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Zhao F, Wang J. Another piece of puzzle for the human microbiome: the gut virome under dietary modulation. J Genet Genomics 2024; 51:983-996. [PMID: 38710286 DOI: 10.1016/j.jgg.2024.04.013] [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: 03/02/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024]
Abstract
The virome is the most abundant and highly variable microbial consortium in the gut. Because of difficulties in isolating and culturing gut viruses and the lack of reference genomes, the virome has remained a relatively elusive aspect of the human microbiome. In recent years, studies on the virome have accumulated growing evidence showing that the virome is diet-modulated and widely involved in regulating health. Here, we review the responses of the gut virome to dietary intake and the potential health implications, presenting changes in the gut viral community and preferences of viral members to particular diets. We further discuss how viral-bacterial interactions and phage lifestyle shifts shape the gut microbiota. We also discuss the specific functions conferred by diet on the gut virome and bacterial community in the context of horizontal gene transfer, as well as the import of new viral members along with the diet. Collating these studies will expand our understanding of the dietary regulation of the gut virome and inspire dietary interventions and health maintenance strategies targeting the gut microbiota.
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Affiliation(s)
- Fengxiang Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jinfeng Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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Xiao L, Zhou T, Zuo Z, Sun N, Zhao F. Spatiotemporal patterns of the pregnancy microbiome and links to reproductive disorders. Sci Bull (Beijing) 2024; 69:1275-1285. [PMID: 38388298 DOI: 10.1016/j.scib.2024.02.001] [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: 09/25/2023] [Revised: 01/04/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024]
Abstract
The microbiome of females undergoes extensive remodeling during pregnancy, which is likely to have an impact on the health of both mothers and offspring. Nevertheless, large-scale integrated investigations characterizing microbiome dynamics across key body habitats are lacking. Here, we performed an extensive meta-analysis that compiles and analyzes microbiome profiles from >10,000 samples across the gut, vagina, and oral cavity of pregnant women from diverse geographical regions. We have unveiled unexpected variations in the taxonomic, functional, and ecological characteristics of microbial communities throughout the course of pregnancy. The gut microbiota showed distinct trajectories between Western and non-Western populations. The vagina microbiota exhibited fluctuating transitions at the genus level across gestation, while the oral microbiota remained relatively stable. We also identified distinctive microbial signatures associated with prevalent pregnancy-related disorders, including opposite variations in the oral and gut microbiota of patients with gestational diabetes and disrupted microbial networks in preterm birth. This study establishes a comprehensive atlas of the pregnancy microbiome by integrating multidimensional datasets and offers foundational insights into the intricate interplay between microbes and host factors that underlie reproductive health.
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Affiliation(s)
- Liwen Xiao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Tian Zhou
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenqiang Zuo
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Ningxia Sun
- Department of Reproductive Medicine, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; Department of Reproductive Medicine, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Xiao L, Zuo Z, Zhao F. Microbiome in Female Reproductive Health: Implications for Fertility and Assisted Reproductive Technologies. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzad005. [PMID: 38862423 PMCID: PMC11104452 DOI: 10.1093/gpbjnl/qzad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 06/13/2024]
Abstract
The microbiome plays a critical role in the process of conception and the outcomes of pregnancy. Disruptions in microbiome homeostasis in women of reproductive age can lead to various pregnancy complications, which significantly impact maternal and fetal health. Recent studies have associated the microbiome in the female reproductive tract (FRT) with assisted reproductive technology (ART) outcomes, and restoring microbiome balance has been shown to improve fertility in infertile couples. This review provides an overview of the role of the microbiome in female reproductive health, including its implications for pregnancy outcomes and ARTs. Additionally, recent advances in the use of microbial biomarkers as indicators of pregnancy disorders are summarized. A comprehensive understanding of the characteristics of the microbiome before and during pregnancy and its impact on reproductive health will greatly promote maternal and fetal health. Such knowledge can also contribute to the development of ARTs and microbiome-based interventions.
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Affiliation(s)
- Liwen Xiao
- CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Beijing Institutes of Life Science/Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenqiang Zuo
- Beijing Institutes of Life Science/Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fangqing Zhao
- CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Beijing Institutes of Life Science/Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Inchingolo AD, Dipalma G, Viapiano F, Netti A, Ferrara I, Ciocia AM, Mancini A, Di Venere D, Palermo A, Inchingolo AM, Inchingolo F. Celiac Disease-Related Enamel Defects: A Systematic Review. J Clin Med 2024; 13:1382. [PMID: 38592254 PMCID: PMC10932357 DOI: 10.3390/jcm13051382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/22/2024] [Accepted: 02/25/2024] [Indexed: 04/10/2024] Open
Abstract
INTRODUCTION This systematic review aims to elucidate the intricate correlation between celiac disease (CD) and dental enamel defects (DED), exploring pathophysiological mechanisms, oral health implications, and a dentist's role in early diagnosis. MATERIALS AND METHODS Following PRISMA guidelines, a comprehensive search from 1 January 2013 to 1 January 2024 across PubMed, Cochrane Library, Scopus, and Web of Science identified 153 publications. After exclusions, 18 studies met the inclusion criteria for qualitative analysis. Inclusion criteria involved study types (RCTs, RCCTs, case series), human participants, English language, and full-text available. RESULTS The search yielded 153 publications, with 18 studies meeting the inclusion criteria for qualitative analysis. Notable findings include a high prevalence of DED in CD patients, ranging from 50 to 94.1%. Symmetrical and chronological defects, according to Aine's classification, were predominant, and significant associations were observed between CD severity and enamel defect extent. CONCLUSIONS The early recognition of oral lesions, particularly through Aine's classification, may signal potential CD even in the absence of gastrointestinal symptoms. Correlations between CD and dental health conditions like molar incisor hypomineralization (MIH) emphasize the dentist's crucial role in early diagnosis. Collaboration between dentists and gastroenterologists is essential for effective monitoring and management. This review consolidates current knowledge, laying the groundwork for future research and promoting interdisciplinary collaboration for improved CD-related oral health outcomes. Further large-scale prospective research is recommended to deepen our understanding of these issues.
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Affiliation(s)
- Alessio Danilo Inchingolo
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.D.); (F.V.); (A.N.); (I.F.); (A.M.C.); (A.M.); (D.D.V.); (A.M.I.)
| | - Gianna Dipalma
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.D.); (F.V.); (A.N.); (I.F.); (A.M.C.); (A.M.); (D.D.V.); (A.M.I.)
| | - Fabio Viapiano
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.D.); (F.V.); (A.N.); (I.F.); (A.M.C.); (A.M.); (D.D.V.); (A.M.I.)
| | - Anna Netti
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.D.); (F.V.); (A.N.); (I.F.); (A.M.C.); (A.M.); (D.D.V.); (A.M.I.)
| | - Irene Ferrara
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.D.); (F.V.); (A.N.); (I.F.); (A.M.C.); (A.M.); (D.D.V.); (A.M.I.)
| | - Anna Maria Ciocia
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.D.); (F.V.); (A.N.); (I.F.); (A.M.C.); (A.M.); (D.D.V.); (A.M.I.)
| | - Antonio Mancini
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.D.); (F.V.); (A.N.); (I.F.); (A.M.C.); (A.M.); (D.D.V.); (A.M.I.)
| | - Daniela Di Venere
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.D.); (F.V.); (A.N.); (I.F.); (A.M.C.); (A.M.); (D.D.V.); (A.M.I.)
| | - Andrea Palermo
- College of Medicine and Dentistry, Birmingham B4 6BN, UK;
| | - Angelo Michele Inchingolo
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.D.); (F.V.); (A.N.); (I.F.); (A.M.C.); (A.M.); (D.D.V.); (A.M.I.)
| | - Francesco Inchingolo
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.I.); (G.D.); (F.V.); (A.N.); (I.F.); (A.M.C.); (A.M.); (D.D.V.); (A.M.I.)
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Zhou T, Xiao L, Zuo Z, Zhao F. MAMI: a comprehensive database of mother-infant microbiome and probiotic resources. Nucleic Acids Res 2024; 52:D738-D746. [PMID: 37819042 PMCID: PMC10767955 DOI: 10.1093/nar/gkad813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/04/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Extensive evidence has demonstrated that the human microbiome and probiotics confer great impacts on human health, particularly during critical developmental stages such as pregnancy and infancy when microbial communities undergo remarkable changes and maturation. However, a major challenge in understanding the microbial community structure and interactions between mothers and infants lies in the current lack of comprehensive microbiome databases specifically focused on maternal and infant health. To address this gap, we have developed an extensive database called MAMI (Microbiome Atlas of Mothers and Infants) that archives data on the maternal and neonatal microbiome, as well as abundant resources on edible probiotic strains. By leveraging this resource, we can gain profound insights into the dynamics of microbial communities, contributing to lifelong wellness for both mothers and infants through precise modulation of the developing microbiota. The functionalities incorporated into MAMI provide a unique perspective on the study of the mother-infant microbiome, which not only advance microbiome-based scientific research but also enhance clinical practice. MAMI is publicly available at https://bioinfo.biols.ac.cn/mami/.
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Affiliation(s)
- Tian Zhou
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Liwen Xiao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenqiang Zuo
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Fangqing Zhao
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Gao S, Wang J. Maternal and infant microbiome: next-generation indicators and targets for intergenerational health and nutrition care. Protein Cell 2023; 14:807-823. [PMID: 37184065 PMCID: PMC10636639 DOI: 10.1093/procel/pwad029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/04/2023] [Indexed: 05/16/2023] Open
Abstract
Microbes are commonly sensitive to shifts in the physiological and pathological state of their hosts, including mothers and babies. From this perspective, the microbiome may be a good indicator for diseases during pregnancy and has the potential to be used for perinatal health monitoring. This is embodied in the application of microbiome from multi body sites for auxiliary diagnosis, early prediction, prolonged monitoring, and retrospective diagnosis of pregnancy and infant complications, as well as nutrition management and health products developments of mothers and babies. Here we summarized the progress in these areas and explained that the microbiome of different body sites is sensitive to different diseases and their microbial biomarkers may overlap between each other, thus we need to make a diagnosis prudently for those diseases. Based on the microbiome variances and additional anthropometric and physical data, individualized responses of mothers and neonates to meals and probiotics/prebiotics were predictable, which is of importance for precise nutrition and probiotics/prebiotics managements and developments. Although a great deal of encouraging performance was manifested in previous studies, the efficacy could be further improved by combining multi-aspect data such as multi-omics and time series analysis in the future. This review reconceptualizes maternal and infant health from a microbiome perspective, and the knowledge in it may inspire the development of new options for the prevention and treatment of adverse pregnancy outcomes and bring a leap forward in perinatal health care.
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Affiliation(s)
- Shengtao Gao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jinfeng Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
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Wilson A, Bogie B, Chaaban H, Burge K. The Nonbacterial Microbiome: Fungal and Viral Contributions to the Preterm Infant Gut in Health and Disease. Microorganisms 2023; 11:909. [PMID: 37110332 PMCID: PMC10144239 DOI: 10.3390/microorganisms11040909] [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: 03/03/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
The intestinal microbiome is frequently implicated in necrotizing enterocolitis (NEC) pathogenesis. While no particular organism has been associated with NEC development, a general reduction in bacterial diversity and increase in pathobiont abundance has been noted preceding disease onset. However, nearly all evaluations of the preterm infant microbiome focus exclusively on the bacterial constituents, completely ignoring any fungi, protozoa, archaea, and viruses present. The abundance, diversity, and function of these nonbacterial microbes within the preterm intestinal ecosystem are largely unknown. Here, we review findings on the role of fungi and viruses, including bacteriophages, in preterm intestinal development and neonatal intestinal inflammation, with potential roles in NEC pathogenesis yet to be determined. In addition, we highlight the importance of host and environmental influences, interkingdom interactions, and the role of human milk in shaping fungal and viral abundance, diversity, and function within the preterm intestinal ecosystem.
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Affiliation(s)
| | | | - Hala Chaaban
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Kathryn Burge
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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