, Gul F, Nasir A. Initial Sequencing and Characterization of the Gastrointestinal and Oral Microbiota in Urban Pakistani Adults. Front Cell Infect Microbiol 2020; 10:409. [PMID: 32850502 PMCID: PMC7428047 DOI: 10.3389/fcimb.2020.00409] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/03/2020] [Indexed: 01/14/2023] Open
Abstract
We report the initial characterization of the gastrointestinal tract (gut) and oral microbiota (bacteria) in 32 urban Pakistani adults. Study participants were between ages 18 and 40, had body mass index between 18 and 25 Kg/m2, and were students or early-career professionals. These individuals donated a total of 61 samples (32 gut and 29 oral) that were subjected to 16S ribosomal RNA (rRNA) gene sequencing. Microbiome composition of Pakistani individuals was compared against the uBiome database of selected individuals who self-reported to be in excellent health. We observed strong gender-based differences in the gut microbiome of Pakistani individuals, a skewness toward Firmicutes, and unusually high levels of Proteobacteria in the Pakistani men. These observations may indicate microbiota dysbiosis, though 16S data alone can neither establish cause nor effect to human health. Albeit conducted on a smaller scale, our report provides a first snapshot about the composition and diversity of gut and oral microbiota communities in Pakistani individuals.
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Affiliation(s)
- Maria Batool
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Syed Baqir Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Ali Jaan
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Kehkishan Khalid
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Syeda Aba Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Kaynat Kamal
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Afraz Ahmed Raja
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Farzana Gul
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Arshan Nasir
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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43
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Autoimmune Hepatitis: Shifts in Gut Microbiota and Metabolic Pathways among Egyptian Patients. Microorganisms 2020; 8:microorganisms8071011. [PMID: 32640728 PMCID: PMC7409351 DOI: 10.3390/microorganisms8071011] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/24/2020] [Accepted: 07/02/2020] [Indexed: 12/11/2022] Open
Abstract
Autoimmune hepatitis (AIH) is a chronic inflammatory disorder with complex immunopathogenesis. Dysbiosis has been linked to many autoimmune diseases, but its detailed role in autoimmune hepatitis (AIH) still needs rigorous evaluation, especially in Egypt. We aimed to identify the shift in the gut microbiota profile and resultant metabolic pathways in AIH Egyptian patients compared to healthy individuals. Stool samples were collected from 15 AIH-naive patients and from 10 healthy individuals. The V3-V4 hyper-variable regions in16S rRNA gene was amplified and sequenced using Illumina MiSeq platform. Significantly lower bacterial diversity in AIH patients was found compared to the controls. A phylum-level analysis showed the overrepresentation of Firmicutes, Bacteroides, and Proteobacteria. At the genus level, AIH-associated enrichment of Faecalibacterium, Blautia, Streptococcus, Haemophilus, Bacteroides, Veillonella, Eubacterium, Lachnospiraceae and Butyricicoccus was reported in contrast to Prevotella, Parabacteroides and Dilaster, which were significantly retracted in such patients. Overall, the predicted metabolic pathways associated with dysbiosis in AIH patients could orchestrate the potential pathogenic roles of gut microbiota in autoimmune disease, though not in a disease-specific manner, calling for future large-scale studies.
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44
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De Filippis F, Pasolli E, Ercolini D. The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health. FEMS Microbiol Rev 2020; 44:454-489. [PMID: 32556166 PMCID: PMC7391071 DOI: 10.1093/femsre/fuaa015] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022] Open
Abstract
Lactic acid bacteria (LAB) are present in foods, the environment and the animal gut, although fermented foods (FFs) are recognized as the primary niche of LAB activity. Several LAB strains have been studied for their health-promoting properties and are employed as probiotics. FFs are recognized for their potential beneficial effects, which we review in this article. They are also an important source of LAB, which are ingested daily upon FF consumption. In this review, we describe the diversity of LAB and their occurrence in food as well as the gut microbiome. We discuss the opportunities to study LAB diversity and functional properties by considering the availability of both genomic and metagenomic data in public repositories, as well as the different latest computational tools for data analysis. In addition, we discuss the role of LAB as potential probiotics by reporting the prevalence of key genomic features in public genomes and by surveying the outcomes of LAB use in clinical trials involving human subjects. Finally, we highlight the need for further studies aimed at improving our knowledge of the link between LAB-fermented foods and the human gut from the perspective of health promotion.
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Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
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45
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Abstract
Investigation of gut microbiome composition and diversity with respect to human personality. Analyses targeted bacterial genera linked to behaviour in animal and human psychiatric studies. Bacterial genera were modelled (using negative binomial regression) with respect to personality. Genera linked to autism are also related to social behaviour in the general population. Sociability is associated with higher diversity, and anxiety and stress with reduced diversity.
The gut microbiome has a measurable impact on the brain, influencing stress, anxiety, depressive symptoms and social behaviour. This microbiome–gut–brain axis may be mediated by various mechanisms including neural, immune and endocrine signalling. To date, the majority of research has been conducted in animal models, while the limited number of human studies has focused on psychiatric conditions. Here the composition and diversity of the gut microbiome is investigated with respect to human personality. Using regression models to control for possible confounding factors, the abundances of specific bacterial genera are shown to be significantly predicted by personality traits. Diversity analyses of the gut microbiome reveal that people with larger social networks tend to have a more diverse microbiome, suggesting that social interactions may shape the microbial community of the human gut. In contrast, anxiety and stress are linked to reduced diversity and an altered microbiome composition. Together, these results add a new dimension to our understanding of personality and reveal that the microbiome–gut–brain axis may also be relevant to behavioural variation in the general population as well as to cases of psychiatric disorders.
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46
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Todorov SD, Kang HJ, Ivanova IV, Holzapfel WH. Bacteriocins From LAB and Other Alternative Approaches for the Control of Clostridium and Clostridiodes Related Gastrointestinal Colitis. Front Bioeng Biotechnol 2020; 8:581778. [PMID: 33042979 PMCID: PMC7517946 DOI: 10.3389/fbioe.2020.581778] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022] Open
Abstract
The gut microbiome is considered as a promising target for future non-conventional therapeutic treatment of inflammatory and infectious diseases. The search for appropriate safe and beneficial (lactic acid bacterial and other) putative probiotic strains and/or their antimicrobial metabolites represents a challenging approach for combating several problematic and emerging infections. The process of selecting suitable strains, especially of lactic acid bacteria (LAB) with superior properties, has been accelerated and intensified during the past two decades, also thanks to recent developments in lab techniques. Currently, special focus is on the potential of antimicrobial metabolites produced by some LAB strains and their application as active therapeutic agents. The vision is to develop a scientific basis for 'biotherapeutics' as alternative to conventional approaches in both human and veterinary medicine. Consequently, innovative and promising applications of LAB to the therapeutic practice are presently emerging. An overview of the existing literature indicates that some antimicrobial metabolites such as bacteriocins, widely produced by different bacterial species including LAB, are promising biotherapeutic agents for controlling infections caused by potential pathogens, such as Clostridium and Clostridiodes. Non-conventional, safe and well designed therapeutic treatments may contribute to the improvement of gut dysbiotic conditions. Thereby gut homeostasis can be restored and inflammatory conditions such as gastrointestinal colitis ameliorated. Combining the knowledge on the production, characterization and application of bacteriocins from probiotic LAB, together with their antibacterial properties, appears to be a promising and novel approach in biotherapy. In this overview, different scenarios for the control of Clostridium spp. by application of bacteriocins as therapeutic agents, also in synergistic combination with antibiotics, will be discussed.
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Affiliation(s)
- Svetoslav D. Todorov
- Advanced Green Energy and Environment Institute (AGEE), Handong Global University, Pohang, South Korea
| | - Hye-Ji Kang
- Advanced Green Energy and Environment Institute (AGEE), Handong Global University, Pohang, South Korea
- HEM Inc., Handong Global University, Pohang, South Korea
| | - Iskra V. Ivanova
- Department of General and Applied Microbiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Wilhelm H. Holzapfel
- Advanced Green Energy and Environment Institute (AGEE), Handong Global University, Pohang, South Korea
- HEM Inc., Handong Global University, Pohang, South Korea
- *Correspondence: Wilhelm H. Holzapfel,
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47
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Batool M, Ali SB, Jaan A, Khalid K, Ali SA, Kamal K, Raja AA, Gul F, Nasir A. Initial Sequencing and Characterization of the Gastrointestinal and Oral Microbiota in Urban Pakistani Adults. Front Cell Infect Microbiol 2020. [PMID: 32850502 DOI: 10.3389/fcimb.2020.00409/bibtex] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
We report the initial characterization of the gastrointestinal tract (gut) and oral microbiota (bacteria) in 32 urban Pakistani adults. Study participants were between ages 18 and 40, had body mass index between 18 and 25 Kg/m2, and were students or early-career professionals. These individuals donated a total of 61 samples (32 gut and 29 oral) that were subjected to 16S ribosomal RNA (rRNA) gene sequencing. Microbiome composition of Pakistani individuals was compared against the uBiome database of selected individuals who self-reported to be in excellent health. We observed strong gender-based differences in the gut microbiome of Pakistani individuals, a skewness toward Firmicutes, and unusually high levels of Proteobacteria in the Pakistani men. These observations may indicate microbiota dysbiosis, though 16S data alone can neither establish cause nor effect to human health. Albeit conducted on a smaller scale, our report provides a first snapshot about the composition and diversity of gut and oral microbiota communities in Pakistani individuals.
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Affiliation(s)
- Maria Batool
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Syed Baqir Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Ali Jaan
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Kehkishan Khalid
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Syeda Aba Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Kaynat Kamal
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Afraz Ahmed Raja
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Farzana Gul
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Arshan Nasir
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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48
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Rashidi A, Kaiser T, Graiziger C, Holtan SG, Rehman TU, Weisdorf DJ, Dunny GM, Khoruts A, Staley C. Gut dysbiosis during antileukemia chemotherapy versus allogeneic hematopoietic cell transplantation. Cancer 2019; 126:1434-1447. [PMID: 31873965 DOI: 10.1002/cncr.32641] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 09/30/2019] [Accepted: 10/19/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND In the field of malignant hematology, most microbiome studies have focused on recipients of allogeneic hematopoietic cell transplantation (allo-HCT). As a result, this population has remained the primary target for novel microbiota therapeutics. Because the types of insults to the microbiome are similar during hematopoietic cell transplantation and intensive antileukemia therapy, this study evaluated whether the dysbiosis states are similar in the 2 settings. METHODS This study compared gut microbiota assemblages and community domination states in 2 cohorts of patients: patients with intensively treated acute leukemia (AL) and allo-HCT recipients. 16S ribosomal RNA gene profiling of thrice weekly stool samples was performed. Linear discriminant analysis effect size was used to determine differentially abundant taxa in groups of interest, and mixed modes were used to determine the predictors of microbiome states. RESULTS Microbiome changes in both cohorts were characterized by a marked loss of diversity and domination of low-diversity communities by Enterococcus. In the AL cohort, the relative abundance of Lactobacillus was also inversely correlated with diversity. Communities dominated by these genera were compositionally different. CONCLUSIONS Similarities in microbiota assemblages between the 2 cohorts support a broader scope for microbiota-directed therapeutics than previously considered, whereas specific differences suggest a personalized aspect to such therapeutics with the possibility of a differential response.
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Affiliation(s)
- Armin Rashidi
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Thomas Kaiser
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota.,BioTechnology Institute, University of Minnesota, St. Paul, Minnesota
| | - Carolyn Graiziger
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Shernan G Holtan
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Tauseef Ur Rehman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Daniel J Weisdorf
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Gary M Dunny
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota
| | - Alexander Khoruts
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota.,Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Christopher Staley
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota.,BioTechnology Institute, University of Minnesota, St. Paul, Minnesota
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49
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King CH, Desai H, Sylvetsky AC, LoTempio J, Ayanyan S, Carrie J, Crandall KA, Fochtman BC, Gasparyan L, Gulzar N, Howell P, Issa N, Krampis K, Mishra L, Morizono H, Pisegna JR, Rao S, Ren Y, Simonyan V, Smith K, VedBrat S, Yao MD, Mazumder R. Baseline human gut microbiota profile in healthy people and standard reporting template. PLoS One 2019; 14:e0206484. [PMID: 31509535 PMCID: PMC6738582 DOI: 10.1371/journal.pone.0206484] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 08/05/2019] [Indexed: 12/19/2022] Open
Abstract
A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or improve therapy outcome. To address this need we present an innovative scalable comprehensive analysis workflow, a healthy human reference microbiome list and abundance profile (GutFeelingKB), and a novel Fecal Biome Population Report (FecalBiome) with clinical applicability. GutFeelingKB provides a list of 157 organisms (8 phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) that forms the baseline biome and therefore can be used as healthy controls for studies related to dysbiosis. This list can be expanded to 863 organisms if closely related proteomes are considered. The incorporation of microbiome science into routine clinical practice necessitates a standard report for comparison of an individual’s microbiome to the growing knowledgebase of “normal” microbiome data. The FecalBiome and the underlying technology of GutFeelingKB address this need. The knowledgebase can be useful to regulatory agencies for the assessment of fecal transplant and other microbiome products, as it contains a list of organisms from healthy individuals. In addition to the list of organisms and their abundances, this study also generated a collection of assembled contiguous sequences (contigs) of metagenomics dark matter. In this study, metagenomic dark matter represents sequences that cannot be mapped to any known sequence but can be assembled into contigs of 10,000 nucleotides or higher. These sequences can be used to create primers to study potential novel organisms. All data is freely available from https://hive.biochemistry.gwu.edu/gfkb and NCBI’s Short Read Archive.
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Affiliation(s)
- Charles H. King
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
- McCormick Genomic and Proteomic Center, George Washington University, Washington, DC, United States of America
| | - Hiral Desai
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Allison C. Sylvetsky
- The Department of Exercise and Nutrition Sciences, Milken Institute School of Public Health, George Washington University, Washington, DC, United States of America
| | - Jonathan LoTempio
- The Institute for Biomedical Science, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States of America
- Center for Genetic Medicine, Children’s National Medical Center, George Washington University, Washington, DC, United States of America
| | - Shant Ayanyan
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Jill Carrie
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Keith A. Crandall
- Computational Biology Institute and The Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States of America
| | - Brian C. Fochtman
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Lusine Gasparyan
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Naila Gulzar
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Paul Howell
- KamTek Inc, Frederick, Maryland, United States of America
| | - Najy Issa
- The Department of Exercise and Nutrition Sciences, Milken Institute School of Public Health, George Washington University, Washington, DC, United States of America
| | - Konstantinos Krampis
- Department of Biological Sciences, Hunter College, City University of New York, New York, New York, United States of America
| | - Lopa Mishra
- Center for Translational Medicine, Department of Surgery, George Washington University, Washington, DC, United States of America
| | - Hiroki Morizono
- Center for Genetic Medicine, Children’s National Medical Center, George Washington University, Washington, DC, United States of America
| | - Joseph R. Pisegna
- Division of Gastroenterology and Hepatology VA Greater Los Angeles Healthcare System and Department of Medicine and Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Shuyun Rao
- Center for Translational Medicine, Department of Surgery, George Washington University, Washington, DC, United States of America
| | - Yao Ren
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Vahan Simonyan
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Krista Smith
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | | | - Michael D. Yao
- Washington DC VA Medical Center, Gastroenterology & Hepatology Section, Washington, DC, United States of America
- Department of Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States of America
| | - Raja Mazumder
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
- Department of Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States of America
- * E-mail:
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Mendez KN, Hoare A, Soto C, Bugueño I, Olivera M, Meneses C, Pérez-Donoso JM, Castro-Nallar E, Bravo D. Variability in Genomic and Virulent Properties of Porphyromonas gingivalis Strains Isolated From Healthy and Severe Chronic Periodontitis Individuals. Front Cell Infect Microbiol 2019; 9:246. [PMID: 31355151 PMCID: PMC6635597 DOI: 10.3389/fcimb.2019.00246] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/24/2019] [Indexed: 12/14/2022] Open
Abstract
Porphyromonas gingivalis has been extensively associated with both the onset and progression of periodontitis. We previously isolated and characterized two P. gingivalis strains, one from a patient exhibiting severe chronic periodontitis (CP3) and another from a periodontally healthy individual (H3). We previously showed that CP3 and H3 exhibit differences in virulence since H3 showed a lower resistance to cationic peptides compared with CP3, and a lower ability to induce proliferation in gingival epithelial cells. Here, we aimed to determine whether differences in virulence between these two strains are associated with the presence or absence of specific genes encoding virulence factors. We sequenced the whole genomes of both P. gingivalis CP3 and H3 and conducted a comparative analysis regarding P. gingivalis virulence genetic determinants. To do so, we performed a homology search of predicted protein sequences in CP3 and H3 genomes against the most characterized virulence genes for P. gingivalis available in the literature. In addition, we performed a genomic comparison of CP3 and H3 with all the 62 genomes of P. gingivalis found in NCBI's RefSeq database. This approach allowed us to determine the evolutionary relationships of CP3 and H3 with other virulent and avirulent strains; and additionally, to detect variability in presence/absence of virulence genes among P. gingivalis genomes. Our results show genetic variability in the hemagglutinin genes. While CP3 possesses one copy of hagA and two of hagC, H3 has no hagA and only one copy of hagC. Experimentally, this finding is related to lower in vitro hemmaglutination ability of H3 compared to CP3. Moreover, while CP3 encodes a gene for a major fimbrium subunit FimA type 4 (CP3_00160), H3 possess a FimA type 1 (H3_01400). Such genetic differences are in agreement with both lower biofilm formation ability and less intracellular invasion to oral epithelial cells exhibited by H3, compared with the virulent strain CP3. Therefore, here we provide new results on the genome sequences, comparative genomics analyses, and phenotypic analyses of two P. gingivalis strains. The genomics comparison of these two strains with the other 62 genomes included in the analysis provided relevant results regarding genetic determinants and their association with P. gingivalis virulence.
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Affiliation(s)
- Katterinne N Mendez
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Anilei Hoare
- Laboratorio de Microbiología Oral, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - Cristopher Soto
- Laboratorio de Microbiología Oral, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - Isaac Bugueño
- Laboratorio de Microbiología Oral, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - Marcela Olivera
- Laboratorio de Microbiología Oral, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
| | - Jose Manuel Pérez-Donoso
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Denisse Bravo
- Laboratorio de Microbiología Oral, Facultad de Odontología, Universidad de Chile, Santiago, Chile
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