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Xue KS, Walton SJ, Goldman DA, Morrison ML, Verster AJ, Parrott AB, Yu FB, Neff NF, Rosenberg NA, Ross BD, Petrov DA, Huang KC, Good BH, Relman DA. Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559480. [PMID: 37808827 PMCID: PMC10557656 DOI: 10.1101/2023.09.26.559480] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Humans constantly encounter new microbes, but few become long-term residents of the adult gut microbiome. Classical theories predict that colonization is determined by the availability of open niches, but it remains unclear whether other ecological barriers limit commensal colonization in natural settings. To disentangle these effects, we used a controlled perturbation with the antibiotic ciprofloxacin to investigate the dynamics of gut microbiome transmission in 22 households of healthy, cohabiting adults. Colonization was rare in three-quarters of antibiotic-taking subjects, whose resident strains rapidly recovered in the week after antibiotics ended. In contrast, the remaining antibiotic-taking subjects exhibited lasting responses, with extensive species losses and transient expansions of potential opportunistic pathogens. These subjects experienced elevated rates of commensal colonization, but only after long delays: many new colonizers underwent sudden, correlated expansions months after the antibiotic perturbation. Furthermore, strains that had previously transmitted between cohabiting partners rarely recolonized after antibiotic disruptions, showing that colonization displays substantial historical contingency. This work demonstrates that there remain substantial ecological barriers to colonization even after major microbiome disruptions, suggesting that dispersal interactions and priority effects limit the pace of community change.
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Affiliation(s)
- Katherine S Xue
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sophie Jean Walton
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Biophysics Training Program, Stanford, CA 94305, USA
| | - Doran A Goldman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Maike L Morrison
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Adrian J Verster
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | | | | | - Norma F Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Benjamin D Ross
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Benjamin H Good
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Applied Physics, Stanford, CA 94305, USA
| | - David A Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA
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Vega-Sagardía M, Delgado J, Ruiz-Moyano S, Garrido D. Proteomic analyses of Bacteroides ovatus and Bifidobacterium longum in xylan bidirectional culture shows sugar cross-feeding interactions. Food Res Int 2023; 170:113025. [PMID: 37316088 DOI: 10.1016/j.foodres.2023.113025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023]
Abstract
The intestinal microbiome is a community of anaerobic microorganisms whose activities significantly impact human health. Its composition can be modulated by consuming foods rich in dietary fiber, such as xylan, a complex polysaccharide that can be considered an emerging prebiotic. In this work, we evaluated how certain gut bacteria acted as primary degraders, fermenting dietary fibers, and releasing metabolites that other bacteria can further use. Different bacterial strains of Lactobacillus, Bifidobacterium, and Bacteroides were evaluated for their ability to consume xylan and interact with one another. Results from unidirectional assays gave indications of possible cross-feeding between bacteria using xylan as a carbon source. Bidirectional assays showed that Bifidobacterium longum PT4 increased its growth in the presence of Bacteroides ovatus HM222. Proteomic analyses indicated that B. ovatus HM222 synthesizes enzymes facilitating xylan degradation, such as β-xylanase, arabinosidase, L-arabinose isomerase, and xylosidase. Interestingly, the relative abundance of these proteins remains largely unaffected in the presence of Bifidobacterium longum PT4. In the presence of B. ovatus, B. longum PT4 increased the production of enzymes such as α-L-arabinosidase, L-arabinose isomerase, xylulose kinase, xylose isomerase, and sugar transporters. These results show an example of positive interaction between bacteria mediated by xylan consumption. Bacteroides degraded this substrate to release xylooligosaccharides, or monosaccharides (xylose, arabinose), which might support the growth of secondary degraders such as B. longum.
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Affiliation(s)
- Marco Vega-Sagardía
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago, Chile
| | - Josué Delgado
- Food Hygiene and Safety, Meat and Meat Products Research Institute, Faculty of Veterinary Science, Universidad de Extremadura, Avenida de las Ciencias s/n, 10003 Caceres, Spain.
| | - Santiago Ruiz-Moyano
- Departamento de Producción Animal y Ciencia de los Alimentos, Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suárez s/n, 06007 Badajoz, Spain; Instituto Universitario de Investigación de Recursos Agrarios (INURA), Universidad de Extremadura, Avda. de la Investigación s/n, Campus Universitario, 06006 Badajoz, Spain
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago, Chile.
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Dauksiene A, Ruzauskas M, Gruzauskas R, Zavistanaviciute P, Starkute V, Lele V, Klupsaite D, Klementaviciute J, Bartkiene E. A Comparison Study of the Caecum Microbial Profiles, Productivity and Production Quality of Broiler Chickens Fed Supplements Based on Medium Chain Fatty and Organic Acids. Animals (Basel) 2021; 11:ani11030610. [PMID: 33652631 PMCID: PMC7996795 DOI: 10.3390/ani11030610] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary The ban of growth promoters in poultry farming in the European Union has resulted in the development of alternatives. Among these alternatives, medium chain fatty acids (MCFAs) or organic acids (OAs) are considered to be suitable for in-feed use. However, their effect on microbiota modulation and the meat quality of broiler chickens are still under-investigated. The aim of this study was to estimate the influence of MCFAs and OAs supplements on the caecum microbial profiles, productivity and production quality characteristics of broiler chickens. The 42-days experiment was conducted using 900-day-old broiler chickens, allocated into three groups, consisting of 300 birds per group. The results indicated that the addition of OAs results in a more appropriate environment in the caecum for beneficial microorganisms rather than diets supplemented with MCFAs. These positive changes led to a higher efficiency of poultry productivity (higher body weight and lower mortality); however, for most of the analysed broilers’, technological parameters were not considerably influenced by treatments. Abstract The aim of this study was to evaluate the influence of medium chain fatty acids (MCFAs) and organic acids (OAs) supplements on the caecum microbial profiles, productivity and production quality characteristics of broiler chickens (BCs). BC (900 chicks) were attributed to three groups: (i) control; (ii) MCFAs group (BCs fed with feed supplemented with MCFAs); (iii) OAs group (BCs fed with feed supplemented with OAs). Broilers were slaughtered at the end of the trial (42 days old), and the caecum microbial profiles, productivity and production quality characteristics were analysed. Supplementation with OAs resulted in a more appropriate environment in the caecum for beneficial microorganisms than with a diet supplemented with MCFAs. This was supported by data on the presence of higher amounts and an increased species variety of probiotic bacteria (Lactobacillus and Bifidobacterium) in the caecum of birds. The above-mentioned changes of the caecum microbiota led to significantly higher villus height (p = 0.003) of the OAs broiler group and significantly lower crypt depth (p = 0.037). Notwithstanding the significant increase of acetic, propionic, isobutyric, butyric, isovaleric, and valeric acids that were established in caecum samples from the MCFAs group, better parameters of broiler production performance (higher body weight and lower mortality) and carcass traits (higher both thigh and shin muscles with skin and bone weight; both shin muscles without skin and bone weight; abdominal fat yield) were found in the OAs-treated group. For chemical, physical and technological characteristics of breast meat samples, increased yellowness and water holding capacity by 14.7% and 2.3%, respectively, were found in MCFAs group samples. A more appropriate environment in the caecum for beneficial microorganisms could be obtained when BCs were fed with OAs supplement, comparing to MCFAs, and these positive changes were associated with higher efficiency of poultry production.
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Affiliation(s)
- Agila Dauksiene
- Institute of Animal Rearing Technologies, Lithuanian University of Health Sciences, Tilzes str. 18, LT-47181 Kaunas, Lithuania; (P.Z.); (V.S.); (V.L.); (D.K.); (J.K.); (E.B.)
- Department of Anatomy and Physiology, Lithuanian University of Health Sciences, Tilzes str. 18, LT-47181 Kaunas, Lithuania;
- Correspondence: ; Tel.: +370-685-25327
| | - Modestas Ruzauskas
- Department of Anatomy and Physiology, Lithuanian University of Health Sciences, Tilzes str. 18, LT-47181 Kaunas, Lithuania;
- Microbiology and Virology Institute, Lithuanian University of Health Sciences, Tilzes str. 18, LT-47181 Kaunas, Lithuania
| | - Romas Gruzauskas
- Department of Food Sciences and Technology, Kaunas University of Technology, Radvilenu str. 19, LT-50254 Kaunas, Lithuania;
| | - Paulina Zavistanaviciute
- Institute of Animal Rearing Technologies, Lithuanian University of Health Sciences, Tilzes str. 18, LT-47181 Kaunas, Lithuania; (P.Z.); (V.S.); (V.L.); (D.K.); (J.K.); (E.B.)
- Department of Food Safety and Quality, Lithuanian University of Health Sciences, Tilzes str. 18, LT-47181 Kaunas, Lithuania
| | - Vytaute Starkute
- Institute of Animal Rearing Technologies, Lithuanian University of Health Sciences, Tilzes str. 18, LT-47181 Kaunas, Lithuania; (P.Z.); (V.S.); (V.L.); (D.K.); (J.K.); (E.B.)
- Department of Food Safety and Quality, Lithuanian University of Health Sciences, Tilzes str. 18, LT-47181 Kaunas, Lithuania
| | - Vita Lele
- Institute of Animal Rearing Technologies, Lithuanian University of Health Sciences, Tilzes str. 18, LT-47181 Kaunas, Lithuania; (P.Z.); (V.S.); (V.L.); (D.K.); (J.K.); (E.B.)
- Department of Food Safety and Quality, Lithuanian University of Health Sciences, Tilzes str. 18, LT-47181 Kaunas, Lithuania
| | - Dovile Klupsaite
- Institute of Animal Rearing Technologies, Lithuanian University of Health Sciences, Tilzes str. 18, LT-47181 Kaunas, Lithuania; (P.Z.); (V.S.); (V.L.); (D.K.); (J.K.); (E.B.)
| | - Jolita Klementaviciute
- Institute of Animal Rearing Technologies, Lithuanian University of Health Sciences, Tilzes str. 18, LT-47181 Kaunas, Lithuania; (P.Z.); (V.S.); (V.L.); (D.K.); (J.K.); (E.B.)
| | - Elena Bartkiene
- Institute of Animal Rearing Technologies, Lithuanian University of Health Sciences, Tilzes str. 18, LT-47181 Kaunas, Lithuania; (P.Z.); (V.S.); (V.L.); (D.K.); (J.K.); (E.B.)
- Department of Food Safety and Quality, Lithuanian University of Health Sciences, Tilzes str. 18, LT-47181 Kaunas, Lithuania
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Donated Human Milk as a Determinant Factor for the Gut Bifidobacterial Ecology in Premature Babies. Microorganisms 2020; 8:microorganisms8050760. [PMID: 32438679 PMCID: PMC7285294 DOI: 10.3390/microorganisms8050760] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022] Open
Abstract
Correct establishment of the gut microbiome is compromised in premature babies, with Bifidobacterium being one of the most affected genera. Prematurity often entails the inability to successfully breastfeed, therefore requiring the implementation of other feeding modes; breast milk expression from a donor mother is the recommended option when their own mother’s milk is not available. Some studies showed different gut microbial profiles in premature infants fed with breast milk and donor human milk, however, it is not known how this affects the species composition of the genus Bifidobacterium. The objective of this study was to assess the effect of donated human milk on shaping the gut bifidobacterial populations of premature babies during the first three months of life. We analyzed the gut bifidobacterial communities of 42 premature babies fed with human donor milk or own-mother milk by the 16S rRNA–23S rRNA internal transcriber spaces (ITS) region sequencing and q-PCR. Moreover, metabolic activity was assessed by gas chromatography. We observed a specific bifidobacterial profile based on feeding type, with higher bifidobacterial diversity in the human donor milk group. Differences in specific Bifidobacterium species composition may contribute to the development of specific new strategies or treatments aimed at mimicking the impact of own-mother milk feeding in neonatal units.
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Zhou S, Yu Z, Chu W. Effect of quorum-quenching bacterium Bacillus sp. QSI-1 on protein profiles and extracellular enzymatic activities of Aeromonas hydrophila YJ-1. BMC Microbiol 2019; 19:135. [PMID: 31226935 PMCID: PMC6588933 DOI: 10.1186/s12866-019-1515-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 06/17/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In natural environments, bacteria always live in communities with others where their physiological characteristics are influenced by each other. Bacteria can communicate with one another by using autoinducers. The current knowledge on the effect of quenching bacteria on others is limited to assess the impact of quorum-quenching bacterium Bacillus sp. QSI-1 on proteins pattern and virulence factors production of Aeromonas hydrophila YJ-1. Proteomic analysis was performed to find out protein changes and virulence factors, after 24 h co-culture. RESULTS Results showed that several proteins of A. hydrophila YJ-1 were altered, seventy-two differentially expressed protein spots were excised from 2-DE gels and analyzed by MALDI-TOF/TOF MS, resulting in 63 individual proteins being clearly identified from 70 spots. Among these proteins, 50 were divided into 22 classes and mapped onto 18 biological pathways. Mixed-culture growth with Bacillus sp. QSI-1 resulted in an increase of A. hydrophilia proteins involved in RNA polymerase activity, biosynthesis of secondary metabolites, flagellar assembly, and two-component systems. In contrast, mixed culture resulted in a decreased level of proteins involved in thiamine metabolism; valine, leucine and isoleucine biosynthesis; pantothenate and CoA biosynthesis. In addition, the two extracellular virulence factors, proteases and hemolysin, were significantly reduced when A. hydrophila was co-cultured with QSI-1, while only lipase activity was observed to increase. CONCLUSIONS The information gathered from our experiment showed that Bacillus sp. QSI-1 has a major impact on the expression of proteins, including virulence factors of A. hydrophila.
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Affiliation(s)
- Shuxin Zhou
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Zixun Yu
- School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Weihua Chu
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China.
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Orihuel A, Terán L, Renaut J, Vignolo GM, De Almeida AM, Saavedra ML, Fadda S. Differential Proteomic Analysis of Lactic Acid Bacteria- Escherichia coli O157:H7 Interaction and Its Contribution to Bioprotection Strategies in Meat. Front Microbiol 2018; 9:1083. [PMID: 29922248 PMCID: PMC5996242 DOI: 10.3389/fmicb.2018.01083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/07/2018] [Indexed: 12/16/2022] Open
Abstract
Human infection by Enterohemorrhagic Escherichia (E.) coli (EHEC) occurs through the ingestion of contaminated foods such as milk, vegetable products, water-based drinks, and particularly minced meats. Indeed EHEC is a pathogen that threatens public health and meat industry. The potential of different Lactic Acid Bacteria (LAB) strains to control EHEC in a meat-based medium was evaluated by using a simple and rapid method and by analyzing the growth kinetics of co-cultures (LAB-EHEC) in a meat-based medium. The activity of LAB toward EHEC in co-cultures showed variable inhibitory effect. Although, LAB were able to control EHEC, neither the produced acid nor bacteriocins were responsible of the inhibition. The bacteriocinogenic Enteroccus (Ent.) mundtii CRL35 presented one of the highest inhibition activities. A proteomic approach was used to evaluate bacterial interaction and antagonistic mechanisms between Ent. mundtii and EHEC. Physiological observations, such as growth kinetics, acidification ability and EHEC inhibitory potential were supported by the proteomic results, demonstrating significant differences in protein expression in LAB: (i) due to the presence of the pathogen and (ii) according to the growth phase analyzed. Most of the identified proteins belonged to carbohydrate/amino acid metabolism, energy production, transcription/translation, and cell division. These results contribute to the knowledge of competition strategies used by Ent. mundtii during its co-culture with EHEC setting new perspectives for the use of LAB to control this pathogen in meat.
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Affiliation(s)
- Alejandra Orihuel
- Technology Department, Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas (CERELA CONICET), San Miguel de Tucumán, Argentina
| | - Lucrecia Terán
- Genetics and Molecular Biology Department, Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas (CERELA CONICET), San Miguel de Tucumán, Argentina
| | - Jenny Renaut
- Luxembourg Institute of Science and Technology "Environmental Research and Innovation" Department, Belvaux, Luxemburg
| | - Graciela M Vignolo
- Technology Department, Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas (CERELA CONICET), San Miguel de Tucumán, Argentina
| | - André M De Almeida
- LEAF - Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
| | - María L Saavedra
- Genetics and Molecular Biology Department, Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas (CERELA CONICET), San Miguel de Tucumán, Argentina
| | - Silvina Fadda
- Technology Department, Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas (CERELA CONICET), San Miguel de Tucumán, Argentina
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