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Ram Das A, Pillai N, Nanduri B, Rothrock MJ, Ramkumar M. Exploring Pathogen Presence Prediction in Pastured Poultry Farms through Transformer-Based Models and Attention Mechanism Explainability. Microorganisms 2024; 12:1274. [PMID: 39065042 PMCID: PMC11278766 DOI: 10.3390/microorganisms12071274] [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: 05/26/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/28/2024] Open
Abstract
In this study, we explore how transformer models, which are known for their attention mechanisms, can improve pathogen prediction in pastured poultry farming. By combining farm management practices with microbiome data, our model outperforms traditional prediction methods in terms of the F1 score-an evaluation metric for model performance-thus fulfilling an essential need in predictive microbiology. Additionally, the emphasis is on making our model's predictions explainable. We introduce a novel approach for identifying feature importance using the model's attention matrix and the PageRank algorithm, offering insights that enhance our comprehension of established techniques such as DeepLIFT. Our results showcase the efficacy of transformer models in pathogen prediction for food safety and mark a noteworthy contribution to the progress of explainable AI within the biomedical sciences. This study sheds light on the impact of effective farm management practices and highlights the importance of technological advancements in ensuring food safety.
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Affiliation(s)
- Athish Ram Das
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA; (A.R.D.); (B.N.)
| | - Nisha Pillai
- Department of Computer Science and Engineering, Mississippi State University, Starkville, MS 39762, USA;
| | - Bindu Nanduri
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA; (A.R.D.); (B.N.)
| | - Michael J. Rothrock
- Egg Safety and Quality Research Unit, USDA-ARS U.S. National Poultry Research Center, Athens, GA 30605, USA;
| | - Mahalingam Ramkumar
- Department of Computer Science and Engineering, Mississippi State University, Starkville, MS 39762, USA;
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2
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Pfau M, Degregori S, Johnson G, Tennenbaum SR, Barber PH, Philson CS, Blumstein DT. The social microbiome: gut microbiome diversity and abundance are negatively associated with sociality in a wild mammal. ROYAL SOCIETY OPEN SCIENCE 2023; 10:231305. [PMID: 37830026 PMCID: PMC10565414 DOI: 10.1098/rsos.231305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023]
Abstract
The gut microbiome has a well-documented relationship with host fitness. Greater microbial diversity and abundance of specific microbes have been associated with improved fitness outcomes. Intestinal microbes also may be associated with patterns of social behaviour. However, these associations have been largely studied in captive animal models; we know less about microbiome composition as a potential driver of individual social behaviour and position in the wild. We used linear mixed models to quantify the relationship between fecal microbial composition, diversity and social network traits in a wild population of yellow-bellied marmots (Marmota flaviventer). We focused our analyses on microbes previously linked to sociability and neurobehavioural alterations in captive rodents, primates and humans. Using 5 years of data, we found microbial diversity (Shannon-Wiener and Faith's phylogenetic diversity) has a modest yet statistically significant negative relationship with the number of social interactions an individual engaged in. We also found a negative relationship between Streptococcus spp. relative abundance and two social network measures (clustering coefficient and embeddedness) that quantify an individual's position relative to others in their social group. These findings highlight a potentially consequential relationship between microbial composition and social behaviour in a wild social mammal.
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Affiliation(s)
- Madison Pfau
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Sam Degregori
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Gina Johnson
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Stavi R. Tennenbaum
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224, USA
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Conner S. Philson
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224, USA
| | - Daniel T. Blumstein
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224, USA
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3
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Park SY, Kwon H, Kim SG, Park SC, Kim JH, Seo S. Characterization of two lytic bacteriophages, infecting Streptococcus bovis/equinus complex (SBSEC) from Korean ruminant. Sci Rep 2023; 13:9110. [PMID: 37277552 DOI: 10.1038/s41598-023-36306-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/31/2023] [Indexed: 06/07/2023] Open
Abstract
Streptococcus bovis/equinus complex (SBSEC) is one of the most important lactic acid-producing rumen bacteria causing subacute ruminal acidosis. Despite the significance of the ruminal bacteria, lytic bacteriophages (phages) capable of infecting SBSEC in the rumen have been rarely characterized. Hence, we describe the biological and genomic characteristics of two lytic phages (designated as vB_SbRt-pBovineB21 and vB_SbRt-pBovineS21) infecting various SBSEC species, including the newly reported S. ruminicola. The isolated SBSEC phages were morphologically similar to Podoviridae and could infect other genera of lactic acid-producing bacteria, including Lactococcus and Lactobacillus. Additionally, they showed high thermal- and pH-stability, and those characteristics induce strong adaptation to the ruminal environment, such as the low pH found in subacute ruminal acidosis. Genome-based phylogeny revealed that both phages were related to Streptococcus phage C1 in the Fischettivirus. However, they had a lower nucleotide similarity and distinct genomic arrangements than phage C1. The phage bacteriolytic activity was evaluated using S. ruminicola, and the phages efficiently inhibited planktonic bacterial growth. Moreover, both phages could prevent bacterial biofilms of various SBSEC strains and other lactic acid-producing bacteria in vitro. Thus, the newly isolated two SBSEC phages were classified as new Fischettivirus members and could be considered as potential biocontrol agents against ruminal SBSEC bacteria and their biofilms.
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Affiliation(s)
- Seon Young Park
- Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, South Korea
| | - Hyemin Kwon
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, South Korea
| | - Sang Guen Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, South Korea
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, South Korea
| | - Ji Hyung Kim
- Department of Food Science and Biotechnology, College of Bionano Technology, Gachon University, Seongnam, 13120, South Korea.
| | - Seongwon Seo
- Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, South Korea.
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4
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Zhang K, Qin Z, Qin H, Wang Y, Wang L, Fu Y, Hou C, Ji C, Yuan Y, Zhang L. First detection of Blastocystis sp. in migratory whooper swans ( Cygnus cygnus) in China. One Health 2023; 16:100486. [PMID: 36683961 PMCID: PMC9846003 DOI: 10.1016/j.onehlt.2023.100486] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/07/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023] Open
Abstract
Blastocystis is a usual intestinal protist that always found in humans and various animals. Currently, the prevalence of Blastocystis in the migratory whooper swan (Cygnus cygnus) is unknown. In our research, we aimed to determine the occurrence, prevalence, subtype distribution and dynamic transmission mechanisms of Blastocystis in the migratory whooper swan in China. We also assessed the zoonotic potential of Blastocystis isolates, as well as possible routes of transmission and impact of this organism on One Health perspective. Fecal samples (n = 770) were collected from whooper swans inhabiting the Sanmenxia Swan Lake National Urban Wetland Park, China. The overall prevalence of Blastocystis was 11.6% (89/770). We identified 9 subtypes of Blastocystis sp., including 5 zoonotic subtypes [ST1 (Cakir et al., 2019 (8)), ST4 (Selma and Karanis, 2011 (4)), ST5 (Stensvold et al., 2009 (1)), ST6 (Fare et al., 2019 (5)) and ST7(58)] and 3 host-specific subtypes [ST10 (Zhao et al., 2018 (7)), ST14 (Tan et al., 2010 (2)), ST23 (Wang et al., 2018 (3)), and ST25 (Stensvold et al., 2009 (1))]. Subtypes ST4, ST5, ST6, ST10, ST14, ST23, and ST25 were first identified in the whooper swan. Among these subtypes, ST23 and ST25 were identified in birds for the first time, indicating that these subtypes are expanding their host range. So far, this is the first research reporting on the prevalence and subtypes distribution of Blastocystis in the migratory whooper swan in China. The findings obtained in this study will provide new insights into the genetic diversity and transmission routes of Blastocystis, and the possible public health concerns posed by this organism.
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Affiliation(s)
- Kaihui Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China,International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450002, Henan Province, PR China,Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China
| | - Ziyang Qin
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China,International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450002, Henan Province, PR China,Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China
| | - Huikai Qin
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China,International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450002, Henan Province, PR China,Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China
| | - Yinlin Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China,International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450002, Henan Province, PR China,Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China
| | - Luyang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China,International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450002, Henan Province, PR China,Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China
| | - Yin Fu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China,International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450002, Henan Province, PR China,Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China
| | - Changjiang Hou
- Sanmenxia Management Office of Henan Yellow River Wetland National Nature Reserve, Sanmenxia 472000, PR China
| | - Chenxiao Ji
- Sanmenxia Management Office of Henan Yellow River Wetland National Nature Reserve, Sanmenxia 472000, PR China
| | - Yuan Yuan
- Sanmenxia Management Office of Henan Yellow River Wetland National Nature Reserve, Sanmenxia 472000, PR China
| | - Longxian Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China,International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450002, Henan Province, PR China,Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, PR China,Corresponding author at: College of Veterinary Medicine, Henan Agricultural University, No. 15 Longzihu University Area, Zhengzhou New District, Zhengzhou 450046, PR China.
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Park SY, Muhammad N, Kim SG, Kwon H, Seo S, Kim JH. Streptococcus ruminicola sp. nov., new species of the Streptococcus bovis/Streptococcus equinus complex (SBSEC) isolated from the rumen of Korean domestic ruminants. Arch Microbiol 2022; 204:636. [PMID: 36127476 DOI: 10.1007/s00203-022-03255-4] [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: 08/11/2022] [Revised: 08/30/2022] [Accepted: 09/12/2022] [Indexed: 11/28/2022]
Abstract
A total of three Gram-positive, and oxidase and catalase-negative facultative anaerobic non-motile bacteria were isolated from the rumen fluid of cows and goats and these strains were designated CNU_G2T, CNU_77-61, and CNU_G3. They grew at 20-45 °C, pH 6.5-7, and 0-6.5% NaCl (w/v). The G + C contents (%) of the three isolates were 37.9, 37.8 and 37.8, respectively. Phylogenomic analysis indicated that these strains were distinct from other Streptococcus species. The average nucleotide identity between the isolates and the closest strain S. infantarius subsp. infantarius ATCC BAA-102T was 94.0-94.5%, while the digital DNA-DNA hybridization (dDDH) values between the isolates and the aforementioned related strain were 58.2-61.4%, respectively. Fatty acid analysis revealed higher proportions of C16:0 (> 28%) in all three isolates, while the proportion of C18:0 was higher in CNU_G2T (25.8%); however, it was less than 12% in all the representing strains used in the study. The C14:0 composition of strains CNU_77-61 (22.1%) and CNU_G3 (24.1%) was higher than that of type strains of CNU_G2T (8.1%). Based on the morphological, biochemical, and molecular phylogenetic features of the three novel isolates, they represent a novel species of the genus Streptococcus, for which we propose as Streptococcus ruminicola sp. nov. The type strain is CNU_G2T (= KCTC 43308T = GDMCC 1.2785T).
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Affiliation(s)
- Seon Young Park
- Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, Korea
| | - Neak Muhammad
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeonbuk, 56212, Korea.,University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Song-Gun Kim
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeonbuk, 56212, Korea.,University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Hyemin Kwon
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea.,Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Korea
| | - Seongwon Seo
- Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, Korea
| | - Ji Hyung Kim
- Department of Food Science and Biotechnology, College of Bio-Nano Technology, Gachon University, Seongnam, 13120, Korea.
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Mohammed AD, Hall N, Chatzistamou I, Jolly A, Kubinak JL. Gluten-free diet exposure prohibits pathobiont expansion and gluten sensitive enteropathy in B cell deficient JH-/- mice. PLoS One 2022; 17:e0264977. [PMID: 35324937 PMCID: PMC8946719 DOI: 10.1371/journal.pone.0264977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/19/2022] [Indexed: 12/19/2022] Open
Abstract
In humans, celiac disease (CeD) is a T-cell-driven gluten-sensitive enteropathy (GSE) localized to the small bowel (duodenum). The presence of antibodies specific for gluten- and self-antigens are commonly used diagnostic biomarkers of CeD and are considered to play a role in GSE pathogenesis. Previously, we have described an apparent T-cell-mediated GSE in CD19-/- mice, which develop weak and abnormal B cell responses. Here, we expand on this observation and use a mouse model of complete B cell deficiency (JH-/- mice), to show that absence of a humoral immune response also promotes development of a GSE. Furthermore, 16S analysis of microbial communities in the small intestine demonstrates that a gluten-free diet suppresses the expansion of anaerobic bacteria in the small intestine and colonization of the small intestine by a specific pathobiont. Finally, we also observe that SI enteropathy in mice fed a gluten-rich diet is positively correlated with the abundance of several microbial peptidase genes, which supports that bacterial metabolism of gluten may be an important driver of GSE in our model. Collectively, results from our experiments indicate that JH-/- mice will be a useful resource to investigators seeking to empirically delineate the contribution of humoral immunity on GSE pathogenesis, and support the hypothesis that humoral immunity promotes tolerance to gluten.
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Affiliation(s)
- Ahmed Dawood Mohammed
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States of America
| | - Nia Hall
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States of America
| | - Ioulia Chatzistamou
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States of America
| | - Amy Jolly
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States of America
| | - Jason Lee Kubinak
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States of America
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Park SY, Lee M, Lim SR, Kwon H, Lee YS, Kim JH, Seo S. Diversity and Antimicrobial Resistance in the Streptococcus bovis/ Streptococcus equinus Complex (SBSEC) Isolated from Korean Domestic Ruminants. Microorganisms 2021; 9:98. [PMID: 33406675 PMCID: PMC7824528 DOI: 10.3390/microorganisms9010098&set/a 837648689+998116719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
S. bovis/S. equinus complex (SBSEC) includes lactic acid-producing bacteria considered as the causative agent associated with acute rumen lactic acidosis in intensive ruminants. Considering the limited information on the detailed characteristics and diversity of SBSEC in Korea and the emergence of antimicrobial resistance (AMR), we investigated the diversity of SBSEC from domestic ruminants and verified the presence of antimicrobial resistance genes (ARGs) against several antimicrobials with their phenotypic resistance. Among 51 SBSEC isolates collected, two SBSEC members (S. equinus and S. lutetiensis) were identified; sodA-based phylogenetic analyses and comparisons of overall genome relatedness revealed potential plasticity and diversity. The AMR rates of these SBSEC against erythromycin, clindamycin, and tetracycline were relatively lower than those of other SBSEC isolates of a clinical origin. An investigation of the ARGs against those antimicrobials indicated that tetracycline resistance of SBSECs generally correlated with the presence of tet(M)-possessing Tn916-like transposon. However, no correlation between the presence of ARGs and phenotypic resistance to erythromycin and clindamycin was observed. Although a limited number of animals and their SBSEC isolates were examined, this study provides insights into the potential intraspecies biodiversity of ruminant-origin SBSEC and the current status on antimicrobial resistance of the bacteria in the Korean livestock industry.
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Affiliation(s)
- Seon Young Park
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (S.Y.P.); (S.R.L.); (H.K.); (Y.S.L.)
- Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea;
| | - Mingyung Lee
- Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea;
| | - Se Ra Lim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (S.Y.P.); (S.R.L.); (H.K.); (Y.S.L.)
| | - Hyemin Kwon
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (S.Y.P.); (S.R.L.); (H.K.); (Y.S.L.)
| | - Ye Seul Lee
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (S.Y.P.); (S.R.L.); (H.K.); (Y.S.L.)
| | - Ji Hyung Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (S.Y.P.); (S.R.L.); (H.K.); (Y.S.L.)
- Correspondence: (J.H.K.); (S.S.); Tel.: +82-(42)-879-8272 (J.H.K.)
| | - Seongwon Seo
- Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea;
- Correspondence: (J.H.K.); (S.S.); Tel.: +82-(42)-879-8272 (J.H.K.)
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Diversity and Antimicrobial Resistance in the Streptococcus bovis/Streptococcus equinus Complex (SBSEC) Isolated from Korean Domestic Ruminants. Microorganisms 2021. [DOI: 10.3390/microorganisms9010098
expr 822437316 + 998765163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
S. bovis/S. equinus complex (SBSEC) includes lactic acid-producing bacteria considered as the causative agent associated with acute rumen lactic acidosis in intensive ruminants. Considering the limited information on the detailed characteristics and diversity of SBSEC in Korea and the emergence of antimicrobial resistance (AMR), we investigated the diversity of SBSEC from domestic ruminants and verified the presence of antimicrobial resistance genes (ARGs) against several antimicrobials with their phenotypic resistance. Among 51 SBSEC isolates collected, two SBSEC members (S. equinus and S. lutetiensis) were identified; sodA-based phylogenetic analyses and comparisons of overall genome relatedness revealed potential plasticity and diversity. The AMR rates of these SBSEC against erythromycin, clindamycin, and tetracycline were relatively lower than those of other SBSEC isolates of a clinical origin. An investigation of the ARGs against those antimicrobials indicated that tetracycline resistance of SBSECs generally correlated with the presence of tet(M)-possessing Tn916-like transposon. However, no correlation between the presence of ARGs and phenotypic resistance to erythromycin and clindamycin was observed. Although a limited number of animals and their SBSEC isolates were examined, this study provides insights into the potential intraspecies biodiversity of ruminant-origin SBSEC and the current status on antimicrobial resistance of the bacteria in the Korean livestock industry.
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9
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Park SY, Lee M, Lim SR, Kwon H, Lee YS, Kim JH, Seo S. Diversity and Antimicrobial Resistance in the Streptococcus bovis/ Streptococcus equinus Complex (SBSEC) Isolated from Korean Domestic Ruminants. Microorganisms 2021; 9:microorganisms9010098. [PMID: 33406675 PMCID: PMC7824528 DOI: 10.3390/microorganisms9010098] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 01/12/2023] Open
Abstract
S. bovis/S. equinus complex (SBSEC) includes lactic acid-producing bacteria considered as the causative agent associated with acute rumen lactic acidosis in intensive ruminants. Considering the limited information on the detailed characteristics and diversity of SBSEC in Korea and the emergence of antimicrobial resistance (AMR), we investigated the diversity of SBSEC from domestic ruminants and verified the presence of antimicrobial resistance genes (ARGs) against several antimicrobials with their phenotypic resistance. Among 51 SBSEC isolates collected, two SBSEC members (S. equinus and S. lutetiensis) were identified; sodA-based phylogenetic analyses and comparisons of overall genome relatedness revealed potential plasticity and diversity. The AMR rates of these SBSEC against erythromycin, clindamycin, and tetracycline were relatively lower than those of other SBSEC isolates of a clinical origin. An investigation of the ARGs against those antimicrobials indicated that tetracycline resistance of SBSECs generally correlated with the presence of tet(M)-possessing Tn916-like transposon. However, no correlation between the presence of ARGs and phenotypic resistance to erythromycin and clindamycin was observed. Although a limited number of animals and their SBSEC isolates were examined, this study provides insights into the potential intraspecies biodiversity of ruminant-origin SBSEC and the current status on antimicrobial resistance of the bacteria in the Korean livestock industry.
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Affiliation(s)
- Seon Young Park
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (S.Y.P.); (S.R.L.); (H.K.); (Y.S.L.)
- Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea;
| | - Mingyung Lee
- Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea;
| | - Se Ra Lim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (S.Y.P.); (S.R.L.); (H.K.); (Y.S.L.)
| | - Hyemin Kwon
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (S.Y.P.); (S.R.L.); (H.K.); (Y.S.L.)
| | - Ye Seul Lee
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (S.Y.P.); (S.R.L.); (H.K.); (Y.S.L.)
| | - Ji Hyung Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (S.Y.P.); (S.R.L.); (H.K.); (Y.S.L.)
- Correspondence: (J.H.K.); (S.S.); Tel.: +82-(42)-879-8272 (J.H.K.)
| | - Seongwon Seo
- Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea;
- Correspondence: (J.H.K.); (S.S.); Tel.: +82-(42)-879-8272 (J.H.K.)
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Silva NOE, de Brito BB, da Silva FAF, Santos MLC, de Melo FF. Probiotics in inflammatory bowel disease: Does it work? World J Meta-Anal 2020; 8:54-66. [DOI: 10.13105/wjma.v8.i2.54] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 03/26/2020] [Accepted: 04/14/2020] [Indexed: 02/06/2023] Open
Abstract
The number of patients with inflammatory bowel disease (IBD), a group of diseases mainly represented by Crohn’s disease (CD) and ulcerative colitis (UC), has increased in recent decades. As a consequence, the number of people undergoing any drug treatment against these diseases has expanded. However, IBD conventional therapies present several limitations, which lead researchers to look for better alternatives to improve the quality of life of patients. Moreover, microbiome imbalance seems to play a crucial role in the pathogenesis of IBD, since important alterations in bacterial, viral, protist and fungal populations are observed in the gut microbiota of affected individuals. Given the importance of such life forms in that context, the use of probiotics becomes a plausible alternative for treating affected patients. Trials have been developed aiming the evaluation of probiotics potential to induce and to maintain remission in CD and UC. Regarding the tested microorganisms, various non-pathogenic bacteria and fungi have been assessed. However, consistent results have been obtained only with some of them, including Escherichia coli Nissle 1917, VSL#3, Saccharomyces boulardii, Lactobacillus, and Bifidobacterium. Therefore, this minireview aims to explore the role of microbiota in the genesis of such a disorder and to compile the most concrete data on probiotic-related efficiency in IBD treatment.
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Affiliation(s)
- Natália Oliveira e Silva
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
| | - Breno Bittencourt de Brito
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
| | | | - Maria Luísa Cordeiro Santos
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
| | - Fabrício Freire de Melo
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
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11
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Exploring Beneficial/Virulence Properties of Two Dairy-Related Strains of Streptococcus infantarius subsp. infantarius. Probiotics Antimicrob Proteins 2020; 12:1524-1541. [DOI: 10.1007/s12602-020-09637-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Todorov SD, Kang HJ, Ivanova IV, Holzapfel WH. Bacteriocins From LAB and Other Alternative Approaches for the Control of Clostridium and Clostridiodes Related Gastrointestinal Colitis. Front Bioeng Biotechnol 2020; 8:581778. [PMID: 33042979 PMCID: PMC7517946 DOI: 10.3389/fbioe.2020.581778] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022] Open
Abstract
The gut microbiome is considered as a promising target for future non-conventional therapeutic treatment of inflammatory and infectious diseases. The search for appropriate safe and beneficial (lactic acid bacterial and other) putative probiotic strains and/or their antimicrobial metabolites represents a challenging approach for combating several problematic and emerging infections. The process of selecting suitable strains, especially of lactic acid bacteria (LAB) with superior properties, has been accelerated and intensified during the past two decades, also thanks to recent developments in lab techniques. Currently, special focus is on the potential of antimicrobial metabolites produced by some LAB strains and their application as active therapeutic agents. The vision is to develop a scientific basis for 'biotherapeutics' as alternative to conventional approaches in both human and veterinary medicine. Consequently, innovative and promising applications of LAB to the therapeutic practice are presently emerging. An overview of the existing literature indicates that some antimicrobial metabolites such as bacteriocins, widely produced by different bacterial species including LAB, are promising biotherapeutic agents for controlling infections caused by potential pathogens, such as Clostridium and Clostridiodes. Non-conventional, safe and well designed therapeutic treatments may contribute to the improvement of gut dysbiotic conditions. Thereby gut homeostasis can be restored and inflammatory conditions such as gastrointestinal colitis ameliorated. Combining the knowledge on the production, characterization and application of bacteriocins from probiotic LAB, together with their antibacterial properties, appears to be a promising and novel approach in biotherapy. In this overview, different scenarios for the control of Clostridium spp. by application of bacteriocins as therapeutic agents, also in synergistic combination with antibiotics, will be discussed.
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Affiliation(s)
- Svetoslav D. Todorov
- Advanced Green Energy and Environment Institute (AGEE), Handong Global University, Pohang, South Korea
| | - Hye-Ji Kang
- Advanced Green Energy and Environment Institute (AGEE), Handong Global University, Pohang, South Korea
- HEM Inc., Handong Global University, Pohang, South Korea
| | - Iskra V. Ivanova
- Department of General and Applied Microbiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Wilhelm H. Holzapfel
- Advanced Green Energy and Environment Institute (AGEE), Handong Global University, Pohang, South Korea
- HEM Inc., Handong Global University, Pohang, South Korea
- *Correspondence: Wilhelm H. Holzapfel,
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13
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Beux S, Todescatto C, Marchi JF, Pereira EA. Selection of raw cow’s milk thermophilic lactic acid bacteria obtained from southwest Parana, Brazil, with potential use as autochthonous starter. BRAZILIAN JOURNAL OF FOOD TECHNOLOGY 2020. [DOI: 10.1590/1981-6723.17019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract This work aimed to isolate and identify Streptococcus and Lactobacillus species from raw cow’s milk obtained from Southwest Paraná - Brazil. We used randomly amplified polymorphic DNA (RAPD)-PCR to identify and type 58Streptococcus and 48 Lactobacillus isolates, of which 04 Streptococcus thermophilus and 02 Streptpcoccus macedonicus were confirmed by species-specific PCR and by sequencing of the 16S ribosomal RNA of 02Streptococcus lutetiensis/infantarius, 10 Lactobacillus fermentum, 03 Lactobacillus delbrueickii subspecies bulgaricus, 01 Lactobacillus rhamnosus/casei and 02 Lactobacillus helveticus. The results indicated predominance of Streptococcus thermophillus and Lactobacillus fermentum. Streptococcus thermophilus and Lactobacillus delbrueickii subspecies bulgaricus strains were tested on the basis of their acidification kinetics. Considerable variation between the Streptococcus thermophilus was observed for the maximum rate of acidification (Vm), with a maximum of -4.5 and minimum of -4.2 pH milliunits min-1. The Lactobacillus delbrueickii subspecies bulgaricus showed values between -8.4 and -7.1 pH milliunits min-1. These results suggest that strains characterized as having a high acidifying capacity, could be used as starters in cheesemaking. The ferments presented an excellent performance in the acidification process, generating adequate curves, characteristics of a starter culture.
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Affiliation(s)
- Simone Beux
- Universidade Tecnológica Federal do Paraná, Brasil
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14
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Gboko KDT, Traoré SG, Sanhoun AR, Kirioua J, Otaru N, Kurt F, Jaeger FN, Isenring J, Kaindi DWM, Kreikemeyer B, Renault P, Hattendorf J, Meile L, Jans C, Nguetta R, Bonfoh B. Risk factors for the carriage of Streptococcus infantarius subspecies infantarius isolated from African fermented dairy products. PLoS One 2019; 14:e0225452. [PMID: 31774832 PMCID: PMC6881063 DOI: 10.1371/journal.pone.0225452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 11/05/2019] [Indexed: 02/07/2023] Open
Abstract
Streptococcus infantarius subsp. infantarius (Sii) has been identified as predominant lactic acid bacteria in spontaneously fermented dairy products (FDPs) in sub-Saharan Africa including Côte d'Ivoire. However, Sii belongs to the Streptococcus bovis/Streptococcus equinus complex (SBSEC). Most SBSEC members are assumed to be involved as opportunistic pathogens in serious diseases in both humans and animals. A population-based cross-sectional survey, including 385 participants was conducted in Korhogo, northern Côte d'Ivoire, to identify risk factors for Sii fecal carriage, including consumption of local FDPs. A structured questionnaire was used to gather participant's socio-demographic and economic characteristics, their relation to livestock and dietary habits. In addition, fresh stool and milk samples were collected. The identification of Sii was done using a SBSEC-specific PCR assay targeting 16S rRNA and groEL genes. The overall prevalence of SBSEC and Sii carriage was 23.2% (confidence interval CI 95% = 18.9-27.5) and 12.0% (CI 95% = 8.4-15.5) for stool, respectively. Prevalence of Sii was significantly higher in consumers of artisanal butter compared with non-consumers (57.1% vs 10.1%, odds ratio OR: 11.9, 95% CI: 3.9-36.6), as well as in persons handling livestock (OR = 3.9; 95% CI = 1.6-9.3) and livestock primary products (OR = 5.7; 95% CI = 2.3-14.3). The closer contact with livestock was a risk factor for Sii fecal carriage. Sii strains were isolated from fresh and fermented milk products with a prevalence of 30.4% and 45.4%, respectively. Analysis of Sii population structure through the SBSEC multi locus sequence typing assay revealed a close relationship across human and dairy isolates, possibly linked to a Kenyan human isolate. All these outcomes underline the interest of in-depth investigations on the ecology, potential reservoirs and pathways of contamination by Sii at the human-animal-environment interface in comparison to yet to be collected data from Europe, Asia and the Americas to further elucidate the various roles of Sii.
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Affiliation(s)
- Kossia D T Gboko
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Adiopodoumé Yopougon, Abidjan, Côte d'Ivoire
| | - Sylvain G Traoré
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Adiopodoumé Yopougon, Abidjan, Côte d'Ivoire.,University of Peleforo Gon Coulibaly, Korhogo, Côte d'Ivoire
| | - Aimé R Sanhoun
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Adiopodoumé Yopougon, Abidjan, Côte d'Ivoire.,University of Nangui Abrogoua, Abidjan, Côte d'Ivoire
| | - Jérôme Kirioua
- University of Peleforo Gon Coulibaly, Korhogo, Côte d'Ivoire
| | - Nize Otaru
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Fabienne Kurt
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Fabienne N Jaeger
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Julia Isenring
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Dasel W M Kaindi
- Department of Food Science, Nutrition and Technology, University of Nairobi, Nairobi, Kenya
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre Rostock, Germany
| | - Pierre Renault
- Institut National de la Recherche Agronomique, UMR 1319 MICALIS, Jouy-en-Josas, France
| | - Jan Hattendorf
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Leo Meile
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Roland Nguetta
- Institut de cardiologie d'Abidjan (ICA), Abidjan, Côte d'Ivoire.,Université Felix Houphouët-Boigny, Abidjan, Côte d'Ivoire
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), Adiopodoumé Yopougon, Abidjan, Côte d'Ivoire.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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15
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Lo Presti A, Zorzi F, Del Chierico F, Altomare A, Cocca S, Avola A, De Biasio F, Russo A, Cella E, Reddel S, Calabrese E, Biancone L, Monteleone G, Cicala M, Angeletti S, Ciccozzi M, Putignani L, Guarino MPL. Fecal and Mucosal Microbiota Profiling in Irritable Bowel Syndrome and Inflammatory Bowel Disease. Front Microbiol 2019; 10:1655. [PMID: 31379797 PMCID: PMC6650632 DOI: 10.3389/fmicb.2019.01655] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 07/04/2019] [Indexed: 12/12/2022] Open
Abstract
An imbalance in the bacterial species resulting in the loss of intestinal homeostasis has been described in inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS). In this prospective study, we investigated whether IBD and IBS patients exhibit specific changes in richness and distribution of fecal and mucosal-associated microbiota. Additionally, we assessed potential 16S rRNA gene amplicons biomarkers for IBD, IBS, and controls (CTRLs) by comparison of taxonomic composition. The relative abundance of bacteria, at phylum and genus/species levels, and the bacterial diversity were determined through 16S rRNA sequence-based fecal and mucosal microbiota analysis. Linear discriminant analysis effect size (LEfSe) was used for biomarker discovery associated to IBD and IBS as compared to CTRLs. In fecal and mucosal samples, the microbiota richness was characterized by a microbial diversity reduction, going from CTRLs to IBS to IBD. β-diversity analysis showed a clear separation between IBD and CTRLs and between IBD and IBS with no significant separation between IBS and CTRLs. β-diversity showed a clear separation between mucosa and stool samples in all the groups. In IBD, there was no difference between inflamed and not inflamed mucosa. Based upon the LEfSe data, the Anaerostipes and Ruminococcaceae were identified as the most differentially abundant bacterial taxa in CTRLs. Erysipelotrichi was identified as potential biomarker for IBS, while Gammaproteobacteria, Enterococcus, and Enterococcaceae for IBD. This study provides an overview of the alterations of microbiota and may aid in identifying potential 16S rRNA gene amplicons mucosal biomarkers for IBD and IBS.
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Affiliation(s)
| | - Francesca Zorzi
- Gastrointestinal Unit, Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | | | - Silvia Cocca
- Unit of Digestive Disease, Campus Bio-Medico University, Rome, Italy
| | - Alessandra Avola
- Unit of Digestive Disease, Campus Bio-Medico University, Rome, Italy
| | - Fabiola De Biasio
- Unit of Digestive Disease, Campus Bio-Medico University, Rome, Italy
| | - Alessandra Russo
- Human Microbiome Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Eleonora Cella
- Unit of Medical Statistics and Molecular Epidemiology, Campus Bio-Medico University, Rome, Italy
| | - Sofia Reddel
- Human Microbiome Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Emma Calabrese
- Gastrointestinal Unit, Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Livia Biancone
- Gastrointestinal Unit, Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Giovanni Monteleone
- Gastrointestinal Unit, Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Michele Cicala
- Unit of Digestive Disease, Campus Bio-Medico University, Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, Campus Bio-Medico University, Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Campus Bio-Medico University, Rome, Italy
| | - Lorenza Putignani
- Human Microbiome Unit and Parasitology Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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16
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Papadimitriou K. Novel insight into the pathogenicity of Streptococcus gallolyticus subsp. gallolyticus belonging to the Streptococcus bovis/Streptococcus equinus complex. Virulence 2018; 9:662-665. [PMID: 29405829 PMCID: PMC5955466 DOI: 10.1080/21505594.2018.1432932] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Konstantinos Papadimitriou
- a Laboratory of Dairy Research, Department of Food Science and Human Nutrition , Agricultural University of Athens , Iera Odos 75, Athens , Greece
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17
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Isenring J, Köhler J, Nakata M, Frank M, Jans C, Renault P, Danne C, Dramsi S, Kreikemeyer B, Oehmcke-Hecht S. Streptococcus gallolyticus subsp. gallolyticus endocarditis isolate interferes with coagulation and activates the contact system. Virulence 2017; 9:248-261. [PMID: 29072555 PMCID: PMC5955193 DOI: 10.1080/21505594.2017.1393600] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Streptococcus gallolyticus subsp. gallolyticus, formerly classified as S. bovis biotype I, is an increasing cause of bacteremia and infective endocarditis in the elderly. The physiopathology of infective endocarditis is poorly understood and involves immune and coagulation systems. In this study, we found that S. gallolyticus subsp. gallolyticus activates the human contact system, which in turn has two consequences: cleavage of high-molecular-weight kininogen (HK) resulting in release of the potent pro-inflammatory peptide bradykinin, and initiation of the intrinsic pathway of coagulation. S. gallolyticus subsp. gallolyticus was found to bind and activate factors of the human contact system at its surface, leading to a significant prolongation of the intrinsic coagulation time and to the release of bradykinin. High-affinity binding of factor XII to the bacterial Pil1 collagen binding protein was demonstrated with a KD of 13 nM. Of note, Pil1 expression was exclusively found in S. gallolyticus subsp. gallolyticus, further supporting an essential contribution of this pilus in virulence.
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Affiliation(s)
- Julia Isenring
- a Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center , Rostock , Germany.,b Nutrition and Health, Laboratory of Food Biotechnology, Institute of Food, ETH Zürich , Zürich , Switzerland
| | - Juliane Köhler
- a Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center , Rostock , Germany
| | - Masanobu Nakata
- a Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center , Rostock , Germany.,c Department of Oral and Molecular Microbiology , Osaka University Graduate School of Dentistry , Suita , Osaka , Japan
| | - Marcus Frank
- d Medical Biology and Electron Microscopy Centre, Rostock University Medical Center , Rostock , Germany
| | - Christoph Jans
- b Nutrition and Health, Laboratory of Food Biotechnology, Institute of Food, ETH Zürich , Zürich , Switzerland
| | - Pierre Renault
- e Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay , Jouy-en-Josas , France
| | - Camille Danne
- f Unité de Biologie des Bactéries Pathogènes à Gram-positif, Institut Pasteur , Paris , France , Centre National de la Recherche Scientifique (CNRS) ERL3526
| | - Shaynoor Dramsi
- f Unité de Biologie des Bactéries Pathogènes à Gram-positif, Institut Pasteur , Paris , France , Centre National de la Recherche Scientifique (CNRS) ERL3526
| | - Bernd Kreikemeyer
- a Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center , Rostock , Germany
| | - Sonja Oehmcke-Hecht
- a Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center , Rostock , Germany
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18
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Bacterial diversity of the Colombian fermented milk "Suero Costeño" assessed by culturing and high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons. Food Microbiol 2017; 68:129-136. [PMID: 28800820 DOI: 10.1016/j.fm.2017.07.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/13/2017] [Accepted: 07/16/2017] [Indexed: 11/22/2022]
Abstract
"Suero Costeño" (SC) is a traditional soured cream elaborated from raw milk in the Northern-Caribbean coast of Colombia. The natural microbiota that characterizes this popular Colombian fermented milk is unknown, although several culturing studies have previously been attempted. In this work, the microbiota associated with SC from three manufacturers in two regions, "Planeta Rica" (Córdoba) and "Caucasia" (Antioquia), was analysed by means of culturing methods in combination with high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons. The bacterial ecosystem of SC samples was revealed to be composed of lactic acid bacteria belonging to the Streptococcaceae and Lactobacillaceae families; the proportions and genera varying among manufacturers and region of elaboration. Members of the Lactobacillus acidophilus group, Lactocococcus lactis, Streptococcus infantarius and Streptococcus salivarius characterized this artisanal product. In comparison with culturing, the use of molecular in deep culture-independent techniques provides a more realistic picture of the overall bacterial communities residing in SC. Besides the descriptive purpose, these approaches will facilitate a rational strategy to follow (culture media and growing conditions) for the isolation of indigenous strains that allow standardization in the manufacture of SC.
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19
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Relative Abundance of Streptococcus spp. and its Association with Disease Activity in Inflammatory Bowel Disease Patients Compared with Controls. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2017. [DOI: 10.5812/archcid.57291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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20
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ISOLATION OF STREPTOCOCCI FROM A FATAL CASE OF MYOCARDITIS IN A CAPTIVE BROWN BEAR (URSUS ARCTOS). J Zoo Wildl Med 2017; 48:269-271. [PMID: 28363068 DOI: 10.1638/2015-0302.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A 10-yr-old, male brown bear ( Ursus arctos ) from Bursa Zoo in Turkey died without any apparent signs. Severe purulent pericarditis and myocarditis with mild ascites, lung edema, and moderate liver congestion were observed during necropsy. Microscopically, there were severe neutrophilic infiltrations in the myocardium and thoracic lymph nodes. A member of the Streptococcus bovis - Streptococcus equinus complex (SBSEC) was isolated and identified phenotypically.
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21
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Tsai CE, Chiu CT, Rayner CK, Wu KL, Chiu YC, Hu ML, Chuah SK, Tai WC, Liang CM, Wang HM. Associated factors in Streptococcus bovis bacteremia and colorectal cancer. Kaohsiung J Med Sci 2016; 32:196-200. [PMID: 27185602 DOI: 10.1016/j.kjms.2016.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/07/2016] [Accepted: 03/15/2016] [Indexed: 02/07/2023] Open
Abstract
Reports suggest that between 25% and 80% of patients with Streptococcus bovis/gallolyticus bacteremia have concomitant colorectal tumors. This retrospective study was aimed to identify associations between clinical characteristics and a finding of colorectal neoplasm in patients with S. bovis bacteremia who had colonoscopy examination. We retrospectively reviewed the records of patients with S. bovis bacteremia from Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan, between January 2004 and January 2014. Clinical data including age, sex, comorbidities, blood culture, and colonoscopy findings were collected and their relationship to a finding of colorectal cancer was examined. A total of 107 patients with S. bovis bacteremia were identified, of whom 49 (72% male; age 65 ± 12 years) were investigated with colonoscopy; 15 of these patients (30.6%) had colorectal adenocarcinoma. Female sex (p = 0.014) and a history of noncolorectal malignancy (p = 0.004) were associated with a finding of colorectal adenocarcinoma. There were no associations with age, percentage of blood cultures, or the presence of diabetes mellitus, chronic liver disease, heart disease, or end-stage renal disease. Our results show that S. bovis bacteremia is associated with the presence of colorectal adenocarcinoma, especially in female patients, and concomitant existence of other malignancies.
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Affiliation(s)
- Cheng-En Tsai
- Division of Hepatogastroenterology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Cheng-Tang Chiu
- Division of Hepatogastroenterology, Department of Internal Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Christopher K Rayner
- Discipline of Medicine, Royal Adelaide Hospital, University of Adelaide, Adelaide, Australia
| | - Keng-Liang Wu
- Division of Hepatogastroenterology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; College of Medicine, Chung Gung University, Taoyuan, Taiwan; Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, Taiwan.
| | - Yi-Chun Chiu
- Division of Hepatogastroenterology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; College of Medicine, Chung Gung University, Taoyuan, Taiwan
| | - Ming-Luen Hu
- Division of Hepatogastroenterology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; College of Medicine, Chung Gung University, Taoyuan, Taiwan
| | - Seng-Kee Chuah
- Division of Hepatogastroenterology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; College of Medicine, Chung Gung University, Taoyuan, Taiwan
| | - Wei-Chen Tai
- Division of Hepatogastroenterology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; College of Medicine, Chung Gung University, Taoyuan, Taiwan
| | - Chih-Ming Liang
- Division of Hepatogastroenterology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; College of Medicine, Chung Gung University, Taoyuan, Taiwan
| | - Hsin-Ming Wang
- Division of Hepatogastroenterology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
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22
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Roto SM, Rubinelli PM, Ricke SC. An Introduction to the Avian Gut Microbiota and the Effects of Yeast-Based Prebiotic-Type Compounds as Potential Feed Additives. Front Vet Sci 2015; 2:28. [PMID: 26664957 PMCID: PMC4672232 DOI: 10.3389/fvets.2015.00028] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 08/20/2015] [Indexed: 01/30/2023] Open
Abstract
The poultry industry has been searching for a replacement for antibiotic growth promoters in poultry feed as public concerns over the use of antibiotics and the appearance of antibiotic resistance has become more intense. An ideal replacement would be feed amendments that could eliminate pathogens and disease while retaining economic value via improvements on body weight and feed conversion ratios. Establishing a healthy gut microbiota can have a positive impact on growth and development of both body weight and the immune system of poultry while reducing pathogen invasion and disease. The addition of prebiotics to poultry feed represents one such recognized way to establish a healthy gut microbiota. Prebiotics are feed additives, mainly in the form of specific types of carbohydrates that are indigestible to the host while serving as substrates to select beneficial bacteria and altering the gut microbiota. Beneficial bacteria in the ceca easily ferment commonly studied prebiotics, producing short-chain fatty acids, while pathogenic bacteria and the host are unable to digest their molecular bonds. Prebiotic-like substances are less commonly studied, but show promise in their effects on the prevention of pathogen colonization, improvements on the immune system, and host growth. Inclusion of yeast and yeast derivatives as probiotic and prebiotic-like substances, respectively, in animal feed has demonstrated positive associations with growth performance and modification of gut morphology. This review will aim to link together how such prebiotics and prebiotic-like substances function to influence the native and beneficial microorganisms that result in a diverse and well-developed gut microbiota.
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Affiliation(s)
- Stephanie M. Roto
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - Peter M. Rubinelli
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - Steven C. Ricke
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
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Abstract
BACKGROUND Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide whose incidence has increased rapidly in recent years. There is growing evidence that the complex gut microbiota community plays an important role in the development of intestinal tumorigenesis. SUMMARY This review aimed to explore the correlation between gut microbiota and CRC as well as to identify the pathogens and their metabolites that affect CRC and the potential models of gut microbiota action. It promotes our understanding of the correlation between gut microbiota and CRC. KEY MESSAGE Our knowledge of the risk factors associated with gut microbiota for CRC development, as well as of the mechanism how intestinal bacteria act on colorectal tumorigenesis, has improved, leading to a better understanding of the correlation between gut microbiota and CRC. PRACTICAL IMPLICATIONS The intestinal microbiota community has a close relationship with CRC by influencing the mechanism of the body and by regulating the physiological function of the colorectum and even the entire digestive system. Gut microbiota have been linked to CRC based upon their toxic and genotoxic metabolites production by fermentation of dietary ingredients. These metabolites could bind specific intestinal cell surface receptors and subsequently affect intracellular signal transduction. The mechanisms by which gut microbiota affect CRC development include the 'Alpha-bug' model, the 'driver-passenger' model and the 'intestinal microbiota adaptions' model. This review promotes our understanding of the correlation between gut microbiota and CRC.
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Affiliation(s)
- Ya-Na Yu
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jing-Yua Fang
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai Institute of Digestive Disease, Shanghai, China ; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai, China ; State Key Laboratory of Oncogene and Related Genes, Shanghai, China
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Zhao S, Wang J, Zheng N, Bu D, Sun P, Yu Z. Reducing microbial ureolytic activity in the rumen by immunization against urease therein. BMC Vet Res 2015; 11:94. [PMID: 25889568 PMCID: PMC4404106 DOI: 10.1186/s12917-015-0409-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 04/07/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Ureolytic activity of rumen bacteria leads to rapid urea conversion to ammonia in the rumen of dairy cows, resulting possible toxicity, excessive ammonia excretion to the environment, and poor nitrogen utilization. The present study investigated immunization of dairy cows against urease in the rumen as an approach to mitigate bacterial ureolytic activity therein. RESULTS Most alpha subunit of rumen urease (UreC) proteins shared very similar amino acid sequences, which were also highly similar to that of H. pylori. Anti-urease titers in the serum and the saliva of the immunized cows were evaluated following repeated immunization with the UreC of H. pylori as the vaccine. After the fourth booster, the vaccinated cows had a significantly reduced urease activity (by 17%) in the rumen than the control cows that were mock immunized cows. The anti-urease antibody significantly reduced ureolysis and corresponding ammonia formation in rumen fluid in vitro. Western blotting revealed that the H. pylori UreC had high immunological homology with the UreC from rumen bacteria. CONCLUSIONS Vaccine developed based on UreC of H. pylori can be a useful approach to decrease bacterial ureolysis in the rumen.
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Affiliation(s)
- Shengguo Zhao
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanyingyuan West Road, Beijing, 100193, PR China. .,State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanyingyuan West Road, Beijing, 100193, PR China.
| | - Jiaqi Wang
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanyingyuan West Road, Beijing, 100193, PR China. .,State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanyingyuan West Road, Beijing, 100193, PR China.
| | - Nan Zheng
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanyingyuan West Road, Beijing, 100193, PR China. .,State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanyingyuan West Road, Beijing, 100193, PR China.
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanyingyuan West Road, Beijing, 100193, PR China.
| | - Peng Sun
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanyingyuan West Road, Beijing, 100193, PR China.
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA.
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Pathogenesis of Streptococcus infantarius subspecies coli Isolated from Sea Otters with Infective Endocarditis. Comp Immunol Microbiol Infect Dis 2015; 40:7-17. [PMID: 25838157 DOI: 10.1016/j.cimid.2015.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 02/24/2015] [Accepted: 03/11/2015] [Indexed: 11/21/2022]
Abstract
The Gram positive bacterial coccus Streptococcus infantarius subspecies coli is increasingly linked with development of fatal vegetative infective endocarditis and septicemia in humans, sea otters (Enhydra lutris) and other animals. However, the pathogenesis of these infections is poorly understood. Using S. infantarius subsp. coli strains isolated from sea otters with infective endocarditis, this study evaluated adherence and invasion of epithelial and endothelial cells, adherence to extracellular matrix components, and macrophage survival. Significant adherence to endothelial-derived cells was observed for 62% of isolates, 24% adhered to epithelial cell lines, and 95% invaded one or both cell types in vitro. The importance of the hyaluronic acid capsule in host cell adherence and invasion was also evaluated. Capsule removal significantly reduced epithelial adherence and invasion for most S. infantarius subsp. coli isolates, suggesting that the capsule facilitates attachment to and invasion of epithelium. Enzyme-linked immunosorbent assay testing revealed that all isolates adhered significantly to the extracellular matrix components collagen IV, fibronectin, laminin and hyaluronic acid. Finally, significant bacterial survival following phagocytosis by macrophages was apparent for 81% of isolates at one or more time points. Taken collectively these findings indicate that S. infantarius subsp. coli has multiple pathogenic properties that may be important to host colonization, invasion and disease.
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26
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Dudek M, Adams J, Swain M, Hegarty M, Huws S, Gallagher J. Metaphylogenomic and potential functionality of the limpet Patella pellucida's gastrointestinal tract microbiome. Int J Mol Sci 2014; 15:18819-39. [PMID: 25334059 PMCID: PMC4227249 DOI: 10.3390/ijms151018819] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/30/2014] [Accepted: 10/11/2014] [Indexed: 11/16/2022] Open
Abstract
This study investigated the microbial diversity associated with the digestive tract of the seaweed grazing marine limpet Patella pellucida. Using a modified indirect DNA extraction protocol and performing metagenomic profiling based on specific prokaryotic marker genes, the abundance of bacterial groups was identified from the analyzed metagenome. The members of three significantly abundant phyla of Proteobacteria, Firmicutes and Bacteroidetes were characterized through the literature and their predicted functions towards the host, as well as potential applications in the industrial environment assessed.
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Affiliation(s)
- Magda Dudek
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales SY23 3EE, UK.
| | - Jessica Adams
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales SY23 3EE, UK.
| | - Martin Swain
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales SY23 3EE, UK.
| | - Matthew Hegarty
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales SY23 3EE, UK.
| | - Sharon Huws
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales SY23 3EE, UK.
| | - Joe Gallagher
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales SY23 3EE, UK.
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DePeters EJ, George LW. Rumen transfaunation. Immunol Lett 2014; 162:69-76. [PMID: 25262872 DOI: 10.1016/j.imlet.2014.05.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 04/26/2014] [Accepted: 05/17/2014] [Indexed: 02/07/2023]
Abstract
The aim of this invited mini-review is to summarize the rumen transfaunation literature. Rumen transfaunation using the cud from a healthy donor animal to treat a sick recipient animal was practiced long before our understanding of rumen microorganisms. Around the mid-1900 s, scientists began to explore the benefits of rumen transfaunation and the associated microbial populations. Rumen transfaunation has been used clinically to treat indigestion and to enhance the return of normal rumen function following surgical correction of a left-displaced abomasum. Rumen transfaunation was also used to introduce unique rumen microorganisms into animals that were exposed to toxic compounds in plants. Rumen liquor contains chemical constituents that likely contribute to the beneficial effects of re-establishing a normal reticulo-rumen anaerobic fermentation. Recommendations for collecting rumen fluid, storage and volumes transferred are discussed. Rumen transfaunation is a common practice to treat indigestion on dairy and livestock operations. The support of a healthy microbial community in the digestive tract is also used for humans. Fecal microbiota transplantation has been used to treat digestive disorders in humans. Rumen transfaunation, although not widely studied with respect to mode of action, is an effective, practical, and easy method to treat simple indigestion of ruminants.
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Affiliation(s)
- E J DePeters
- Department of Animal Science, University of California, Davis, CA, USA.
| | - L W George
- School of Veterinary Medicine, University of California, Davis, CA, USA.
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28
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Jans C, Meile L, Lacroix C, Stevens MJA. Genomics, evolution, and molecular epidemiology of the Streptococcus bovis/Streptococcus equinus complex (SBSEC). INFECTION GENETICS AND EVOLUTION 2014; 33:419-36. [PMID: 25233845 DOI: 10.1016/j.meegid.2014.09.017] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/10/2014] [Accepted: 09/11/2014] [Indexed: 02/07/2023]
Abstract
The Streptococcus bovis/Streptococcus equinus complex (SBSEC) is a group of human and animal derived streptococci that are commensals (rumen and gastrointestinal tract), opportunistic pathogens or food fermentation associates. The classification of SBSEC has undergone massive changes and currently comprises 7 (sub)species grouped into four branches based on sequences identities: the Streptococcus gallolyticus, the Streptococcus equinus, the Streptococcus infantarius and the Streptococcus alactolyticus branch. In animals, SBSEC are causative agents for ruminal acidosis, potentially laminitis and infective endocarditis (IE). In humans, a strong association was established between bacteraemia, IE and colorectal cancer. Especially the SBSEC-species S. gallolyticus subsp. gallolyticus is an emerging pathogen for IE and prosthetic joint infections. S. gallolyticus subsp. pasteurianus and the S. infantarius branch are further associated with biliary and urinary tract infections. Knowledge on pathogenic mechanisms is so far limited to colonization factors such as pili and biofilm formation. Certain strain variants of S. gallolyticus subsp. macedonicus and S. infantarius subsp. infantarius are associated with traditional dairy and plant-based food fermentations and display traits suggesting safety. However, due to their close relationship to virulent strains, their use in food fermentation has to be critically assessed. Additionally, implementing accurate and up-to-date taxonomy is critical to enable appropriate treatment of patients and risk assessment of species and strains via recently developed multilocus sequence typing schemes to enable comparative global epidemiology. Comparative genomics revealed that SBSEC strains harbour genomics islands (GI) that seem acquired from other streptococci by horizontal gene transfer. In case of virulent strains these GI frequently encode putative virulence factors, in strains from food fermentation the GI encode functions that are pivotal for strain performance during fermentation. Comparative genomics is a powerful tool to identify acquired pathogenic functions, but there is still an urgent need for more physiological and epidemiological data to understand SBSEC-specific traits.
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Affiliation(s)
- Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Leo Meile
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Marc J A Stevens
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
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Luo G, Angelidaki I. Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing. WATER RESEARCH 2014; 60:156-163. [PMID: 24852413 DOI: 10.1016/j.watres.2014.04.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/22/2014] [Accepted: 04/27/2014] [Indexed: 05/13/2023]
Abstract
The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors.
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Affiliation(s)
- Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 200433 Shanghai, China; Department of Environmental Engineering, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark.
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30
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Papadimitriou K, Anastasiou R, Mavrogonatou E, Blom J, Papandreou NC, Hamodrakas SJ, Ferreira S, Renault P, Supply P, Pot B, Tsakalidou E. Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex. BMC Genomics 2014; 15:272. [PMID: 24713045 PMCID: PMC4051162 DOI: 10.1186/1471-2164-15-272] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 04/01/2014] [Indexed: 12/21/2022] Open
Abstract
Background Within the genus Streptococcus, only Streptococcus
thermophilus is used as a starter culture in food fermentations.
Streptococcus macedonicus though, which belongs to the
Streptococcus bovis/Streptococcus equinus complex
(SBSEC), is also frequently isolated from fermented foods mainly of dairy
origin. Members of the SBSEC have been implicated in human endocarditis and
colon cancer. Here we compare the genome sequence of the dairy isolate
S. macedonicus ACA-DC 198 to the other SBSEC genomes in order
to assess in silico its potential adaptation to milk and its
pathogenicity status. Results Despite the fact that the SBSEC species were found tightly related based on
whole genome phylogeny of streptococci, two distinct patterns of evolution
were identified among them. Streptococcus macedonicus, Streptococcus
infantarius CJ18 and Streptococcus pasteurianus ATCC 43144
seem to have undergone reductive evolution resulting in significantly
diminished genome sizes and increased percentages of potential pseudogenes
when compared to Streptococcus gallolyticus subsp.
gallolyticus. In addition, the three species seem to have lost
genes for catabolizing complex plant carbohydrates and for detoxifying toxic
substances previously linked to the ability of S. gallolyticus to
survive in the rumen. Analysis of the S. macedonicus genome
revealed features that could support adaptation to milk, including an extra
gene cluster for lactose and galactose metabolism, a proteolytic system for
casein hydrolysis, auxotrophy for several vitamins, an increased ability to
resist bacteriophages and horizontal gene transfer events with the dairy
Lactococcus lactis and S. thermophilus as potential
donors. In addition, S. macedonicus lacks several
pathogenicity-related genes found in S. gallolyticus. For example,
S. macedonicus has retained only one (i.e. the pil3)
of the three pilus gene clusters which may mediate the binding of S.
gallolyticus to the extracellular matrix. Unexpectedly, similar
findings were obtained not only for the dairy S. infantarius CJ18,
but also for the blood isolate S. pasteurianus ATCC 43144. Conclusions Our whole genome analyses suggest traits of adaptation of S.
macedonicus to the nutrient-rich dairy environment. During this
process the bacterium gained genes presumably important for this new
ecological niche. Finally, S. macedonicus carries a reduced number
of putative SBSEC virulence factors, which suggests a diminished pathogenic
potential.
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Affiliation(s)
- Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece.
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31
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Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev 2014; 26:547-603. [PMID: 23824373 DOI: 10.1128/cmr.00072-12] [Citation(s) in RCA: 511] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.
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32
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Vélez Balestro LM, Baroni MR, Ochoteco MC, Zurbriggen ML, Virgolini SM. [Streptococcus gallolyticus subsp. pasteurianus isolated from cerebrospinal fluid in a pediatric patient]. Rev Argent Microbiol 2014; 45:254-6. [PMID: 24401779 DOI: 10.1016/s0325-7541(13)70032-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 08/08/2013] [Indexed: 11/28/2022] Open
Abstract
Streptococcus gallolyticus subsp. pasteurianus is known to cause bacterial meningitis in adults, and most of the few pediatric cases observed occurred in neonates. We report the case of a 9-month old boy with a history of repeated hospitalizations due to respiratory diseases, who presented meningitis and bacteremia by Streptococcus gallolyticus subsp. pasterianus. To our knowledge, this is the first reported case in Santa Fe to this date.
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Affiliation(s)
- Liz M Vélez Balestro
- Sección Bacteriología, División Laboratorio, Hospital de Niños «Dr. O. Alassia», Mendoza 4158, Santa Fe, Argentina.
| | - María R Baroni
- Sección Bacteriología, División Laboratorio, Hospital de Niños «Dr. O. Alassia», Mendoza 4158, Santa Fe, Argentina
| | - Maria C Ochoteco
- Sección Bacteriología, División Laboratorio, Hospital de Niños «Dr. O. Alassia», Mendoza 4158, Santa Fe, Argentina
| | - María L Zurbriggen
- Sección Bacteriología, División Laboratorio, Hospital de Niños «Dr. O. Alassia», Mendoza 4158, Santa Fe, Argentina
| | - Stella M Virgolini
- Sección Bacteriología, División Laboratorio, Hospital de Niños «Dr. O. Alassia», Mendoza 4158, Santa Fe, Argentina
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Peretz A, Dinisman-Zavulunov E, Koifman A, Brodsky D, Isakovich N, Glyatman T, Pastukh N, Paritsky M. Susceptibility of 45 Streptococcus bovis isolates to five antibiotic agents. Int J Antimicrob Agents 2013; 43:298-9. [PMID: 24560425 DOI: 10.1016/j.ijantimicag.2013.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 12/04/2013] [Accepted: 12/05/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Avi Peretz
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Poria, Affiliated to the Faculty of Medicine, Bar-Ilan University, Galilee, Israel.
| | - Eleonora Dinisman-Zavulunov
- Pharmacy Services, Baruch Padeh Medical Center, Poria, Affiliated to the Faculty of Medicine, Bar-Ilan University, Galilee, Israel
| | - Anna Koifman
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Poria, Affiliated to the Faculty of Medicine, Bar-Ilan University, Galilee, Israel
| | - Diana Brodsky
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Poria, Affiliated to the Faculty of Medicine, Bar-Ilan University, Galilee, Israel
| | - Natalya Isakovich
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Poria, Affiliated to the Faculty of Medicine, Bar-Ilan University, Galilee, Israel
| | - Tatyana Glyatman
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Poria, Affiliated to the Faculty of Medicine, Bar-Ilan University, Galilee, Israel
| | - Nina Pastukh
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Poria, Affiliated to the Faculty of Medicine, Bar-Ilan University, Galilee, Israel
| | - Maya Paritsky
- Gastrointestinal Unit, Baruch Padeh Medical Center, Poria, Affiliated to the Faculty of Medicine, Bar-Ilan University, Galilee, Israel
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Stein RA. Streptococcus infantarius and carcinogenesis: a new chapter in colorectal pathology. Int J Clin Pract 2013; 67:1220-4. [PMID: 24246203 DOI: 10.1111/ijcp.12295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/17/2013] [Indexed: 12/14/2022] Open
Abstract
As mirrored by several topics throughout history, the causal link between infectious diseases and cancer was initially viewed with disbelief and subsequently forgotten, only to be rediscovered decades later, when it started flourishing into a vibrant multidisciplinary field . Just a few years ago, it was estimated that over 20% of all cancers are causally linked to infectious diseases, most frequently caused by bacteria, viruses, and parasites .
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Affiliation(s)
- R A Stein
- Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA. ,
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Abstract
The gastrointestinal tract (GIT) microbiomes of production animals are now firmly established as a key feature underscoring animal health, development, and productivity. In particular, early gut colonization is critically important to the morphological and immunological development of the GIT, development of a functional fermentative environment, and neonatal resistance to pathogenic challenge. Although perturbations of an animal's GIT microbiome at any age can have profound consequences, perturbations during early GIT development can be particularly severe and result in significant and long-lasting sequelae. As the GIT microbiome matures, it exhibits significant diversity, ostensibly an important indicator of ecosystem health. Recognition of the immense importance of the GIT microbiota to the host has led to the development of probiotic and prebiotic feedstuffs with the express aim of ensuring animal health. We herein review the current collective understanding of the GIT microbiota of production animals.
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Affiliation(s)
- Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana 59717-2900;
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Jans C, Kaindi DWM, Böck D, Njage PMK, Kouamé-Sina SM, Bonfoh B, Lacroix C, Meile L. Prevalence and comparison of Streptococcus infantarius subsp. infantarius and Streptococcus gallolyticus subsp. macedonicus in raw and fermented dairy products from East and West Africa. Int J Food Microbiol 2013; 167:186-95. [PMID: 24131584 DOI: 10.1016/j.ijfoodmicro.2013.09.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 08/12/2013] [Accepted: 09/14/2013] [Indexed: 01/25/2023]
Abstract
Streptococcus infantarius subsp. infantarius (Sii) and Streptococcus gallolyticus subsp. macedonicus are members of the Streptococcus bovis/Streptococcus equinus complex (SBSEC) associated with human infections. SBSEC-related endocarditis was furthermore associated with rural residency in Southern Europe. SBSEC members are increasingly isolated as predominant species from fermented dairy products in Europe, Asia and Africa. African variants of Sii displayed dairy adaptations to lactose metabolism paralleling those of Streptococcus thermophilus including genome decay. In this study, the aim was to assess the prevalence of Sii and possibly other SBSEC members in dairy products of East and West Africa in order to identify their habitat, estimate their importance in dairy fermentation processes and determine geographic areas affected by this potential health risk. Presumptive SBSEC members were isolated on semi-selective M17 and SM agar media. Subsequent genotypic identification of isolates was based on rep-PCR fingerprinting and SBSEC-specific16S rRNA gene PCR assay. Detailed identification was achieved through application of novel primers enhancing the binding stringency in partial groES/groEL gene amplification and subsequent DNA sequencing. The presence of S. thermophilus-like lacS and lacZ genes in the SBSEC isolates was determined to elucidate the prevalence of this dairy adaptation. Isolates (n = 754) were obtained from 72 raw and 95 fermented milk samples from Côte d'Ivoire and Kenya on semi-selective agar media. Colonies of Sii were not detected from raw milk despite high microbial titers of approximately 10(6)CFU/mL on M17 agar medium. However, after spontaneous milk fermentation Sii was genotypically identified in 94.1% of Kenyan samples and 60.8% of Kenyan isolates. Sii prevalence in Côte d'Ivoire displayed seasonal variations in samples from 32.3% (June) to 40.0% (Dec/Jan) and isolates from 20.5% (June) to 27.7% (Dec/Jan) present at titers of 10(6)-10(8)CFU/mL. lacS and lacZ genes were detected in all Kenyan and 25.8% (June) to 65.4% (Dec/Jan) of Ivorian Sii isolates. Regional differences in prevalence of Sii and dairy adaptations were observed, but no clear effect of dairy animal, fermentation procedure and climate was revealed. Conclusively, the high prevalence of Sii in Kenya, Côte d'Ivoire in addition to Somalia, Sudan and Mali strongly indicates a pivotal role of Sii in traditional African dairy fermentations potentially paralleling that of typical western dairy species S. thermophilus. Putative health risks associated with the consumption of high amounts of live Sii and potential different degrees of evolutionary adaptation or ecological colonization require further epidemiologic and genomic investigations, particularly in Africa.
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Affiliation(s)
- Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
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Xie G, Duff GC, Hall LW, Allen JD, Burrows CD, Bernal-Rigoli JC, Dowd SE, Guerriero V, Yeoman CJ. Alteration of digestive tract microbiome in neonatal Holstein bull calves by bacitracin methylene disalicylate treatment and scours. J Anim Sci 2013; 91:4984-90. [PMID: 23942707 DOI: 10.2527/jas.2013-6304] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The effects of bacitracin methylene disalicylate (BMD) and scours on the fecal microbiome, animal performance, and health were studied in Holstein bull calves. Holstein bull calves (n = 150) were obtained from a single source at 12 to 24 h of age. Bull calves were randomly assigned to 1 of 2 treatments including CON (no BMD; n = 75 calves) and BMD (n = 75 calves). Starting 3 d after arrival, BMD was added into milk replacer (0.5 g/feeding; twice daily) and fed to the calves for 10 consecutive d. No differences (P > 0.10) were observed in ADG for d 0 to 28 and d 0 to 56, DMI for d 0 to 28, d 29 to 56, and d 0 to 56, or G:F for d 0 to 28, d 29 to 56, and d 0 to 56; ADG for d 29 to 56 tended to increase (P < 0.10) for BMD-treated calves compared with controls. Fecal samples were collected from 15 scouring calves and 10 cohorts (nonscouring calves received on the same day and administered the same treatment as the scouring calves). Animal morbidity and fecal score did not vary between the 2 treatments. Mortality was not influenced by the treatments in the BMD administration period or throughout the experiment. Fecal samples were subjected to pyrotagged 454 FLX pyrosequencing of 16S rRNA gene amplicon to examine compositional dynamics of fecal microbes. Escherichia, Enterococcus, and Shigella had greater (P < 0.05) populations in the BMD group whereas Dorea, Roseburia, Fecalibacterium, Papillibacter, Collinsella, Eubacterium, Peptostreptococcus, and Prevotella were decreased (P < 0.05) by BMD treatment. Genus populations were also compared between scouring and nonscouring calves. Streptococcus was the only genus that had notable increase (P < 0.05) in fecal samples from scouring calves whereas populations of Bacteroides, Roseburia, and Eubacterium were markedly (P < 0.05) greater in nonscouring calves. These results show that BMD has the ability to alter the composition of the fecal microbiome but failed to improve performance in Holstein bull calves. Discrepancy of microorganism profiles between scouring and nonscouring calves might be associated with the occurrence of scours and bacterial genera identified might be potential target of treating diarrhea.
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Affiliation(s)
- G Xie
- Department of Animal Sciences, University of Arizona, Tucson 85719
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Sharara AI, Abou Hamdan T, Malli A, El-Halabi MM, Hashash JG, Ghaith OA, Kanj SS. Association of Streptococcus bovis endocarditis and advanced colorectal neoplasia: a case-control study. J Dig Dis 2013; 14:382-7. [PMID: 23551389 DOI: 10.1111/1751-2980.12059] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To study the association between Streptococcus bovis (S. bovis) endocarditis and advanced colorectal neoplasia. METHODS This was a case-control study of patients with S. bovis endocarditis undergoing colonoscopic evaluation. Patients were matched 1:20 with controls by gender and age (±2 years) from a large screening colonoscopy database. The baseline, colonoscopic and clinicopathological characteristics of patients with S. bovis endocarditis were analyzed. RESULTS From 1996 to 2010, 18 adult patients with S. bovis bacteremia were identified, of whom 10 with infective endocarditis (IE) underwent colonoscopic evaluation. Endocarditis involved a native or prosthetic valve in six and four of those patients, respectively. All 10 patients recovered without recurrence of IE (mean follow-up duration 49.6 months). None had a concurrent or preceding history of colon disease and only one had subclinical chronic liver disease. Advanced neoplasia, defined as the presence of polyps ≥1 cm (n = 6), villous histology (n = 3), high-grade focal dysplasia (n = 1) or cancer (n = 1), was found under colonoscopy in 6 of the 10 cases (60.0%) compared with 13/200 (6.5%) matched controls (OR 21.6, 95% CI 5.4-86.1, P < 0.0001). CONCLUSIONS S. bovis endocarditis is strongly associated with the presence of advanced colorectal neoplasia. In the absence of any contraindication, colonoscopic examination is strongly recommended in patients with endocarditis. The exact pathophysiological mechanisms underlying this association and the predilection for S. bovis bacteremia in patients with advanced colonic neoplasia remain unclear.
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Affiliation(s)
- Ala I Sharara
- Division of Gastroenterology, American University of Beirut Medical Center, Beirut, Lebanon.
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Hao GJ, Zhang K, Zhang JY, Wang XR, Qin Z, Wang XZ, Wang L, Meng JR, Yang ZQ, Li JX. RT-qPCR analysis of dexB and galE gene expression of Streptococcus alactolyticus in Astragalus membranaceus fermentation. Appl Microbiol Biotechnol 2013; 97:6009-18. [DOI: 10.1007/s00253-013-4873-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 03/19/2013] [Accepted: 03/20/2013] [Indexed: 11/28/2022]
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Jans C, Follador R, Hochstrasser M, Lacroix C, Meile L, Stevens MJA. Comparative genome analysis of Streptococcus infantarius subsp. infantarius CJ18, an African fermented camel milk isolate with adaptations to dairy environment. BMC Genomics 2013; 14:200. [PMID: 23521820 PMCID: PMC3640971 DOI: 10.1186/1471-2164-14-200] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 03/13/2013] [Indexed: 12/14/2022] Open
Abstract
Background Streptococcus infantarius subsp. infantarius (Sii) belongs to the Streptococcus bovis/Streptococcus equinus complex associated with several human and animal infections. Sii is a predominant bacterium in spontaneously fermented milk products in Africa. The genome sequence of Sii strain CJ18 was compared with that of other Streptococcus species to identify dairy adaptations including genome decay such as in Streptococcus thermophilus, traits for its competitiveness in spontaneous milk fermentation and to assess potential health risks for consumers. Results The genome of Sii CJ18 harbors several unique regions in comparison to Sii ATCC BAA-102T, among others an enlarged exo- and capsular polysaccharide operon; Streptococcus thermophilus-associated genes; a region containing metabolic and hypothetical genes mostly unique to CJ18 and the dairy isolate Streptococcus gallolyticus subsp. macedonicus; and a second oligopeptide transport operon. Dairy adaptations in CJ18 are reflected by a high percentage of pseudogenes (4.9%) representing genome decay which includes the inactivation of the lactose phosphotransferase system (lacIIABC) by multiple transposases integration. The presence of lacS and lacZ genes is the major dairy adaptation affecting lactose metabolism pathways also due to the disruption of lacIIABC. We constructed mutant strains of lacS, lacZ and lacIIABC and analyzed the resulting strains of CJ18 to confirm the redirection of lactose metabolism via LacS and LacZ. Natural competence genes are conserved in both Sii strains, but CJ18 contains a lower number of CRISPR spacers which indicates a reduced defense capability against alien DNA. No classical streptococcal virulence factors were detected in both Sii strains apart from those involved in adhesion which should be considered niche factors. Sii-specific virulence factors are not described. Several Sii-specific regions encoding uncharacterized proteins provide new leads for virulence analyses and investigation of the unclear association of dairy and clinical Sii with human diseases. Conclusions The genome of the African dairy isolate Sii CJ18 clearly differs from the human isolate ATCC BAA-102T. CJ18 possesses a high natural competence predisposition likely explaining the enlarged genome. Metabolic adaptations to the dairy environment are evident and especially lactose uptake corresponds to S. thermophilus. Genome decay is not as advanced as in S. thermophilus (10-19%) possibly due to a shorter history in dairy fermentations.
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Affiliation(s)
- Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, ETH Zurich, Zurich, CH 8092, Switzerland
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Wullschleger S, Lacroix C, Bonfoh B, Sissoko-Thiam A, Hugenschmidt S, Romanens E, Baumgartner S, Traoré I, Yaffee M, Jans C, Meile L. Analysis of lactic acid bacteria communities and their seasonal variations in a spontaneously fermented dairy product (Malian fènè) by applying a cultivation/genotype-based binary model. Int Dairy J 2013. [DOI: 10.1016/j.idairyj.2012.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Paiva AD, Fernandes KM, Dias RS, Rocha AS, de Oliveira LL, Neves CA, de Paula SO, Mantovani HC. Effects of the oral administration of viable and heat-killed Streptococcus bovis HC5 cells to pre-sensitized BALB/c mice. PLoS One 2012; 7:e48313. [PMID: 23144752 PMCID: PMC3483269 DOI: 10.1371/journal.pone.0048313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 09/24/2012] [Indexed: 12/26/2022] Open
Abstract
Antimicrobial peptides have been suggested as an alternative to classical antibiotics in livestock production and bacteriocin-producing bacteria could be added to animal feeds to deliver bacteriocins in the gastrointestinal (GI) tract of ruminant and monogastric animals. In this study, viable (V) and heat-killed (HK) Streptococcus bovis HC5 cells were orally administered to pre-sensitized mice in order to assess the effects of a bacteriocin-producing bacteria on histological parameters and the immune response of the GI tract of monogastric animals. The administration of V and HK S. bovis HC5 cells during 58 days to BALB/c mice did not affect weight gain, but an increase in gut permeability was detected in animals receiving the HK cells. Viable and heat killed cells caused similar morphological alterations in the GI tract of the animals, but the most prominent effects were detected in the small intestine. The oral administration of S. bovis HC5 also influenced cytokine production in the small intestine, and the immune-mediated activity differed between V and HK cells. The relative expression of IL-12 and INF-γ was significantly higher in the small intestine of mice treated with V cells, while an increase in IL-5, IL-13 and TNF-α expression was only detected in mice treated with HK cells. Considering that even under a condition of severe challenge (pre-sensitization followed by daily exposure to the same bacterial immunogen) the general health of the animals was maintained, it appears that oral administration of S. bovis HC5 cells could be a useful route to deliver bacteriocin in the GI tract of livestock animals.
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Affiliation(s)
- Aline D. Paiva
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Kenner M. Fernandes
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Roberto S. Dias
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Alípio S. Rocha
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Leandro L. de Oliveira
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Clóvis A. Neves
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Sérgio O. de Paula
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Hilário C. Mantovani
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- * E-mail:
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Novel Streptococcus infantarius subsp. infantarius variants harboring lactose metabolism genes homologous to Streptococcus thermophilus. Food Microbiol 2012; 31:33-42. [DOI: 10.1016/j.fm.2012.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 02/03/2012] [Accepted: 02/06/2012] [Indexed: 02/07/2023]
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Barile S, Devirgiliis C, Perozzi G. Molecular characterization of a novel mosaic tet(S/M) gene encoding tetracycline resistance in foodborne strains of Streptococcus bovis. MICROBIOLOGY-SGM 2012; 158:2353-2362. [PMID: 22723288 PMCID: PMC3542815 DOI: 10.1099/mic.0.058206-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The presence of antibiotic-resistance (AR) genes in foodborne bacteria of enteric origin represents a relevant threat to human health in the case of opportunistic pathogens, which can reach the human gut through the food chain. Streptococcus bovis is a human opportunistic pathogen often associated with infections in immune-compromised or cancer patients, and it can also be detected in the environment, including fermented foods. We have focused on the molecular characterization of a tetracycline (Tet)-resistance gene present in 39 foodborne isolates of S. bovis phenotypically resistant to this drug. The gene was identified as a novel tet(S/M) fusion, encoding a mosaic protein composed of the N-terminal 33 amino acids of Tet(S), in-frame with the Tet(M) coding sequence. Heterologous expression of the mosaic gene was found to confer Tet resistance upon Escherichia coli recipients. Moreover, the tet(S/M) gene was found to be transcriptionally inducible by Tet under the endogenous tet(S) promoter in both S. bovis and E. coli. Nucleotide sequencing of the surrounding genomic region of 16.2 kb revealed large blocks of homology with the genomes of Streptococcus infantarius and Lactococcus lactis. A subregion of about 4 kb containing mosaic tet(S/M) was flanked by two copies of the IS1216 mobile element. PCR amplification with primers directed outwards from the tet(S/M) gene identified the presence of a 4.3 kb circular form corresponding to the intervening chromosomal region between the two IS1216 elements, but lacking a replication origin. The circular element shared extensive overall homology with a region of the multidrug-resistance plasmid pK214 from Lc. lactis, containing tet(S), as well as the IS1216 transposase-containing element and intervening non-coding sequences. Linear reconstruction of the insertion events likely to have occurred within this genomic region, inferred from sequence homology, provides further evidence of the chromosomal rearrangements that drive genomic evolution in complex bacterial communities such as the gut and food microbiota.
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Affiliation(s)
- Simona Barile
- INRAN - National Research Institute on Food & Nutrition, Via Ardeatina 546, 00178 Roma, Italy
| | - Chiara Devirgiliis
- INRAN - National Research Institute on Food & Nutrition, Via Ardeatina 546, 00178 Roma, Italy
| | - Giuditta Perozzi
- INRAN - National Research Institute on Food & Nutrition, Via Ardeatina 546, 00178 Roma, Italy
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Complete genome sequence of the African dairy isolate Streptococcus infantarius subsp. infantarius strain CJ18. J Bacteriol 2012; 194:2105-6. [PMID: 22461547 DOI: 10.1128/jb.00160-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus infantarius subsp. infantarius, a member of the Streptococcus bovis/Streptococcus equinus complex, is highly prevalent in artisanal dairy fermentations in Africa. Here the complete genome sequence of the dairy-adapted S. infantarius subsp. infantarius CJ18 strain--a strain predominant in traditionally fermented camel milk (suusac) from Kenya--is presented.
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Wang Y, Majak W, McAllister TA. Frothy bloat in ruminants: Cause, occurrence, and mitigation strategies. Anim Feed Sci Technol 2012. [DOI: 10.1016/j.anifeedsci.2011.12.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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47
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Božic AK, Anderson RC, Ricke SC, Crandall PG, O'Bryan CA. Comparison of nitroethane, 2-nitro-1-propanol, lauric acid, Lauricidin® and the Hawaiian marine algae, Chaetoceros, for potential broad-spectrum control of anaerobically grown lactic acid bacteria. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2012; 47:269-274. [PMID: 22428888 DOI: 10.1080/03601234.2012.638883] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The gastrointestinal tract of bovines often contains bacteria that contribute to disorders of the rumen, and may also contain foodborne or opportunistic human pathogens as well as bacteria capable of causing mastitis in cows. Thus there is a need to develop broad-spectrum therapies that are effective while not leading to unacceptably long antibiotic withdrawal times. The effects of the CH(4)-inhibitors nitroethane (2 mg/mL), 2-nitro-1-propanol (2 mg/mL), lauric acid (5 mg/mL), the commercial product Lauricidin® (5 mg/mL), and a finely ground product of the Hawaiian marine algae, Chaetoceros (10 mg/mL), were compared in pure cultures of Streptococcus agalactia, Enterococcus faecium, Streptococcus bovis, and in a mixed lactic acid rumen bacterial culture. Lauricidin® and lauric acid exhibited the most bactericidal acidity against all bacteria. These results suggest potential animal health benefits from supplementing cattle diets with lauric acid or Lauricidin® to improve the health of the rumen and help prevent shedding of human pathogens.
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Affiliation(s)
- Aleksandar K Božic
- Department of Animal Science, Faculty of Agriculture, University of Novi Sad, Republic of Serbia
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Harrison S, Benziger H, Koerner R. Streptococcus bovis infections, colorectal cancer and liver dysfunction. ANZ J Surg 2011; 81:762-3. [DOI: 10.1111/j.1445-2197.2011.05874.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Stanton TB, Humphrey SB. Persistence of antibiotic resistance: evaluation of a probiotic approach using antibiotic-sensitive Megasphaera elsdenii strains to prevent colonization of swine by antibiotic-resistant strains. Appl Environ Microbiol 2011; 77:7158-66. [PMID: 21821757 PMCID: PMC3194883 DOI: 10.1128/aem.00647-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 07/25/2011] [Indexed: 11/20/2022] Open
Abstract
Megasphaera elsdenii is a lactate-fermenting, obligately anaerobic bacterium commonly present in the gastrointestinal tracts of mammals, including humans. Swine M. elsdenii strains were previously shown to have high levels of tetracycline resistance (MIC=64 to >256 μg/ml) and to carry mosaic (recombinant) tetracycline resistance genes. Baby pigs inherit intestinal microbiota from the mother sow. In these investigations we addressed two questions. When do M. elsdenii strains from the sow colonize baby pigs? Can five antibiotic-sensitive M. elsdenii strains administered intragastrically to newborn pigs affect natural colonization of the piglets by antibiotic-resistant (AR) M. elsdenii strains from the mother? M. elsdenii natural colonization of newborn pigs was undetectable (<10(4) CFU/g [wet weight] of feces) prior to weaning (20 days after birth). After weaning, all pigs became colonized (4 × 10(5) to 2 × 10(8) CFU/g feces). In a separate study, 61% (76/125) of M. elsdenii isolates from a gravid sow never exposed to antibiotics were resistant to chlortetracycline, ampicillin, or tylosin. The inoculation of the sow's offspring with mixtures of M. elsdenii antibiotic-sensitive strains prevented colonization of the offspring by maternal AR strains until at least 11 days postweaning. At 25 and 53 days postweaning, however, AR strains predominated. Antibiotic susceptibility phenotypes and single nucleotide polymorphism (SNP)-based identities of M. elsdenii isolated from sow and offspring were unexpectedly diverse. These results suggest that dosing newborn piglets with M. elsdenii antibiotic-sensitive strains delays but does not prevent colonization by maternal resistant strains. M. elsdenii subspecies diversity offers an explanation for the persistence of resistant strains in the absence of antibiotic selection.
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Affiliation(s)
- Thad B Stanton
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA.
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Lin CY, Tseng SB, Lu PL, Chen TC, Lin WR, Chen YH, Lin KS. Isolation of Streptococcus bovis from apheresis platelets of asymptomatic donor warranted colonoscopy investigation: case report and literature review. Transfusion 2011; 51:2023-7. [DOI: 10.1111/j.1537-2995.2011.03088.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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