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Qian T, Zhu H, Zhu L, Chen C, Shen C, Zhang R. Small intestinal microbiota composition and the prognosis of infants with ileostomy resulting from distinct primary diseases. BMC Gastroenterol 2020; 20:224. [PMID: 32660555 PMCID: PMC7359560 DOI: 10.1186/s12876-020-01366-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 07/02/2020] [Indexed: 11/10/2022] Open
Abstract
Background Studies of microbiota composition of infants with small intestinal ostomy due to various etiologies are limited. Here, we characterized the intestinal microbiota of neonates with ileostomy resulting from distinct primary diseases. Methods Fifteen patients with necrotizing enterocolitis, eight patients with meconium peritonitis, and seven patients with Hirschsprung’s disease were included in the study. The small intestinal microbiota composition in infants with ileostomy caused by these diseases was studied. Results Microbial diversity in neonatal ileostomy fluid was generally low, and was dominated by members of the Proteobacteria and Firmicutes phyla. At the genus level, the most abundant were Klebsiella, Escherichia-Shigella, Streptococcus, Clostridium sensu stricto 1, Enterococcus, and Lactobacillus. Streptococcus and Veillonella are related to carbohydrate metabolism and immunity, and breastfeeding can increase the proportion of these potentially beneficial bacteria. The proportion of Bifidobacterium in the breastfeeding group was higher than that in the non-breastfeeding group, and incidence of colitis and sepsis was reduced in the breastfeeding group. The proportion of Bifidobacterium increased and incidence of colitis and sepsis decreased in the breastfeeding group compared with the non- breastfeeding group, but there was no significant difference. The increase in body weight in the breastfeeding group was observed to be higher than in the non-breastfeeding group. Conclusions Excessive Klebsiella and Escherichia-Shigella and low abundance of Streptococcus, Veillonella and Faecalibacterium suggests that the small intestinal microbiota is in an unhealthy state after ileostomy. However, Streptococcus, Faecalibacterium, and Veillonella species were frequently present, suggesting that expansion of these bacteria might assist the development of the immune system after surgery.
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Affiliation(s)
- Tian Qian
- Department of Neonatology, Children's Hospital of Fudan University, 399 Wanyuan Rd, Shanghai, 201102, P. R. China.,Department of Clinical Nutrition, Children's Hospital of Fudan University, 399 Wanyuan Rd, Shanghai, 201102, P. R. China
| | - Haitao Zhu
- Department of Pediatric Surgery, Children's Hospital of Fudan University, 399 Wanyuan Rd, Shanghai, 201102, P. R. China
| | - Li Zhu
- Department of Neonatology, Children's Hospital of Fudan University, 399 Wanyuan Rd, Shanghai, 201102, P. R. China
| | - Chao Chen
- Department of Neonatology, Children's Hospital of Fudan University, 399 Wanyuan Rd, Shanghai, 201102, P. R. China
| | - Chun Shen
- Department of Pediatric Surgery, Children's Hospital of Fudan University, 399 Wanyuan Rd, Shanghai, 201102, P. R. China.
| | - Rong Zhang
- Department of Neonatology, Children's Hospital of Fudan University, 399 Wanyuan Rd, Shanghai, 201102, P. R. China.
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Johnston JM, Bulloch EM. Advances in menaquinone biosynthesis: sublocalisation and allosteric regulation. Curr Opin Struct Biol 2020; 65:33-41. [PMID: 32634692 DOI: 10.1016/j.sbi.2020.05.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 12/31/2022]
Abstract
Menaquinones (vitamin K2) are a family of redox-active small molecules with critical functions across all domains of life, including energy generation in bacteria and bone health in humans. The enzymes involved in menaquinone biosynthesis also have bioengineering applications and are potential antimicrobial drug targets. New insights into the essential roles of menaquinones, and their potential to cause redox-related toxicity, have highlighted the need for this pathway to be tightly controlled. Here, we provide an overview of our current understanding of the classical menaquinone biosynthesis pathway in bacteria. We also review recent discoveries on protein-level allostery and sublocalisation of membrane-bound enzymes that have provided insight into the regulation of flux through this biosynthetic pathway.
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Affiliation(s)
- Jodie M Johnston
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre, and Maurice Wilkins Centre for MolecularBiodiscovery, University of Canterbury, Christchurch 8041, New Zealand.
| | - Esther Mm Bulloch
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for MolecularBiodiscovery, University of Auckland, Private Bag 92019, Auckland, New Zealand
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Cheng D, Song J, Xie M, Song D. The bidirectional relationship between host physiology and microbiota and health benefits of probiotics: A review. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.07.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Dicks L, Geldenhuys J, Mikkelsen L, Brandsborg E, Marcotte H. Our gut microbiota: a long walk to homeostasis. Benef Microbes 2018; 9:3-20. [DOI: 10.3920/bm2017.0066] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The microbiome of the human gastrointestinal tract (GIT) consists of billions of bacteria, fungi and viruses, of which bacteria play the most important role in nutrition, immune development, production of vitamins and maintaining a well-balanced (homeostatic) microbial population. Many papers have been published on the microbiota in the human GIT, but little is known about the first group of bacteria that colonises an infant. The intestinal tract of an unborn is, despite general belief, not sterile, but contains bacteria that have been transferred from the mother. This opens a new research field and may change our understanding about the role bacteria play in early life, the selection of strains with probiotic properties and the treatment of diseases related to bacterial infections. Differences in bacterial populations isolated from meconia may provide answers to the prevention of certain forms of diabetes. More research is now focusing on the effect that a genetically diverse group, versus a much simpler microbial population, may have on the development of a homeostatic gut microbiome. The effect different bacterial species have on the gut-associated lymphoid tissue and cascade of immune responses has been well researched, but we still fail in identifying the ideal group of intestinal bacteria and if we do, it will certainly not be possible to maintain homeostasis with so many challenges the gut faces. Changes in diet, antibiotics, food preservatives and stress are some of the factors we would like to control, but more than often fail to do so. The physiology and genetics of the GIT changes with age and so the microbiome. This review summarises factors involved in the regulation of a gut microbiome.
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Affiliation(s)
- L.M.T. Dicks
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7600, South Africa
| | - J. Geldenhuys
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7600, South Africa
| | | | - E. Brandsborg
- Bifodan A/S, Bogbinderivej 6, 3390 Hundested, Denmark
| | - H. Marcotte
- Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge 141 86, Sweden
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Bäckhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P, Li Y, Xia Y, Xie H, Zhong H, Khan M, Zhang J, Li J, Xiao L, Al-Aama J, Zhang D, Lee Y, Kotowska D, Colding C, Tremaroli V, Yin Y, Bergman S, Xu X, Madsen L, Kristiansen K, Dahlgren J, Wang J, Jun W. Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. Cell Host Microbe 2015; 17:690-703. [DOI: 10.1016/j.chom.2015.04.004] [Citation(s) in RCA: 1795] [Impact Index Per Article: 199.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/27/2015] [Accepted: 04/08/2015] [Indexed: 02/07/2023]
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Latham JA, Chen D, Allen KN, Dunaway-Mariano D. Divergence of substrate specificity and function in the Escherichia coli hotdog-fold thioesterase paralogs YdiI and YbdB. Biochemistry 2014; 53:4775-87. [PMID: 24992697 PMCID: PMC4116150 DOI: 10.1021/bi500333m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The work described in this paper, and its companion paper (Wu, R., Latham, J. A., Chen, D., Farelli, J., Zhao, H., Matthews, K. Allen, K. N., and Dunaway-Mariano, D. (2014) Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB. Biochemistry, DOI: 10.1021/bi500334v), focuses on the evolution of a pair of paralogous hotdog-fold superfamily thioesterases of E. coli, YbdB and YdiI, which share a high level of sequence identity but perform different biological functions (viz., proofreader of 2,3-dihydroxybenzoyl-holoEntB in the enterobactin biosynthetic pathway and catalyst of the 1,4-dihydoxynapthoyl-CoA hydrolysis step in the menaquinone biosynthetic pathway, respectively). In vitro substrate activity screening of a library of thioester metabolites showed that YbdB displays high activity with benzoyl-holoEntB and benzoyl-CoA substrates, marginal activity with acyl-CoA thioesters, and no activity with 1,4-dihydoxynapthoyl-CoA. YdiI, on the other hand, showed a high level of activity with its physiological substrate, significant activity toward a wide range of acyl-CoA thioesters, and minimal activity toward benzoyl-holoEntB. These results were interpreted as evidence for substrate promiscuity that facilitates YbdB and YdiI evolvability, and divergence in substrate preference, which correlates with their assumed biological function. YdiI support of the menaquinone biosynthetic pathway was confirmed by demonstrating reduced anaerobic growth of the E. coli ydiI-knockout mutant (vs wild-type E. coli) on glucose in the presence of the electron acceptor fumarate. Bioinformatic analysis revealed that a small biological range exists for YbdB orthologs (i.e., limited to Enterobacteriales) relative to that of YdiI orthologs. The divergence in YbdB and YdiI substrate specificity detailed in this paper set the stage for their structural analyses reported in the companion paper.
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Affiliation(s)
- John A Latham
- Department of Chemistry & Chemical Biology, University of New Mexico , Albuquerque, New Mexico 87131, United States
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Wu R, Latham JA, Chen D, Farelli J, Zhao H, Matthews K, Allen KN, Dunaway-Mariano D. Structure and catalysis in the Escherichia coli hotdog-fold thioesterase paralogs YdiI and YbdB. Biochemistry 2014; 53:4788-805. [PMID: 25010423 PMCID: PMC4116151 DOI: 10.1021/bi500334v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Herein,
the structural determinants for substrate recognition and
catalysis in two hotdog-fold thioesterase paralogs, YbdB and YdiI
from Escherichia coli, are identified and analyzed
to provide insight into the evolution of biological function in the
hotdog-fold enzyme superfamily. The X-ray crystal structures of YbdB
and YdiI, in complex with inert substrate analogs, determined in this
study revealed the locations of the respective thioester substrate
binding sites and the identity of the residues positioned for substrate
binding and catalysis. The importance of each of these residues was
assessed through amino acid replacements followed by steady-state
kinetic analyses of the corresponding site-directed mutants. Transient
kinetic and solvent 18O-labeling studies were then carried
out to provide insight into the role of Glu63 posited to function
as the nucleophile or general base in catalysis. Finally, the structure–function–mechanism
profiles of the two paralogs, along with that of a more distant homolog,
were compared to identify conserved elements of substrate recognition
and catalysis, which define the core traits of the hotdog-fold thioesterase
family, as well as structural features that are unique to each thioesterase.
Founded on the insight gained from this analysis, we conclude that
the promiscuity revealed by in vitro substrate activity
determinations, and posited to facilitate the evolution of new biological
function, is the product of intrinsic plasticity in substrate binding
as well as in the catalytic mechanism.
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Affiliation(s)
- Rui Wu
- Department of Chemistry, Boston University , Boston, Massachusetts 02215, United States
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