1
|
Li H, Wang Y, Zhao X, Yan Z, Song C, Wang S. Chirality of tyrosine controls biofilm formation via the regulation of bacterial adhesion. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
|
2
|
Wu T, Wang G, Tang H, Xiong Z, Song X, Xia Y, Lai PFH, Ai L. Genes encoding bile salt hydrolase differentially affect adhesion of Lactiplantibacillus plantarum AR113. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:1522-1530. [PMID: 34402069 DOI: 10.1002/jsfa.11487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/23/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Adhesion is considered important for Lactiplantibacillus to persist in the human gut and for it to exert probiotic effects. Lactiplantibacillus plantarum contains a considerable number and variety of genes encoding bile salt hydrolases (bsh), but their effects on microbial adhesion remain poorly understood. To clarify the effects of four bsh on adhesion, we tried to knock out bsh (Δbsh) of L. plantarum AR113 using the CRISPR-Cas9 method, and compared the growth, auto-aggregation (RAA ), co-aggregation (RCA ), surface hydrophobicity (AHC ) of AR113 wild-type and Δbsh strains and their adhesion abilities to HT29 cells. RESULTS We first obtained the AR113 Δbsh1,3,2,4 strain with four bsh knocked out. Their growth was significantly slower than the wild-type strain cultured in De Man, Rogosa, and Sharpe medium (MRS) with 3.0 g L-1 glyco- or tauro-conjugated bile acid. Bsh had no significant effect on the growth of ten strains cultured in MRS, but Δbsh1 inhibited their growth when cultured in MRS containing 3.0 g L-1 sodium glycocholate, whereas Δbsh4 instead promoted their growth in MRS with 3.0 g L-1 sodium glycocholate and sodium taurocholate. RCA and RAA were linearly positive for all strains except AR113 Δbsh2,4, and AHC and RAA were negatively correlated for most strains excluding AR113 Δbsh2, with RAA = 6.38-25.05%, RCA = 5.17-9.22%, and ACH = 3.22-47.71%. The adhesion ability of ten strains cultured in MRS was higher than that of strains cultured in MRS with 3.0 g L-1 bovine bile, and it was related to bsh2. CONCLUSION Bsh differentially affected the adhesion of AR113 series strains. This adds to the available information about substrate-gene-performance, and provides new information to enable engineering to regulate the colonization of Lactiplantibacillus. © 2021 Society of Chemical Industry.
Collapse
Affiliation(s)
- Taoying Wu
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
- Hunan Key Laboratory of Bean Products Processing and Safety Control, School of Food and Chemical Engineering, Shaoyang University, Shaoyang, China
| | - Guangqiang Wang
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Hongyu Tang
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Zhiqiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xin Song
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yongjun Xia
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Phoency F-H Lai
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Lianzhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| |
Collapse
|
3
|
Leng RA. Unravelling methanogenesis in ruminants, horses and kangaroos: the links between gut anatomy, microbial biofilms and host immunity. ANIMAL PRODUCTION SCIENCE 2018. [DOI: 10.1071/an15710] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The present essay aims to resolve the question as to why macropod marsupials (e.g. kangaroos and wallabies, hereinafter termed ‘macropods) and horses produce much less methane (CH4) than do ruminants when digesting the same feed. In herbivores, gases produced during fermentation of fibrous feeds do not pose a major problem in regions of the gut that have mechanisms to eliminate them (e.g. eructation in the rumen and flatus in the lower bowel). In contrast, gas pressure build-up in the tubiform forestomach of macropods or in the enlarged tubiform caecum of equids would be potentially damaging. It is hypothesised that, to prevent this problem, evolution has favoured development of controls over gut microbiota that enable enteric gas production (H2 and CH4) to be differently regulated in the forestomach of macropods and the caecum of all three species, from the forestomach of ruminants. The hypothesised regulation depends on interactions between their gut anatomy and host-tissue immune responses that have evolved to modify the species composition of their gut microbiota which, importantly, are mainly in biofilms. Obligatory H2 production during forage fermentation is, thus, captured in CH4 in the ruminant where ruminal gases are readily released by eructation, or in acetate in the macropod forestomach and equid caecum–colon where a build-up in gas pressure could potentially damage these organs. So as to maintain appropriate gut microbiota in different species, it is hypothesised that blind sacs at the cranial end of the haustral anatomy of the macropod forestomach and the equid caecum are sites of release of protobiofilm particles that develop in close association with the mucosal lymphoid tissues. These tissues release immune secretions such as antimicrobial peptides, immunoglobulins, innate lymphoid cells and mucin that eliminate or suppress methanogenic Archaea and support the growth of acetogenic microbiota. The present review draws on microbiological studies of the mammalian gut as well as other microbial environments. Hypotheses are advanced to account for published findings relating to the gut anatomy of herbivores and humans, the kinetics of digesta in ruminants, macropods and equids, and also the composition of biofilm microbiota in the human gut as well as aquatic and other environments where the microbiota exist in biofilms.
Collapse
|
4
|
Davison M, Treangen TJ, Koren S, Pop M, Bhaya D. Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers. PLoS One 2016; 11:e0160574. [PMID: 27611571 PMCID: PMC5017753 DOI: 10.1371/journal.pone.0160574] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/21/2016] [Indexed: 12/13/2022] Open
Abstract
The polymicrobial biofilm communities in Mushroom and Octopus Spring in Yellowstone National Park (YNP) are well characterized, yet little is known about the phage populations. Dominant species, Synechococcus sp. JA-2-3B'a(2–13), Synechococcus sp. JA-3-3Ab, Chloroflexus sp. Y-400-fl, and Roseiflexus sp. RS-1, contain multiple CRISPR-Cas arrays, suggesting complex interactions with phage predators. To analyze phage populations from Octopus Spring biofilms, we sequenced a viral enriched fraction. To assemble and analyze phage metagenomic data, we developed a custom module, VIRITAS, implemented within the MetAMOS framework. This module bins contigs into groups based on tetranucleotide frequencies and CRISPR spacer-protospacer matching and ORF calling. Using this pipeline we were able to assemble phage sequences into contigs and bin them into three clusters that corroborated with their potential host range. The virome contained 52,348 predicted ORFs; some were clearly phage-like; 9319 ORFs had a recognizable Pfam domain while the rest were hypothetical. Of the recognized domains with CRISPR spacer matches, was the phage endolysin used by lytic phage to disrupt cells. Analysis of the endolysins present in the thermophilic cyanophage contigs revealed a subset of characterized endolysins as well as a Glyco_hydro_108 (PF05838) domain not previously associated with sequenced cyanophages. A search for CRISPR spacer matches to all identified phage endolysins demonstrated that a majority of endolysin domains were targets. This strategy provides a general way to link host and phage as endolysins are known to be widely distributed in bacteriophage. Endolysins can also provide information about host cell wall composition and have the additional potential to be used as targets for novel therapeutics.
Collapse
Affiliation(s)
- Michelle Davison
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, United States of America
- Stanford University, Department of Biology, Stanford, CA, 94305, United States of America
- * E-mail: (MD); (DB)
| | - Todd J. Treangen
- Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, College Park, MD, 20742, United States of America
| | - Sergey Koren
- Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, College Park, MD, 20742, United States of America
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, College Park, MD, 20742, United States of America
- Department of Computer Science, University of Maryland, College Park, MD, 20742, United States of America
| | - Devaki Bhaya
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, United States of America
- Stanford University, Department of Biology, Stanford, CA, 94305, United States of America
- * E-mail: (MD); (DB)
| |
Collapse
|
5
|
Hanning I, Diaz-Sanchez S. The functionality of the gastrointestinal microbiome in non-human animals. MICROBIOME 2015; 3:51. [PMID: 26552373 PMCID: PMC4640220 DOI: 10.1186/s40168-015-0113-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 09/28/2015] [Indexed: 05/04/2023]
Abstract
Due to the significance of the microbiome on human health, much of the current data available regarding microbiome functionality is centered on human medicine. For agriculturally important taxa, the functionality of gastrointestinal bacteria has been studied with the primary goals of improving animal health and production performance. With respect to cattle, the digestive functions of bacteria in cattle are unarguably critical to digestion and positively impact production performance. Conversely, some research suggests that the gastrointestinal microbiome in chickens competes with the host for nutrients and produces toxins that can harm the host resulting in decreased growth efficiency. Concerning many other species including reptiles and cetaceans, some cataloging of fecal bacteria has been conducted, but the functionality within the host remains ambiguous. These taxa could provide interesting gastrointestinal insight into functionality and symbiosis considering the extreme feeding regimes (snakes), highly specialized diets (vampire bats), and living environments (polar bears), which warrants further exploration.
Collapse
Affiliation(s)
- Irene Hanning
- College of Genome Sciences and Technology, University of Tennessee, Knoxville, TN, USA.
- Department of Science, Lincoln International Academy, Managua, Nicaragua.
| | - Sandra Diaz-Sanchez
- Department of Food Science and Technology, University of Tennessee, Knoxville, TN, USA
| |
Collapse
|
6
|
Chuzeville S, Dramsi S, Madec JY, Haenni M, Payot S. Antigen I/II encoded by integrative and conjugative elements of Streptococcus agalactiae and role in biofilm formation. Microb Pathog 2015; 88:1-9. [PMID: 26232503 DOI: 10.1016/j.micpath.2015.07.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 07/13/2015] [Accepted: 07/20/2015] [Indexed: 10/23/2022]
Abstract
Streptococcus agalactiae (i.e. Group B streptococcus, GBS) is a major human and animal pathogen. Genes encoding putative surface proteins and in particular an antigen I/II have been identified on Integrative and Conjugative Elements (ICEs) found in GBS. Antigens I/II are multimodal adhesins promoting colonization of the oral cavity by streptococci such as Streptococcus gordonii and Streptococcus mutans. The prevalence and diversity of antigens I/II in GBS were studied by a bioinformatic analysis. It revealed that antigens I/II, which are acquired by horizontal transfer via ICEs, exhibit diversity and are widespread in GBS, in particular in the serotype Ia/ST23 invasive strains. This study aimed at characterizing the impact on GBS biology of proteins encoded by a previously characterized ICE of S. agalactiae (ICE_515_tRNA(Lys)). The production and surface exposition of the antigen I/II encoded by this ICE was examined using RT-PCR and immunoblotting experiments. Surface proteins of ICE_515_tRNA(Lys) were found to contribute to GBS biofilm formation and to fibrinogen binding. Contribution of antigen I/II encoded by SAL_2056 to biofilm formation was also demonstrated. These results highlight the potential for ICEs to spread microbial adhesins between species.
Collapse
Affiliation(s)
- Sarah Chuzeville
- INRA, UMR1128 DynAMic, F-54506 Vandoeuvre-lès-Nancy, France; Université de Lorraine, UMR1128 DynAMic, F-54506 Vandoeuvre-lès-Nancy, France; ANSES Site de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Shaynoor Dramsi
- Institut Pasteur, Unité de Biologie des Bactéries Pathogènes à Gram-Positif, Paris, France; CNRS ERL3526, Paris, France
| | - Jean-Yves Madec
- ANSES Site de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marisa Haenni
- ANSES Site de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Sophie Payot
- INRA, UMR1128 DynAMic, F-54506 Vandoeuvre-lès-Nancy, France; Université de Lorraine, UMR1128 DynAMic, F-54506 Vandoeuvre-lès-Nancy, France.
| |
Collapse
|
7
|
Lv XM, Shao MF, Li J, Li CL. Metagenomic Analysis of the Sludge Microbial Community in a Lab-Scale Denitrifying Phosphorus Removal Reactor. Appl Biochem Biotechnol 2015; 175:3258-70. [DOI: 10.1007/s12010-015-1491-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/12/2015] [Indexed: 11/29/2022]
|
8
|
Xing SF, Sun XF, Taylor AA, Walker SL, Wang YF, Wang SG. D-amino acids inhibit initial bacterial adhesion: thermodynamic evidence. Biotechnol Bioeng 2014; 112:696-704. [PMID: 25333717 DOI: 10.1002/bit.25479] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 10/13/2014] [Accepted: 10/15/2014] [Indexed: 02/02/2023]
Abstract
Bacterial biofilms are structured communities of cells enclosed in a self-produced hydrated polymeric matrix that can adhere to inert or living surfaces. D-Amino acids were previously identified as self-produced compounds that mediate biofilm disassembly by causing the release of the protein component of the polymeric matrix. However, whether exogenous D-amino acids could inhibit initial bacterial adhesion is still unknown. Here, the effect of the exogenous amino acid D-tyrosine on initial bacterial adhesion was determined by combined use of chemical analysis, force spectroscopic measurement, and theoretical predictions. The surface thermodynamic theory demonstrated that the total interaction energy increased with more D-tyrosine, and the contribution of Lewis acid-base interactions relative to the change in the total interaction energy was much greater than the overall nonspecific interactions. Finally, atomic force microscopy analysis implied that the hydrogen bond numbers and adhesion forces decreased with the increase in D-tyrosine concentrations. D-Tyrosine contributed to the repulsive nature of the cell and ultimately led to the inhibition of bacterial adhesion. This study provides a new way to regulate biofilm formation by manipulating the contents of D-amino acids in natural or engineered systems.
Collapse
Affiliation(s)
- Su-Fang Xing
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China
| | | | | | | | | | | |
Collapse
|
9
|
Development and validation of a microarray for the investigation of the CAZymes encoded by the human gut microbiome. PLoS One 2013; 8:e84033. [PMID: 24391873 PMCID: PMC3877134 DOI: 10.1371/journal.pone.0084033] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 11/11/2013] [Indexed: 12/14/2022] Open
Abstract
Distal gut bacteria play a pivotal role in the digestion of dietary polysaccharides by producing a large number of carbohydrate-active enzymes (CAZymes) that the host otherwise does not produce. We report here the design of a custom microarray that we used to spot non-redundant DNA probes for more than 6,500 genes encoding glycoside hydrolases and lyases selected from 174 reference genomes from distal gut bacteria. The custom microarray was tested and validated by the hybridization of bacterial DNA extracted from the stool samples of lean, obese and anorexic individuals. Our results suggest that a microarray-based study can detect genes from low-abundance bacteria better than metagenomic-based studies. A striking example was the finding that a gene encoding a GH6-family cellulase was present in all subjects examined, whereas metagenomic studies have consistently failed to detect this gene in both human and animal gut microbiomes. In addition, an examination of eight stool samples allowed the identification of a corresponding CAZome core containing 46 families of glycoside hydrolases and polysaccharide lyases, which suggests the functional stability of the gut microbiota despite large taxonomical variations between individuals.
Collapse
|