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An S, Cho EY, Hwang J, Yang H, Hwang J, Shin K, Jung S, Kim BT, Kim KN, Lee W. Methane gas in breath test is associated with non-alcoholic fatty liver disease. J Breath Res 2024; 18:046005. [PMID: 38968933 DOI: 10.1088/1752-7163/ad5faf] [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: 11/08/2023] [Accepted: 07/05/2024] [Indexed: 07/07/2024]
Abstract
Although the associations between a patient's body mass index (BMI) and metabolic diseases, as well as their breath test results, have been studied, the relationship between breath hydrogen/methane levels and metabolic diseases needs to be further clarified. We aimed to investigate how the composition of exhaled breath gases relates to metabolic disorders, such as diabetes mellitus, dyslipidemia, hypertension, and nonalcoholic fatty liver disease (NAFLD), and their key risk factors. An analysis was performed using the medical records, including the lactulose breath test (LBT) data of patients who visited the Ajou University Medical Center, Suwon, Republic of Korea, between January 2016 and December 2021. The patients were grouped according to four different criteria for LBT hydrogen and methane levels. Of 441 patients, 325 (72.1%) had positive results for methane only (hydrogen < 20 parts per million [ppm] and methane ⩾ 3 ppm). BMIs and NAFLD prevalence were higher in patients with only methane positivity than in patients with hydrogen and methane positivity (hydrogen ⩾ 20 ppm and methane ⩾ 3 ppm). According to a multivariate analysis, the odds ratio of only methane positivity was 2.002 (95% confidence interval [CI]: 1.244-3.221,P= 0.004) for NAFLD. Our results demonstrate that breath methane positivity is related to NAFLD and suggest that increased methane gas on the breath tests has the potential to be an easily measurable biomarker for NAFLD diagnosis.
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Affiliation(s)
- Sanggwon An
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Eui-Young Cho
- Department of Nursing Science, Paichai University, 155-40 Baejae-ro, Seo-gu, Daejeon 35345, Republic of Korea
| | - Junho Hwang
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hyunseong Yang
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Jungho Hwang
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Kyusik Shin
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Susie Jung
- Department of Family Practice and Community Health, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Bom-Taeck Kim
- Department of Family Practice and Community Health, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Kyu-Nam Kim
- Department of Family Practice and Community Health, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Wooyoung Lee
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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Moodley S, Kroon E, Naidoo CC, Nyawo GR, Wu BG, Naidoo S, Chiyaka TL, Tshivhula H, Singh S, Li Y, Warren RM, Hoal EG, Schurr E, Clemente JC, Segal LN, Möller M, Theron G. Latent Tuberculosis Infection Is Associated with an Enrichment of Short-Chain Fatty Acid-Producing Bacteria in the Stool of Women Living with HIV. Microorganisms 2024; 12:1048. [PMID: 38930430 PMCID: PMC11205370 DOI: 10.3390/microorganisms12061048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 06/28/2024] Open
Abstract
Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high-TB-burden settings. Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI in PLHIV. We characterised the stool microbiota of PLHIV with [interferon-γ release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST-negative) LTBI (n = 25 per group). The 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet-Multinomial Mixtures, DESeq2, and PICRUSt2. No α- or β-diversity differences occurred by LTBI status; however, LTBI-positive people were Faecalibacterium-, Blautia-, Gemmiger-, and Bacteroides-enriched and Moryella-, Atopobium-, Corynebacterium-, and Streptococcus-depleted. Inferred metagenome data showed that LTBI-negative-enriched pathways included several metabolite degradation pathways. Stool from LTBI-positive people demonstrated differential taxa abundance based on a quantitative response to antigen stimulation. In LTBI-positive people, older people had different β-diversities than younger people, whereas in LTBI-negative people, no differences occurred across age groups. Amongst female PLHIV, those with LTBI were, vs. those without LTBI, Faecalibacterium-, Blautia-, Gemmiger-, and Bacteriodes-enriched, which are producers of short-chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome's potential role in LTBI.
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Affiliation(s)
- Suventha Moodley
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Elouise Kroon
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
| | - Charissa C. Naidoo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Georgina R. Nyawo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Benjamin G. Wu
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY 10016, USA; (B.G.W.); (S.S.); (Y.L.); (L.N.S.)
| | - Selisha Naidoo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
| | - Tinaye L. Chiyaka
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Happy Tshivhula
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Shivani Singh
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY 10016, USA; (B.G.W.); (S.S.); (Y.L.); (L.N.S.)
| | - Yonghua Li
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY 10016, USA; (B.G.W.); (S.S.); (Y.L.); (L.N.S.)
| | - Robin M. Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
| | - Eileen G. Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
| | - Erwin Schurr
- Department of Biochemistry, McGill University, Montreal, QC H3A 1Y6, Canada;
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, 1001 Boul Décarie, Site Glen Block E, Room EM3.3210, Montréal, QC H4A 3J1, Canada
- McGill International TB Centre, McGill University, Montréal, QC H3A3J1, Canada
- Departments of Medicine and Human Genetics, McGill University, Montréal, QC H3A0C7, Canada
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Leopoldo N. Segal
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY 10016, USA; (B.G.W.); (S.S.); (Y.L.); (L.N.S.)
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
| | - Grant Theron
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa; (S.M.); (E.K.); (C.C.N.); (G.R.N.); (S.N.); (T.L.C.); (H.T.); (R.M.W.); (E.G.H.); (M.M.)
- African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
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Cena JAD, Belmok A, Kyaw CM, Dame-Teixeira N. The Archaea domain: Exploring historical and contemporary perspectives with in silico primer coverage analysis for future research in Dentistry. Arch Oral Biol 2024; 161:105936. [PMID: 38422909 DOI: 10.1016/j.archoralbio.2024.105936] [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: 01/13/2024] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVE The complete picture of how the human microbiome interacts with its host is still largely unknown, particularly concerning microorganisms beyond bacteria. Although existing in very low abundance and not directly linked to causing diseases, archaea have been detected in various sites of the human body, including the gastrointestinal tract, oral cavity, skin, eyes, respiratory and urinary systems. But what exactly are these microorganisms? In the early 1990 s, archaea were classified as a distinct domain of life, sharing a more recent common ancestor with eukaryotes than with bacteria. While archaea's presence and potential significance in Dentistry remain under-recognized, there are concerns that they may contribute to oral dysbiosis. However, detecting archaea in oral samples presents challenges, including difficulties in culturing, the selection of DNA extraction methods, primer design, bioinformatic analysis, and databases. DESIGN This is a comprehensive review on the oral archaeome, presenting an in-depth in silico analysis of various primers commonly used for detecting archaea in human body sites. RESULTS Among several primer pairs used for detecting archaea in human samples across the literature, only one specifically designed for detecting methanogenic archaea in stool samples, exhibited exceptional coverage levels for the domain and various archaea phyla. CONCLUSIONS Our in silico analysis underscores the need for designing new primers targeting not only methanogenic archaea but also nanoarchaeal and thaumarchaeota groups to gain a comprehensive understanding of the archaeal oral community. By doing so, researchers can pave the way for further advancements in the field of oral archaeome research.
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Affiliation(s)
| | - Aline Belmok
- Institute of Biology, University of Brasilia, Brazil
| | | | - Naile Dame-Teixeira
- Department of Dentistry, School of Health Sciences, University of Brasilia, Brazil; Division of Oral Biology, School of Dentistry, University of Leeds, UK.
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Moodley S, Kroon E, Naidoo CC, Nyawo GR, Wu BG, Naidoo S, Chiyaka TL, Tshivhula H, Singh S, Li Y, Warren RM, Hoal EG, Schurr E, Clemente J, Segal LN, Möller M, Theron G. Latent tuberculosis infection is associated with an enrichment of short chain fatty acid producing bacteria in the stool of women living with HIV. RESEARCH SQUARE 2024:rs.3.rs-4182285. [PMID: 38645218 PMCID: PMC11030539 DOI: 10.21203/rs.3.rs-4182285/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high TB burden settings. Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI, including in PLHIV. Method Within a parent study that recruited adult females with HIV from Cape Town, South Africa into predefined age categories (18-25, 35-60 years), we characterised the stool microbiota of those with [interferon-γ release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST- negative) LTBI (n=25 per group). 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet Multinomial Mixtures, DESeq2 and PICRUSt2. Results No α- or β-diversity differences occurred by LTBI status; however, LTBI-positives were Faecalibacterium-, Blautia-, Gemmiger-, Bacteroides-enriched and Moryella-, Atopobium-, Corynebacterium-, Streptococcus-depleted. Inferred metagenome data showed LTBI-negative-enriched pathways included several involved in methylglyoxal degradation, L-arginine, putrescine, 4-aminobutanoate degradation and L-arginine and ornithine degradation. Stool from LTBI-positives demonstrated differential taxa abundance based on a quantitative response to antigen stimulation (Acidaminococcus-enrichment and Megamonas-, Alistipes-, and Paraprevotella-depletion associated with higher IGRA or TST responses, respectively). In LTBI-positives, older people had different β-diversities than younger people whereas, in LTBI-negatives, no differences occurred across age groups. Conclusion Amongst female PLHIV, those with LTBI had, vs. those without LTBI, Faecalibacterium, Blautia, Gemmiger, Bacteriodes-enriched, which are producers of short chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome's potential role in LTBI.
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Yang J, Chen R, Peng Y, Chai J, Li Y, Deng F. The role of gut archaea in the pig gut microbiome: a mini-review. Front Microbiol 2023; 14:1284603. [PMID: 37876779 PMCID: PMC10593451 DOI: 10.3389/fmicb.2023.1284603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023] Open
Abstract
The gastrointestinal microbiota of swine harbors an essential but often overlooked component: the gut archaea. These enigmatic microorganisms play pivotal roles in swine growth, health, and yield quality. Recent insights indicate that the diversity of gut archaea is influenced by various factors including breed, age, and diet. Such factors orchestrate the metabolic interactions within the porcine gastrointestinal environment. Through symbiotic relationships with bacteria, these archaea modulate the host's energy metabolism and digestive processes. Contemporary research elucidates a strong association between the abundance of these archaea and economically significant traits in swine. This review elucidates the multifaceted roles of gut archaea in swine and underscores the imperative for strategic interventions to modulate their population and functionality. By exploring the probiotic potential of gut archaea, we envisage novel avenues to enhance swine growth, health, and product excellence. By spotlighting this crucial, yet under-investigated, facet of the swine gut microbiome, we aim to galvanize further scientific exploration into harnessing their myriad benefits.
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Affiliation(s)
- Jianbo Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Routing Chen
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Yunjuan Peng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Jianmin Chai
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Feilong Deng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
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Guo W, Bi SS, Wang WW, Zhou M, Neves ALA, Degen AA, Guan LL, Long RJ. Maternal rumen and milk microbiota shape the establishment of early-life rumen microbiota in grazing yak calves. J Dairy Sci 2023; 106:2054-2070. [PMID: 36710176 DOI: 10.3168/jds.2022-22655] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/05/2022] [Indexed: 01/30/2023]
Abstract
Early-life gut microbial colonization and development exert a profound impact on the health and metabolism of the host throughout the life span. The transmission of microbes from the mother to the offspring affects the succession and establishment of the early-life rumen microbiome in newborns, but the contributions of different maternal sites to the rumen microbial establishment remain unclear. In the present study, samples from different dam sites (namely, oral, rumen fluid, milk, and teat skin) and rumen fluid of yak calves were collected at 6 time points between d 7 and 180 postpartum to determine the contributions of the different maternal sites to the establishment of the bacterial and archaeal communities in the rumen during early life. Our analysis demonstrated that the dam's microbial communities clustered according to the sites, and the calves' rumen microbiota resembled that of the dam consistently regardless of fluctuations at d 7 and 14. The dam's rumen microbiota was the major source of the calves' rumen bacteria (7.9%) and archaea (49.7%) compared with the other sites, whereas the potential sources of the calf rumen microbiota from other sites varied according to the age. The contribution of dam's rumen bacteria increased with age from 0.36% at d 7 to 14.8% at d 180, whereas the contribution of the milk microbiota showed the opposite trend, with its contribution reduced from 2.7% at d 7 to 0.2% at d 180. Maternal oral archaea were the main sources of the calves' rumen archaea at d 14 (50.4%), but maternal rumen archaea became the main source gradually and reached 66.2% at d 180. These findings demonstrated the potential microbial transfer from the dam to the offspring that could influence the rumen microbiota colonization and establishment in yak calves raised under grazing regimens, providing the basis for future microbiota manipulation strategies during their early life.
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Affiliation(s)
- W Guo
- State Key Laboratory of Grassland Agro-ecosystems, International Centre of Tibetan Plateau Ecosystem Management, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China; Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - S S Bi
- State Key Laboratory of Grassland Agro-ecosystems, International Centre of Tibetan Plateau Ecosystem Management, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - W W Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - M Zhou
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - A L A Neves
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870, Frederiksberg C, Denmark
| | - A A Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva 8410500, Israel
| | - L L Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada.
| | - R J Long
- State Key Laboratory of Grassland Agro-ecosystems, International Centre of Tibetan Plateau Ecosystem Management, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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Liu H, Han X, Zhao N, Hu L, Wang X, Luo C, Chen Y, Zhao X, Xu S. The Gut Microbiota Determines the High-Altitude Adaptability of Tibetan Wild Asses (Equus kiang) in Qinghai-Tibet Plateau. Front Microbiol 2022; 13:949002. [PMID: 35923394 PMCID: PMC9342865 DOI: 10.3389/fmicb.2022.949002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/17/2022] [Indexed: 12/14/2022] Open
Abstract
It was acknowledged long ago that microorganisms have played critical roles in animal evolution. Tibetan wild asses (TWA, Equus kiang) are the only wild perissodactyls on the Qinghai-Tibet Plateau (QTP) and the first national protected animals; however, knowledge about the relationships between their gut microbiota and the host's adaptability remains poorly understood. Herein, 16S rRNA and meta-genomic sequencing approaches were employed to investigate the gut microbiota–host associations in TWA and were compared against those of the co-resident livestock of yak (Bos grunnies) and Tibetan sheep (Ovis aries). Results revealed that the gut microbiota of yak and Tibetan sheep underwent convergent evolution. By contrast, the intestinal microflora of TWA diverged in a direction enabling the host to subsist on sparse and low-quality forage. Meanwhile, high microbial diversity (Shannon and Chao1 indices), cellulolytic activity, and abundant indicator species such as Spirochaetes, Bacteroidetes, Prevotella_1, and Treponema_2 supported forage digestion and short-chain fatty acid production in the gut of TWA. Meanwhile, the enterotype identification analysis showed that TWA shifted their enterotype in response to low-quality forage for a better utilization of forage nitrogen and short-chain fatty acid production. Metagenomic analysis revealed that plant biomass degrading microbial consortia, genes, and enzymes like the cellulolytic strains (Prevotella ruminicola, Ruminococcus flavefaciens, Ruminococcus albus, Butyrivibrio fibrisolvens, and Ruminobacter amylophilus), as well as carbohydrate metabolism genes (GH43, GH3, GH31, GH5, and GH10) and enzymes (β-glucosidase, xylanase, and β-xylosidase, etc.) had a significantly higher enrichment in TWA. Our results indicate that gut microbiota can improve the adaptability of TWA through plant biomass degradation and energy maintenance by the functions of gut microbiota in the face of nutritional deficiencies and also provide a strong rationale for understanding the roles of gut microbiota in the adaptation of QTP wildlife when facing harsh feeding environments.
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Affiliation(s)
- Hongjin Liu
- Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
| | - Xueping Han
- Technology Extension Service of Animal Husbandry of Qinghai, Xining, China
| | - Na Zhao
- Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
| | - Linyong Hu
- Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
| | - Xungang Wang
- Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
| | - Chongliang Luo
- Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
| | - Yongwei Chen
- Technology Extension Service of Animal Husbandry of Qinghai, Xining, China
| | - Xinquan Zhao
- Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- Xinquan Zhao
| | - Shixiao Xu
- Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
- *Correspondence: Shixiao Xu
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8
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Archaeome in Colorectal Cancer: High Abundance of Methanogenic Archaea in Colorectal Cancer Patients. INTERNATIONAL JOURNAL OF CANCER MANAGEMENT 2022. [DOI: 10.5812/ijcm-117843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background: The importance of microbiome in the progression and development of colorectal cancer (CRC) has been discussed in the last decade. Like colon bacteria, other intestinal microorganisms, including archaea, could also be involved in the CRC progression, so it's important to work out the archaeal microbiome (archaeome) composition among CRC patients. Objectives: The aim of this study was to determine the archaeome composition of CRC and healthy controls based on age and gender. Methods: Total bacterial DNA was extracted from 30 biopsy samples (17 CRC and 13 healthy controls). Archaeome communities were profiled by 16S rRNA high throughput sequencing, then compared to clinicopathological features, including CRC patients’ gender and age. Results: In the CRC patients, archaeal methanogens including Methanobrevibacter (86%) and Methanomassiliicoccus (8%) were overrepresented at the genus level. In contrast in the healthy controls, only two genera of haloarchaea including Natronococcus (58%) and Haloterrigena (42%) were presented. The results showed that the number of archaeal genera in men is higher than women in both the CRC and healthy controls. moreover, our results showed that the most genera of archaea are present in the CRC-32-50 group, six archaeal genera. The differential abundance taxa analysis results showed significant differences between healthy controls and CRC patients (P ≤ 0.05). Conclusions: The high abundance of methanogens in the colon archaeome of CRC patients compared to healthy controls suggests that methanogens may be involved in CRC development.
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The Relevance of the Bacterial Microbiome, Archaeome and Mycobiome in Pediatric Asthma and Respiratory Disorders. Cells 2022; 11:cells11081287. [PMID: 35455967 PMCID: PMC9024940 DOI: 10.3390/cells11081287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 03/30/2022] [Accepted: 04/07/2022] [Indexed: 02/04/2023] Open
Abstract
Bacteria, as well as eukaryotes, principally fungi, of the upper respiratory tract play key roles in the etiopathogenesis of respiratory diseases, whereas the potential role of archaea remains poorly understood. In this review, we discuss the contribution of all three domains of cellular life to human naso- and oropharyngeal microbiomes, i.e., bacterial microbiota, eukaryotes (mostly fungi), as well as the archaeome and their relation to respiratory and atopic disorders in infancy and adolescence. With this review, we aim to summarize state-of-the-art contributions to the field published in the last decade. In particular, we intend to build bridges between basic and clinical science.
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10
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Liu H, Tang Y, Zhang S, Liu H, Wang Z, Li Y, Wang X, Ren L, Yang K, Qin L. Anti-infection mechanism of a novel dental implant made of titanium-copper (TiCu) alloy and its mechanism associated with oral microbiology. Bioact Mater 2022; 8:381-395. [PMID: 34541408 PMCID: PMC8429474 DOI: 10.1016/j.bioactmat.2021.05.053] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/19/2021] [Accepted: 05/30/2021] [Indexed: 12/13/2022] Open
Abstract
This work was focused on study of anti-infection ability and its underlying mechanism of a novel dental implant made of titanium-copper (TiCu) alloy. In general, most studies on antibacterial implants have used a single pathogen to test their anti-infection ability using infectious animal models. However, dental implant-associated infections are polymicrobial diseases. We innovatively combine the classic ligature model in dogs with sucrose-rich diets to induce oral infections via the canine native oral bacteria. The anti-infection ability, biocompatibility and underlying mechanism of TiCu implant were systematically investigated in comparison with pure Ti implant via general inspection, hematology, imageology (micro-CT), microbiology (16S rDNA and metagenome), histology, and Cu ion detections. Compared with Ti implant, TiCu implant demonstrated remarkable anti-infection potentials with excellent biocompatibility. Additionally, the underlying anti-infection mechanism of TiCu implant was considered to involve maintaining the oral microbiota homeostasis. It was found that the carbohydrates in the plaques formed on the surface of TiCu implant were metabolized through the tricarboxylic acid cycle (TCA) cycles, which prevented the formation of an acidic microenvironment and inhibited the accumulation of acidogens and pathogens, thereby maintaining the microflora balance between aerobic and anaerobic bacteria.
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Affiliation(s)
- Hui Liu
- School of Materials Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, 230026, China
- Shi-changxu Innovation Center for Advanced Materials, Institute of Metal Research, Chinese Academy of Sciences, 72 Wenhua Road, Shenyang, 110016, China
| | - Yulong Tang
- Department of Stomatology, General Hospital of Northern Military Area, 83 Wenhua Road, Shenyang, 110016, China
| | - Shuyuan Zhang
- Shi-changxu Innovation Center for Advanced Materials, Institute of Metal Research, Chinese Academy of Sciences, 72 Wenhua Road, Shenyang, 110016, China
| | - Huan Liu
- School of Materials Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, 230026, China
- Shi-changxu Innovation Center for Advanced Materials, Institute of Metal Research, Chinese Academy of Sciences, 72 Wenhua Road, Shenyang, 110016, China
| | - Zijian Wang
- Department of Stomatology, General Hospital of Northern Military Area, 83 Wenhua Road, Shenyang, 110016, China
| | - Yue Li
- Department of Stomatology, General Hospital of Northern Military Area, 83 Wenhua Road, Shenyang, 110016, China
| | - Xinluan Wang
- Translational Medicine R&D Center, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518057, China
- Musculoskeletal Research Laboratory of Department of Orthopaedics & Traumatology and Innovative Orthopaedic Biomaterial and Drug Translational Research Laboratory of Li Ka Shing Institute of Health, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Ling Ren
- Shi-changxu Innovation Center for Advanced Materials, Institute of Metal Research, Chinese Academy of Sciences, 72 Wenhua Road, Shenyang, 110016, China
| | - Ke Yang
- Shi-changxu Innovation Center for Advanced Materials, Institute of Metal Research, Chinese Academy of Sciences, 72 Wenhua Road, Shenyang, 110016, China
| | - Ling Qin
- Translational Medicine R&D Center, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518057, China
- Musculoskeletal Research Laboratory of Department of Orthopaedics & Traumatology and Innovative Orthopaedic Biomaterial and Drug Translational Research Laboratory of Li Ka Shing Institute of Health, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
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11
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Meta-analyses on the Periodontal Archaeome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1373:69-93. [DOI: 10.1007/978-3-030-96881-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Ghosh S, Pramanik S. Structural diversity, functional aspects and future therapeutic applications of human gut microbiome. Arch Microbiol 2021; 203:5281-5308. [PMID: 34405262 PMCID: PMC8370661 DOI: 10.1007/s00203-021-02516-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/29/2021] [Accepted: 08/06/2021] [Indexed: 02/06/2023]
Abstract
The research on human gut microbiome, regarded as the black box of the human body, is still at the stage of infancy as the functional properties of the complex gut microbiome have not yet been understood. Ongoing metagenomic studies have deciphered that the predominant microbial communities belong to eubacterial phyla Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Cyanobacteria, Verrucomicrobia and archaebacterial phylum Euryarchaeota. The indigenous commensal microbial flora prevents opportunistic pathogenic infection and play undeniable roles in digestion, metabolite and signaling molecule production and controlling host's cellular health, immunity and neuropsychiatric behavior. Besides maintaining intestinal health via short-chain fatty acid (SCFA) production, gut microbes also aid in neuro-immuno-endocrine modulatory molecule production, immune cell differentiation and glucose and lipid metabolism. Interdependence of diet and intestinal microbial diversity suggests the effectiveness of pre- and pro-biotics in maintenance of gut and systemic health. Several companies worldwide have started potentially exploiting the microbial contribution to human health and have translated their use in disease management and therapeutic applications. The present review discusses the vast diversity of microorganisms playing intricate roles in human metabolism. The contribution of the intestinal microbiota to regulate systemic activities including gut-brain-immunity crosstalk has been focused. To the best of our knowledge, this review is the first of its kind to collate and discuss the companies worldwide translating the multi-therapeutic potential of human intestinal microbiota, based on the multi-omics studies, i.e. metagenomics and metabolomics, as ready solutions for several metabolic and systemic disorders.
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Affiliation(s)
- Soma Ghosh
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute, i-8 Sector-C, East Kolkata Township, Kolkata, 700107, India.
| | - Sreemanta Pramanik
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute, i-8 Sector-C, East Kolkata Township, Kolkata, 700107, India
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13
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Ding L, Liu Y, Wu X, Wu M, Luo X, Ouyang H, Xia J, Liu X, Ding T. Pathogen Metagenomics Reveals Distinct Lung Microbiota Signatures Between Bacteriologically Confirmed and Negative Tuberculosis Patients. Front Cell Infect Microbiol 2021; 11:708827. [PMID: 34589441 PMCID: PMC8475726 DOI: 10.3389/fcimb.2021.708827] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the dynamics of lung microbiota in tuberculosis patients, especially those who cannot be confirmed bacteriologically in clinical practice, is imperative for accurate diagnosis and effective treatment. This study aims to characterize the distinct lung microbial features between bacteriologically confirmed and negative tuberculosis patients to understand the influence of microbiota on tuberculosis patients. We collected specimens of bronchoalveolar lavage fluid from 123 tuberculosis patients. Samples were subjected to metagenomic next-generation sequencing to reveal the lung microbial signatures. By combining conventional bacterial detection and metagenomic sequencing, 101/123 (82%) tuberculosis patients were bacteriologically confirmed. In addition to Mycobacterium tuberculosis, Staphylococcus aureus, Kluyveromyces lactis, and Pyricularia pennisetigena were also enriched in the bacteriological confirmation group. In contrast, Haemophilus parainfluenzae was enriched in the bacteriologically negative group. Besides, microbial interaction exhibits a different state between bacteriologically confirmed and negative tuberculosis patients. Mycobacterium tuberculosis was confirmed correlated with clinical characteristics such as albumin and chest cavities. Our study comprehensively demonstrates the correlation between unique features of lung microbial dynamics and the clinical characteristics of tuberculosis patients, suggesting the importance of studying the pulmonary microbiome in tuberculosis disease and providing new insights for future precision diagnosis and treatment.
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Affiliation(s)
- Li Ding
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Yanmin Liu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaorong Wu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Minhao Wu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaoqing Luo
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Hui Ouyang
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Jinyu Xia
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Xi Liu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Tao Ding
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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14
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Dwivedi M, Powali S, Rastogi S, Singh A, Gupta DK. Microbial community in human gut: a therapeutic prospect and implication in health and diseases. Lett Appl Microbiol 2021; 73:553-568. [PMID: 34365651 DOI: 10.1111/lam.13549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022]
Abstract
The interest in the working and functionality of the human gut microbiome has increased drastically over the years. Though the existence of gut microbes has long been speculated for long over the last few decades, a lot of research has sprung up in studying and understanding the role of gut microbes in the human digestive tract. The microbes present in the gut are highly instrumental in maintaining the metabolism in the body. Further research is going on in this field to understand how gut microbes can be employed as potential sources of novel therapeutics; moreover, probiotics have also elucidated their significant place in this direction. As regards the clinical perspective, microbes can be engineered to afford defence mechanisms while interacting with foreign pathogenic bodies. More investigations in this field may assist us to evaluate and understand how these cells communicate with human cells and promote immune interactions. Here we elaborate on the possible implication of human gut microbiota into the immune system as well as explore the probiotics in the various human ailments. Comprehensive information on the human gut microbiome at the same platform may contribute effectively to our understanding of the human microbiome and possible mechanisms of associated human diseases.
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Affiliation(s)
- M Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - S Powali
- Maulana Abdul Kalam Azad University of Technology, Kolkatta, India
| | - S Rastogi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - A Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - D K Gupta
- Department of Biochemistry, University of Allahabad, Prayagraj, India
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15
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Radaic A, Kapila YL. The oralome and its dysbiosis: New insights into oral microbiome-host interactions. Comput Struct Biotechnol J 2021; 19:1335-1360. [PMID: 33777334 PMCID: PMC7960681 DOI: 10.1016/j.csbj.2021.02.010] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
The oralome is the summary of the dynamic interactions orchestrated between the ecological community of oral microorganisms (comprised of up to approximately 1000 species of bacteria, fungi, viruses, archaea and protozoa - the oral microbiome) that live in the oral cavity and the host. These microorganisms form a complex ecosystem that thrive in the dynamic oral environment in a symbiotic relationship with the human host. However, the microbial composition is significantly affected by interspecies and host-microbial interactions, which in turn, can impact the health and disease status of the host. In this review, we discuss the composition of the oralome and inter-species and host-microbial interactions that take place in the oral cavity and examine how these interactions change from healthy (eubiotic) to disease (dysbiotic) states. We further discuss the dysbiotic signatures associated with periodontitis and caries and their sequalae, (e.g., tooth/bone loss and pulpitis), and the systemic diseases associated with these oral diseases, such as infective endocarditis, atherosclerosis, diabetes, Alzheimer's disease and head and neck/oral cancer. We then discuss current computational techniques to assess dysbiotic oral microbiome changes. Lastly, we discuss current and novel techniques for modulation of the dysbiotic oral microbiome that may help in disease prevention and treatment, including standard hygiene methods, prebiotics, probiotics, use of nano-sized drug delivery systems (nano-DDS), extracellular polymeric matrix (EPM) disruption, and host response modulators.
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Affiliation(s)
- Allan Radaic
- Kapila Laboratory, Orofacial Sciences Department, School of Dentistry, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Yvonne L. Kapila
- Kapila Laboratory, Orofacial Sciences Department, School of Dentistry, University of California, San Francisco (UCSF), San Francisco, CA, USA
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16
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García-Montero C, Fraile-Martínez O, Gómez-Lahoz AM, Pekarek L, Castellanos AJ, Noguerales-Fraguas F, Coca S, Guijarro LG, García-Honduvilla N, Asúnsolo A, Sanchez-Trujillo L, Lahera G, Bujan J, Monserrat J, Álvarez-Mon M, Álvarez-Mon MA, Ortega MA. Nutritional Components in Western Diet Versus Mediterranean Diet at the Gut Microbiota-Immune System Interplay. Implications for Health and Disease. Nutrients 2021; 13:699. [PMID: 33671569 PMCID: PMC7927055 DOI: 10.3390/nu13020699] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
The most prevalent diseases of our time, non-communicable diseases (NCDs) (including obesity, type 2 diabetes, cardiovascular diseases and some types of cancer) are rising worldwide. All of them share the condition of an "inflammatory disorder", with impaired immune functions frequently caused or accompanied by alterations in gut microbiota. These multifactorial maladies also have in common malnutrition related to physiopathology. In this context, diet is the greatest modulator of immune system-microbiota crosstalk, and much interest, and new challenges, are arising in the area of precision nutrition as a way towards treatment and prevention. It is a fact that the westernized diet (WD) is partly responsible for the increased prevalence of NCDs, negatively affecting both gut microbiota and the immune system. Conversely, other nutritional approaches, such as Mediterranean diet (MD), positively influence immune system and gut microbiota, and is proposed not only as a potential tool in the clinical management of different disease conditions, but also for prevention and health promotion globally. Thus, the purpose of this review is to determine the regulatory role of nutritional components of WD and MD in the gut microbiota and immune system interplay, in order to understand, and create awareness of, the influence of diet over both key components.
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Affiliation(s)
- Cielo García-Montero
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (C.G.-M.); (O.F.-M.); (A.M.G.-L.); (L.P.); (A.J.C.); (N.G.-H.); (J.B.); (J.M.)
| | - Oscar Fraile-Martínez
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (C.G.-M.); (O.F.-M.); (A.M.G.-L.); (L.P.); (A.J.C.); (N.G.-H.); (J.B.); (J.M.)
| | - Ana M. Gómez-Lahoz
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (C.G.-M.); (O.F.-M.); (A.M.G.-L.); (L.P.); (A.J.C.); (N.G.-H.); (J.B.); (J.M.)
| | - Leonel Pekarek
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (C.G.-M.); (O.F.-M.); (A.M.G.-L.); (L.P.); (A.J.C.); (N.G.-H.); (J.B.); (J.M.)
| | - Alejandro J. Castellanos
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (C.G.-M.); (O.F.-M.); (A.M.G.-L.); (L.P.); (A.J.C.); (N.G.-H.); (J.B.); (J.M.)
| | - Fernando Noguerales-Fraguas
- Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain; (F.N.-F.); (A.A.)
- Department of General Surgery, Príncipe de Asturias Hospital, 28806 Alcalá de Henares, Spain
| | - Santiago Coca
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (C.G.-M.); (O.F.-M.); (A.M.G.-L.); (L.P.); (A.J.C.); (N.G.-H.); (J.B.); (J.M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (S.C.); (L.S.-T.)
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
| | - Luis G. Guijarro
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (S.C.); (L.S.-T.)
- Unit of Biochemistry and Molecular Biology (CIBEREHD), Department of System Biology, University of Alcalá, 28801 Alcalá de Henares, Spain;
| | - Natalio García-Honduvilla
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (C.G.-M.); (O.F.-M.); (A.M.G.-L.); (L.P.); (A.J.C.); (N.G.-H.); (J.B.); (J.M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (S.C.); (L.S.-T.)
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
| | - Angel Asúnsolo
- Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain; (F.N.-F.); (A.A.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (S.C.); (L.S.-T.)
| | - Lara Sanchez-Trujillo
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (C.G.-M.); (O.F.-M.); (A.M.G.-L.); (L.P.); (A.J.C.); (N.G.-H.); (J.B.); (J.M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (S.C.); (L.S.-T.)
- Service of Pediatric, Hospital Universitario Principe de Asturias, Alcalá de Henares,28806 Madrid, Spain
| | - Guillermo Lahera
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (C.G.-M.); (O.F.-M.); (A.M.G.-L.); (L.P.); (A.J.C.); (N.G.-H.); (J.B.); (J.M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (S.C.); (L.S.-T.)
- Psychiatry Service, Center for Biomedical Research in the Mental Health Network, University Hospital Príncipe de Asturias, 28806 Alcalá de Henares, Spain;
| | - Julia Bujan
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (C.G.-M.); (O.F.-M.); (A.M.G.-L.); (L.P.); (A.J.C.); (N.G.-H.); (J.B.); (J.M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (S.C.); (L.S.-T.)
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
| | - Jorge Monserrat
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (C.G.-M.); (O.F.-M.); (A.M.G.-L.); (L.P.); (A.J.C.); (N.G.-H.); (J.B.); (J.M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (S.C.); (L.S.-T.)
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
| | - Melchor Álvarez-Mon
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (C.G.-M.); (O.F.-M.); (A.M.G.-L.); (L.P.); (A.J.C.); (N.G.-H.); (J.B.); (J.M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (S.C.); (L.S.-T.)
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
- Immune System Diseases-Rheumatology, Oncology Service an Internal Medicine, University Hospital Príncipe de Asturias, (CIBEREHD), 28806 Alcalá de Henares, Spain;
| | - Miguel A. Álvarez-Mon
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (C.G.-M.); (O.F.-M.); (A.M.G.-L.); (L.P.); (A.J.C.); (N.G.-H.); (J.B.); (J.M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (S.C.); (L.S.-T.)
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
- Department of Psychiatry and Medical Psychology, Hospital Universitario Infanta Leonor, 28031 Madrid, Spain
| | - Miguel A. Ortega
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (C.G.-M.); (O.F.-M.); (A.M.G.-L.); (L.P.); (A.J.C.); (N.G.-H.); (J.B.); (J.M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain; (S.C.); (L.S.-T.)
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
- Cancer Registry and Pathology Department, Hospital Universitario Principe de Asturias, 28806 Alcalá de Henares, Spain;
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Vitkova V, Mitkova D, Yordanova V, Pohl P, Bakowsky U, Staneva G, Batishchev O. Elasticity and phase behaviour of biomimetic membrane systems containing tetraether archaeal lipids. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.124974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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18
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Chaisuwan W, Jantanasakulwong K, Wangtueai S, Phimolsiripol Y, Chaiyaso T, Techapun C, Phongthai S, You S, Regenstein JM, Seesuriyachan P. Microbial exopolysaccharides for immune enhancement: Fermentation, modifications and bioactivities. FOOD BIOSCI 2020. [DOI: 10.1016/j.fbio.2020.100564] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Abstract
The Archaea domain was recognized as a separate phylogenetic lineage in the tree of life nearly 3 decades ago. It is now known as part of the human microbiome; however, given that its roles in oral sites are still poorly understood, this review aimed to establish the current level of evidence regarding archaea in the oral cavity to guide future research, providing insights on the present knowledge about the human oral archaeome. A scoping review was conducted with the PRISMA Extension for Scoping Reviews checklist. Five electronic databases were searched, as well as gray literature. Two independent reviewers performed the selection and characterization of the studies. Clinical studies were included when the target population consisted of humans of any age who were donors of samples from the oral cavity. A qualitative analysis was performed, based on the type of oral site and by considering the methods employed for archaeal identification and taxonomy, including the DNA extraction protocols, primers, and probes used. Fifty articles were included in the final scoping review, published from 1987 to 2019. Most studies sampled periodontal sites. Methanogens were the most abundant archaea in those sites, and their presence could be associated with other periodontal pathogens. No consistent relationship with different disease conditions was observed in studies that evaluated the microbiota surviving in endodontic sites. Few articles analyzed the presence of archaea in dental caries, saliva, or tongue microbiota, as well as in archaeologic samples, also showing a relationship with healthy microbiota. Archaea have been detected in different oral niches of individuals from diverse geographic locations and clinical conditions, suggesting potential roles in oral diseases. Methodological limitations may hamper our current knowledge about archaeal diversity and prevalence in oral samples, and future research with diversified methodological approaches may lead to a better comprehension of the human oral archaeome.
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Affiliation(s)
- A Belmok
- Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - J A de Cena
- Department of Dentistry, Faculty of Heath Sciences, University of Brasília, Brasília, Brazil
| | - C M Kyaw
- Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - N Damé-Teixeira
- Department of Dentistry, Faculty of Heath Sciences, University of Brasília, Brasília, Brazil
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20
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Presence of Archaea in dental caries biofilms. Arch Oral Biol 2020; 110:104606. [DOI: 10.1016/j.archoralbio.2019.104606] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/31/2019] [Accepted: 11/08/2019] [Indexed: 12/21/2022]
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21
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Park CH, Eun CS, Han DS. Intestinal microbiota, chronic inflammation, and colorectal cancer. Intest Res 2018; 16:338-345. [PMID: 30090032 PMCID: PMC6077304 DOI: 10.5217/ir.2018.16.3.338] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 05/03/2018] [Accepted: 05/03/2018] [Indexed: 12/22/2022] Open
Abstract
In addition to genetic and epigenetic factors, various environmental factors, including diet, play important roles in the development of colorectal cancer (CRC). Recently, there is increasing interest in the intestinal microbiota as an environmental risk factor for CRC, because diet also influences the composition of the intestinal microbiota. The human intestinal microbiota comprises about 100 trillion microbes. This microbiome thrives on undigested dietary residues in the intestinal lumen and produces various metabolites. It is well known that the dietary risk factors for CRC are mediated by dysbiosis of the intestinal microbiota and their metabolites. In this review, we describe the bacterial taxa associated with CRC, including Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, Escherichia coli, and butyrate-producing bacteria. We also discuss the host-diet interaction in colorectal carcinogenesis.
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Affiliation(s)
- Chan Hyuk Park
- Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Korea
| | - Chang Soo Eun
- Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Korea
| | - Dong Soo Han
- Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Korea
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Ramiro FS, de Lira E, Soares G, Retamal-Valdes B, Feres M, Figueiredo LC, Faveri M. Effects of different periodontal treatments in changing the prevalence and levels of Archaea present in the subgingival biofilm of subjects with periodontitis: A secondary analysis from a randomized controlled clinical trial. Int J Dent Hyg 2018; 16:569-575. [PMID: 29797436 DOI: 10.1111/idh.12347] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2018] [Indexed: 11/30/2022]
Abstract
OBJECTIVE The aim of this randomized double-blind and placebo-controlled study was to assess if periodontal treatment with or without systemic antibiotic would change the mean level of Archaea. METHODS Fifty-nine (59) subjects were randomly assigned to receive scaling and root planing (SRP) alone or combined with metronidazole (MTZ; 400 mg/TID) or either with MTZ and amoxicillin (AMX; 500 mg/TID) for 14 days. Clinical and microbiological examinations were performed at baseline and at 6 months post-SRP. Six subgingival plaque samples per subject were analysed for the presence and levels of Archaea using quantitative polymerase chain reaction. RESULTS Scaling and root planing alone or combined with MTZ or MTZ + AMX significantly reduced the prevalence of subjects colonized by Archaea at 6 months post-therapy, without significant differences among groups (P > .05). Both therapies led to a statistically significant decrease in the mean percentage of sites colonized by Archaea (P < .05). The MTZ and MTZ + AMX group had a significantly lower mean number of sites colonized by Archaea and lower levels of these micro-organisms at sites with probing depth ≥5 mm at 6 months compared with SRP group (P < .05). CONCLUSION Periodontal treatments including adjunctive MTZ or MTZ + AMX are more effective than mechanical treatment alone in reducing the levels and prevalence of sites colonized by Archaea in subjects with chronic periodontitis.
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Affiliation(s)
- F S Ramiro
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, Brazil
| | - Eag de Lira
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, Brazil
| | - Gms Soares
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, Brazil
| | - B Retamal-Valdes
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, Brazil
| | - M Feres
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, Brazil
| | - L C Figueiredo
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, Brazil
| | - M Faveri
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, Brazil
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Comparison of Oral Microbe Quantities from Tongue Samples and Subgingival Pockets. Int J Dent 2018; 2018:2048390. [PMID: 29853892 PMCID: PMC5944217 DOI: 10.1155/2018/2048390] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/08/2018] [Accepted: 03/22/2018] [Indexed: 12/17/2022] Open
Abstract
Objectives To improve understanding of periodontitis pathology, we need more profound knowledge of relative abundances of single prokaryotic species and colonization dynamics between habitats. Thus, we quantified oral microbes from two oral habitats to gain insights into colonization variability and correlation to the clinical periodontal status. Methods We analyzed tongue scrapings and subgingival pocket samples from 237 subjects (35–54 years) with at least 10 teeth and no recent periodontal treatment from the 11-year follow-up of the Study of Health in Pomerania. Relative abundances of Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum, Streptococcus sanguinis, total bacteria, and Archaea were correlated to clinically assessed pocket depths (PD) and clinical attachment levels (CAL). Results Increased relative abundances of P. gingivalis, A. actinomycetemcomitans, and F. nucleatum were linked to increased levels of PD and CAL (i) on the subject level (mean PD, mean CAL) and (ii) in subgingival pockets. Relative abundances of Archaea from tongue samples correlated negatively with mean PD or mean CAL. Detection and quantity of bacterial species correlated weakly to moderately between the tongue and subgingival pocket, except for Archaea. Conclusions Relative abundances of specific oral species correlated weakly to moderately between habitats. Single species, total bacteria, and Archaea were linked to clinically assessed severity of periodontitis in a habitat-dependent manner.
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Wilder-Smith CH, Olesen SS, Materna A, Drewes AM. Breath methane concentrations and markers of obesity in patients with functional gastrointestinal disorders. United European Gastroenterol J 2017; 6:595-603. [PMID: 29881615 DOI: 10.1177/2050640617744457] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/30/2017] [Indexed: 12/14/2022] Open
Abstract
Background Obesity is associated with changes in the intestinal microbiome and methane-producing archaea may be involved in energy homeostasis. Objective The objective of this article is to investigate the associations between intestinal methane production, waist circumference and body mass index (BMI) as biomarkers for obesity. Methods Breath methane and hydrogen concentrations were measured over five hours following fructose or lactose ingestion in 1647 patients with functional gastrointestinal disorders. The relationships between gas concentrations and measures of obesity were investigated by stratifying gas concentration-time profiles by BMI and waist circumference, and, conversely, BMI and waist circumference by peak breath hydrogen and methane concentrations. Results Following fructose ingestion, patients with lower BMI and lesser waist circumference had greater breath methane concentrations (all p < 0.003). Conversely, patients with increased methane concentrations had lower BMI (p < 0.001) and waist circumference (p = 0.02). After lactose ingestion, BMI and waist circumference were not associated with significant differences in methane. However, greater methane concentrations were associated with a lower BMI (p < 0.002), but not with waist circumference. Conclusion In this large group of patients mainly negative associations between breath methane concentrations and anthropometric biomarkers of obesity were evident. Studies investigating microbial methane production and energy homoeostasis in different populations are of substantial interest to distinguish epiphenomena from true causality.A follow-up study was registered at Clinical trials.gov NCT02085889.
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Affiliation(s)
| | - Søren S Olesen
- Mech-Sense, Department of Gastroenterology and Hepatology, Clinical Institute, Aalborg University Hospital, Aalborg, Denmark
| | - Andrea Materna
- Brain-Gut Research Group, Gastroenterology Group Practice, Bern, Switzerland
| | - Asbjørn M Drewes
- Mech-Sense, Department of Gastroenterology and Hepatology, Clinical Institute, Aalborg University Hospital, Aalborg, Denmark
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25
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van den Hoogen WJ, Laman JD, 't Hart BA. Modulation of Multiple Sclerosis and Its Animal Model Experimental Autoimmune Encephalomyelitis by Food and Gut Microbiota. Front Immunol 2017; 8:1081. [PMID: 28928747 PMCID: PMC5591889 DOI: 10.3389/fimmu.2017.01081] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 08/21/2017] [Indexed: 12/11/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune neurological disease characterized by chronic inflammation of the central nervous system (CNS), leading to demyelination, axonal damage, and symptoms such as fatigue and disability. Although the cause of MS is not known, the infiltration of peripherally activated immune cells into the CNS has a key pathogenic role. Accumulating evidence supports an important role of diet and gut microbiota in immune-mediated diseases. Preclinical as well as clinical studies suggest a role for gut microbiota and dietary components in MS. Here, we review these recent studies on gut microbiota and dietary interventions in MS and its animal model experimental autoimmune encephalomyelitis. We also propose directions for future research.
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Affiliation(s)
| | - Jon D Laman
- Department of Neuroscience, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Bert A 't Hart
- Department of Neuroscience, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,Department of Immunobiology, Biomedical Primate Research Center, Rijswijk, Netherlands
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26
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Nkamga VD, Henrissat B, Drancourt M. Archaea: Essential inhabitants of the human digestive microbiota. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.humic.2016.11.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Hoffman DJ, Campos-Ponce M, Taddei CR, Doak CM. Microbiome, growth retardation and metabolism: are they related? Ann Hum Biol 2017; 44:201-207. [PMID: 27927018 DOI: 10.1080/03014460.2016.1267261] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
CONTEXT Despite an improvement in food security and the delivery of nutritional supplements to children living in impoverished parts of the world, poor growth is still highly prevalent. Given that the microbiome is related to both nutrient absorption, as well as overweight/obesity, it may play a central role in limiting or modifying normal growth processes while contributing to chronic disease risks. OBJECTIVE The objective of this paper is to describe normal growth processes, the role of the microbiome in supporting or disrupting normal growth processes, and its potential impact on long-term health. METHODS A literature search of relevant human and laboratory research on growth, microbiome and the relationship between poor growth and chronic diseases was conducted. This review focuses on potential mechanisms that implicate the microbiome as a mediator of poor growth and later metabolic outcomes. In this relationship, attention was given to the potential for gastrointestinal infections to disrupt the microbiome. RESULTS Based on the studies reviewed, it is clear that exposure to infections disturbs both intestinal functioning as well as normal growth and changes in the microbiome may influence micronutrient availability and metabolic processes. CONCLUSIONS The microbiome may play a significant role in limiting human growth, but little is known about changes in the microbiome during periods of undernutrition. Thus, it is of great scientific and public health importance to improve the understanding of how the microbiome changes during nutrient deprivation. To best address the issue of the double burden and poor growth in low-income countries, research is warranted to advance the knowledge of the long-term role of the microbiome in the health of children exposed to undernutrition.
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Affiliation(s)
- Daniel J Hoffman
- a Department of Nutritional Sciences and the New Jersey Institute for Food, Nutrition, and Health , Rutgers, the State University of New Jersey , New Brunswick , NJ , USA
| | - Maiza Campos-Ponce
- b Department of Health Sciences , VU University , Amsterdam , The Netherlands
| | - Carla R Taddei
- c Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences , University of São Paulo , São Paulo, SP , Brazil.,d School of Arts, Science and Humanities , University of São Paulo , São Paulo, SP , Brazil
| | - Colleen M Doak
- b Department of Health Sciences , VU University , Amsterdam , The Netherlands
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Sampaio-Maia B, Caldas IM, Pereira ML, Pérez-Mongiovi D, Araujo R. The Oral Microbiome in Health and Its Implication in Oral and Systemic Diseases. ADVANCES IN APPLIED MICROBIOLOGY 2016; 97:171-210. [PMID: 27926431 DOI: 10.1016/bs.aambs.2016.08.002] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The oral microbiome can alter the balance between health and disease, locally and systemically. Within the oral cavity, bacteria, archaea, fungi, protozoa, and viruses may all be found, each having a particular role, but strongly interacting with each other and with the host, in sickness or in health. A description on how colonization occurs and how the oral microbiome dynamically evolves throughout the host's life is given. In this chapter the authors also address oral and nonoral conditions in which oral microorganisms may play a role in the etiology and progression, presenting the up-to-date knowledge on oral dysbiosis as well as the known underlying pathophysiologic mechanisms involving oral microorganisms in each condition. In oral pathology, oral microorganisms are associated with several diseases, namely dental caries, periodontal diseases, endodontic infections, and also oral cancer. In systemic diseases, nonoral infections, adverse pregnancy outcomes, cardiovascular diseases, and diabetes are among the most prevalent pathologies linked with oral cavity microorganisms. The knowledge on how colonization occurs, how oral microbiome coevolves with the host, and how oral microorganisms interact with each other may be a key factor to understand diseases etiology and progression.
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Affiliation(s)
| | - I M Caldas
- Universidade do Porto, Portugal; Institute of Research and Advanced Training in Health Sciences and Technologies, University Institute of Health Sciences (IUCS), CESPU, CRL, Gandra, Portugal; Universidade de Coimbra, Portugal
| | | | - D Pérez-Mongiovi
- Institute of Research and Advanced Training in Health Sciences and Technologies, University Institute of Health Sciences (IUCS), CESPU, CRL, Gandra, Portugal
| | - R Araujo
- Universidade do Porto, Portugal; Flinders University, Adelaide, SA, Australia
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Hoedt EC, Cuív PÓ, Morrison M. Methane matters: from blue-tinged moos, to boozy roos, and the health of humans too. Anim Front 2016. [DOI: 10.2527/af.2016-0029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Emily C. Hoedt
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072 Australia
| | - Páraic Ó Cuív
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD, 4102 Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD, 4102 Australia
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Kortman GAM, Dutilh BE, Maathuis AJH, Engelke UF, Boekhorst J, Keegan KP, Nielsen FGG, Betley J, Weir JC, Kingsbury Z, Kluijtmans LAJ, Swinkels DW, Venema K, Tjalsma H. Microbial Metabolism Shifts Towards an Adverse Profile with Supplementary Iron in the TIM-2 In vitro Model of the Human Colon. Front Microbiol 2016; 6:1481. [PMID: 26779139 PMCID: PMC4701948 DOI: 10.3389/fmicb.2015.01481] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 12/08/2015] [Indexed: 12/11/2022] Open
Abstract
Oral iron administration in African children can increase the risk for infections. However, it remains unclear to what extent supplementary iron affects the intestinal microbiome. We here explored the impact of iron preparations on microbial growth and metabolism in the well-controlled TNO's in vitro model of the large intestine (TIM-2). The model was inoculated with a human microbiota, without supplementary iron, or with 50 or 250 μmol/L ferrous sulfate, 50 or 250 μmol/L ferric citrate, or 50 μmol/L hemin. High resolution responses of the microbiota were examined by 16S rDNA pyrosequencing, microarray analysis, and metagenomic sequencing. The metabolome was assessed by fatty acid quantification, gas chromatography-mass spectrometry (GC-MS), and 1H-NMR spectroscopy. Cultured intestinal epithelial Caco-2 cells were used to assess fecal water toxicity. Microbiome analysis showed, among others, that supplementary iron induced decreased levels of Bifidobacteriaceae and Lactobacillaceae, while it caused higher levels of Roseburia and Prevotella. Metagenomic analyses showed an enrichment of microbial motility-chemotaxis systems, while the metabolome markedly changed from a saccharolytic to a proteolytic profile in response to iron. Branched chain fatty acids and ammonia levels increased significantly, in particular with ferrous sulfate. Importantly, the metabolite-containing effluent from iron-rich conditions showed increased cytotoxicity to Caco-2 cells. Our explorations indicate that in the absence of host influences, iron induces a more hostile environment characterized by a reduction of microbes that are generally beneficial, and increased levels of bacterial metabolites that can impair the barrier function of a cultured intestinal epithelial monolayer.
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Affiliation(s)
- Guus A M Kortman
- Department of Laboratory Medicine - Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Netherlands
| | - Bas E Dutilh
- Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Radboud University Medical CenterNijmegen, Netherlands; Theoretical Biology and Bioinformatics, Utrecht UniversityUtrecht, Netherlands; Department of Marine Biology, Institute of Biology, Federal University of Rio de JaneiroRio de Janeiro, Brazil
| | | | - Udo F Engelke
- Department of Laboratory Medicine - Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Netherlands
| | | | - Kevin P Keegan
- Argonne National Laboratory, University of Chicago Lemont, IL, USA
| | - Fiona G G Nielsen
- Illumina Inc., Chesterford Research ParkLittle Chesterford, UK; DNAdigest, Future Business CentreCambridge, UK
| | - Jason Betley
- Illumina Inc., Chesterford Research Park Little Chesterford, UK
| | | | - Zoya Kingsbury
- Illumina Inc., Chesterford Research Park Little Chesterford, UK
| | - Leo A J Kluijtmans
- Department of Laboratory Medicine - Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Netherlands
| | - Dorine W Swinkels
- Department of Laboratory Medicine - Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Netherlands
| | | | - Harold Tjalsma
- Department of Laboratory Medicine - Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Netherlands
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The oral microbiome diversity and its relation to human diseases. Folia Microbiol (Praha) 2014; 60:69-80. [PMID: 25147055 DOI: 10.1007/s12223-014-0342-2] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 08/11/2014] [Indexed: 02/07/2023]
Abstract
As one of the most clinically relevant human habitats, the human mouth is colonized by a set of microorganisms, including bacteria, archaea, fungi, and viruses. Increasing evidence has supported that these microbiota contribute to the two commonest oral diseases of man (dental caries and periodontal diseases), presenting significant risk factors to human health conditions, such as tumor, diabetes mellitus, cardiovascular diseases, bacteremia, preterm birth, and low birth weight in infants. It is widely accepted that oral microorganisms cause diseases mainly by a synergistic or cooperative way, and the interspecies interactions within the oral community play a crucial role in determining whether oral microbiota elicit diseases or not. Since a comprehensive understanding of the complex interspecies interactions within a community needs the knowledge of its endogenous residents, a plenty of research have been carried out to explore the oral microbial diversity. In this review, we focus on the recent progress in this field, including the oral microbiome composition and its association with human diseases.
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Göhler A, Hetzer A, Holtfreter B, Geisel MH, Schmidt CO, Steinmetz I, Kocher T. Quantitative molecular detection of putative periodontal pathogens in clinically healthy and periodontally diseased subjects. PLoS One 2014; 9:e99244. [PMID: 25029268 PMCID: PMC4100758 DOI: 10.1371/journal.pone.0099244] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 05/13/2014] [Indexed: 01/11/2023] Open
Abstract
Periodontitis is a multi-microbial oral infection with high prevalence among adults. Putative oral pathogens are commonly found in periodontally diseased individuals. However, these organisms can be also detected in the oral cavity of healthy subjects. This leads to the hypothesis, that alterations in the proportion of these organisms relative to the total amount of oral microorganisms, namely their abundance, rather than their simple presence might be important in the transition from health to disease. Therefore, we developed a quantitative molecular method to determine the abundance of various oral microorganisms and the portion of bacterial and archaeal nucleic acid relative to the total nucleic acid extracted from individual samples. We applied quantitative real-time PCRs targeting single-copy genes of periodontal bacteria and 16S-rRNA genes of Bacteria and Archaea. Testing tongue scrapings of 88 matched pairs of periodontally diseased and healthy subjects revealed a significantly higher abundance of P. gingivalis and a higher total bacterial abundance in diseased subjects. In fully adjusted models the risk of being periodontally diseased was significantly higher in subjects with high P. gingivalis and total bacterial abundance. Interestingly, we found that moderate abundances of A. actinomycetemcomitans were associated with reduced risk for periodontal disease compared to subjects with low abundances, whereas for high abundances, this protective effect leveled off. Moderate archaeal abundances were health associated compared to subjects with low abundances. In conclusion, our methodological approach unraveled associations of the oral flora with periodontal disease, which would have gone undetected if only qualitative data had been determined.
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Affiliation(s)
- André Göhler
- Friedrich Loeffler Institute of Medical Microbiology, Ernst Moritz Arndt University, Greifswald, Germany
| | - Adrian Hetzer
- Friedrich Loeffler Institute of Medical Microbiology, Ernst Moritz Arndt University, Greifswald, Germany
| | - Birte Holtfreter
- Unit of Periodontology, Dental School, University Medicine, Ernst Moritz Arndt University, Greifswald, Germany
| | - Marie Henrike Geisel
- Unit of Periodontology, Dental School, University Medicine, Ernst Moritz Arndt University, Greifswald, Germany
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Carsten Oliver Schmidt
- Section Methods in Community Medicine, Institute for Community Medicine, University Medicine Greifswald, Ernst Moritz Arndt University, Greifswald, Germany
| | - Ivo Steinmetz
- Friedrich Loeffler Institute of Medical Microbiology, Ernst Moritz Arndt University, Greifswald, Germany
- * E-mail: (IM); (TK)
| | - Thomas Kocher
- Unit of Periodontology, Dental School, University Medicine, Ernst Moritz Arndt University, Greifswald, Germany
- * E-mail: (IM); (TK)
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Lira EAG, Ramiro FS, Chiarelli FM, Dias RR, Feres M, Figueiredo LC, Faveri M. Reduction in prevalence of Archaea after periodontal therapy in subjects with generalized aggressive periodontitis. Aust Dent J 2014; 58:442-7. [PMID: 24320900 DOI: 10.1111/adj.12123] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2013] [Indexed: 12/12/2022]
Abstract
BACKGROUND There is evidence of a possible relationship between Archaea and periodontal disease; however, to date few studies have assessed the changes in prevalence of this domain after periodontal therapy. The aim of this randomized double-blind and placebo-controlled study was to assess if periodontal treatment with or without systemic antibiotic would change the prevalence of Archaea after periodontal therapy. METHODS Thirty subjects were randomly assigned to receive scaling and root planing (SRP) alone or combined with metronidazole (MTZ) + amoxicillin (AMX) for 14 days. Clinical and microbiological examinations were performed at baseline and at six months post-SRP. Nine subgingival plaque samples per subject were analysed for the presence of Archaea. RESULTS SRP alone or combined with MTZ + AMX significantly reduced the prevalence of subjects colonized by Archaea at six months post-therapy. However, no significant differences between treatment groups were observed (p > 0.05). Both therapies led to a statistically significant decrease in the mean percentage of sites colonized by Archaea (p < 0.05). A negative Spearman correlation was observed between the presence of Archaea and the mean clinical attachment gain at six months post-therapy (r(2) = -0.61; 95% CI -0.80- -0.31; p = 0.003). CONCLUSIONS SRP alone or combined with MTZ + AMX provides a similar reduction in the prevalence of Archaea in the subgingival biofilm of subjects with generalized aggressive periodontitis.
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Affiliation(s)
- E A G Lira
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, São Paulo, Brazil
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35
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Triantafyllou K, Chang C, Pimentel M. Methanogens, methane and gastrointestinal motility. J Neurogastroenterol Motil 2013; 20:31-40. [PMID: 24466443 PMCID: PMC3895606 DOI: 10.5056/jnm.2014.20.1.31] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 10/28/2013] [Accepted: 10/29/2013] [Indexed: 12/16/2022] Open
Abstract
Anaerobic fermentation of the undigested polysaccharide fraction of carbohydrates produces hydrogen in the intestine which is the substrate for methane production by intestinal methanogens. Hydrogen and methane are excreted in the flatus and in breath giving the opportunity to indirectly measure their production using breath testing. Although methane is detected in 30%-50% of the healthy adult population worldwide, its production has been epidemiologically and clinically associated with constipation related diseases, like constipation predominant irritable bowel syndrome and chronic constipation. While a causative relation is not proven yet, there is strong evidence from animal studies that methane delays intestinal transit, possibly acting as a neuromuscular transmitter. This evidence is further supported by the universal finding that methane production (measured by breath test) is associated with delayed transit time in clinical studies. There is also preliminary evidence that antibiotic reduction of methanogens (as evidenced by reduced methane production) predicts the clinical response in terms of symptomatic improvement in patients with constipation predominant irritable bowel syndrome. However, we have not identified yet the mechanism of action of methane on intestinal motility, and since methane production does not account for all constipation associated cases, there is need for high quality clinical trials to examine methane as a biomarker for the diagnosis or as a biomarker that predicts antibiotic treatment response in patients with constipation related disorders.
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Affiliation(s)
- Konstantinos Triantafyllou
- GI Motility Program, Division of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA, USA. ; Hepatogastroenterology Unit, Second Department of Internal Medicine and Research Institute, Attikon University General Hospital, Medical School, Athens University, Athens, Greece
| | - Christopher Chang
- GI Motility Program, Division of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mark Pimentel
- GI Motility Program, Division of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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36
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Omics approaches to study host-microbiota interactions. Curr Opin Microbiol 2013; 16:270-7. [PMID: 23891019 DOI: 10.1016/j.mib.2013.07.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 06/25/2013] [Accepted: 07/01/2013] [Indexed: 02/08/2023]
Abstract
The intestinal microbiota has profound effects on our physiology and immune system and disturbances in the equilibrium between microbiota and host have been observed in many disorders. Here we discuss the possibilities to further our understanding of how microbiota impacts on human health and disease through the use of large-scale quantifiable tools such as transcriptomics, metagenomics and metabolomics. Reductionist models, including gnotobiotic mouse models have their place in testing hypotheses and elucidating mechanisms by which specific communities or individual species impact on host biology. Network biology approaches can be combined with studies in animal models and cell lines to create iterative cycle of hypotheses and testing, possibly leading to testing in clinical and nutritional intervention studies.
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37
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Hoffmann C, Dollive S, Grunberg S, Chen J, Li H, Wu GD, Lewis JD, Bushman FD. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One 2013; 8:e66019. [PMID: 23799070 PMCID: PMC3684604 DOI: 10.1371/journal.pone.0066019] [Citation(s) in RCA: 513] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/30/2013] [Indexed: 12/12/2022] Open
Abstract
Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health.
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Affiliation(s)
- Christian Hoffmann
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiania, Goiás, Brazil
| | - Serena Dollive
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Stephanie Grunberg
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jun Chen
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Hongzhe Li
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Gary D. Wu
- Division of Gastroenterology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (GDW); (JDL); (FDB)
| | - James D. Lewis
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (GDW); (JDL); (FDB)
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (GDW); (JDL); (FDB)
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