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Zhuang Y, Liu S, Gao D, Xu Y, Jiang W, Chen T, Xiao J, Wang J, Hou G, Li S, Zhao X, Huang Y, Li S, Zhang S, Li M, Wang W, Li S, Cao Z. The Bifidobacterium-dominated fecal microbiome in dairy calves shapes the characteristic growth phenotype of host. NPJ Biofilms Microbiomes 2024; 10:59. [PMID: 39034349 PMCID: PMC11271470 DOI: 10.1038/s41522-024-00534-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024] Open
Abstract
The dominant bacteria in the hindgut of calves play an important role in their growth and health, which could even lead to lifelong consequences. However, the identification of core probiotics in the hindgut and its mechanism regulating host growth remain unclear. Here, a total of 1045 fecal samples were analyzed by 16S rRNA gene sequencing from the 408 Holstein dairy calves at the age of 0, 14, 28, 42, 56, and 70 days to characterize the dynamic changes of core taxa. Moreover, the mechanisms of nutrient metabolism of calf growth regulated by core bacteria were investigated using multi-omics analyses. Finally, fecal microbiota transplantation (FMT) in mice were conducted to illustrate the potential beneficial effects of core bacteria. Four calf enterotypes were identified and enterotypes dominated by Bifidobacterium and Oscillospiraceae_UCG-005 were representative. The frequency of enterotype conversion shifted from variable to stable. The close relationship observed between phenotype and enterotype, revealing a potential pro-growth effect of Bifidobacterium, might be implemented by promoting the use of carbohydrate, activating the synthesis of volatile fatty acids, amino acids and vitamin B6, and inhibiting methane production in the hindgut. The FMT results indicated the beneficial effect of Bifidobacterium on host growth and hindgut development. These results support the notion that the Bifidobacterium-dominated fecal microbiome would be an important driving force for promoting the host growth in the early life. Our findings provide new insights into the potential probiotic mining and application strategies to promote the growth of young animals or improve their growth retardation.
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Affiliation(s)
- Yimin Zhuang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuai Liu
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Duo Gao
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yiming Xu
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Wen Jiang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Tianyu Chen
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianxin Xiao
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jingjun Wang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Guobin Hou
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Sumin Li
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xinjie Zhao
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yanting Huang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shangru Li
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Siyuan Zhang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Mengmeng Li
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wei Wang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengli Li
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
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2
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Firkins JL, Mitchell KE. Invited review: Rumen modifiers in today's dairy rations. J Dairy Sci 2023; 106:3053-3071. [PMID: 36935236 DOI: 10.3168/jds.2022-22644] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/23/2022] [Indexed: 03/19/2023]
Abstract
Our aim was to review feed additives that have a potential ruminal mechanism of action when fed to dairy cattle. We discuss how additives can influence ruminal fermentation stoichiometry through electron transfer mechanisms, particularly the production and usage of dihydrogen. Lactate accumulation should be avoided, especially when acidogenic conditions suppress ruminal neutral detergent fiber digestibility or lead to subclinical acidosis. Yeast products and other probiotics are purported to influence lactate uptake, but growing evidence also supports that yeast products influence expression of gut epithelial genes promoting barrier function and resulting inflammatory responses by the host to various stresses. We also have summarized methane-suppressing additives for potential usage in dairy rations. We focused on those with potential to decrease methane production without decreasing fiber digestibility or milk production. We identified some mitigating factors that need to be addressed more fully in future research. Growth factors such as branched-chain volatile fatty acids also are part of crucial cross-feeding among groups of microbes, particularly to optimize fiber digestibility in the rumen. Our developments of mechanisms of action for various rumen-active modifiers should help nutrition advisors anticipate when a benefit in field conditions is more likely.
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Affiliation(s)
- J L Firkins
- Department of Animal Sciences, The Ohio State University, Columbus 43210.
| | - K E Mitchell
- Department of Animal Sciences, The Ohio State University, Columbus 43210
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Amin N, Schwarzkopf S, Tröscher-Mußotter J, Camarinha-Silva A, Dänicke S, Huber K, Frahm J, Seifert J. Host metabolome and faecal microbiome shows potential interactions impacted by age and weaning times in calves. Anim Microbiome 2023; 5:12. [PMID: 36788596 PMCID: PMC9926800 DOI: 10.1186/s42523-023-00233-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND Calves undergo nutritional, metabolic, and behavioural changes from birth to the entire weaning period. An appropriate selection of weaning age is essential to reduce the negative effects caused by weaning-related dietary transitions. This study monitored the faecal microbiome and plasma metabolome of 59 female Holstein calves during different developmental stages and weaning times (early vs. late) and identified the potential associations of the measured parameters over an experimental period of 140 days. RESULTS A progressive development of the microbiome and metabolome was observed with significant differences according to the weaning groups (weaned at 7 or 17 weeks of age). Faecal samples of young calves were dominated by bifidobacterial and lactobacilli species, while their respective plasma samples showed high concentrations of amino acids (AAs) and biogenic amines (BAs). However, as the calves matured, the abundances of potential fiber-degrading bacteria and the plasma concentrations of sphingomyelins (SMs), few BAs and acylcarnitines (ACs) were increased. Early-weaning at 7 weeks significantly restructured the microbiome towards potential fiber-degrading bacteria and decreased plasma concentrations of most of the AAs and SMs, few BAs and ACs compared to the late-weaning event. Strong associations between faecal microbes, plasma metabolites and calf growth parameters were observed during days 42-98, where the abundances of Bacteroides, Parabacteroides, and Blautia were positively correlated with the plasma concentrations of AAs, BAs and SMs as well as the live weight gain or average daily gain in calves. CONCLUSION The present study reported that weaning at 17 weeks of age was beneficial due to higher growth rate of late-weaned calves during days 42-98 and a quick adaptability of microbiota to weaning-related dietary changes during day 112, suggesting an age-dependent maturation of the gastrointestinal tract. However, the respective plasma samples of late-weaned calves contained several metabolites with differential concentrations to the early-weaned group, suggesting a less abrupt but more-persistent effect of dietary changes on host metabolome compared to the microbiome.
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Affiliation(s)
- Nida Amin
- grid.9464.f0000 0001 2290 1502HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany ,grid.9464.f0000 0001 2290 1502Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Sarah Schwarzkopf
- grid.9464.f0000 0001 2290 1502HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany ,grid.9464.f0000 0001 2290 1502Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Johanna Tröscher-Mußotter
- grid.9464.f0000 0001 2290 1502HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany ,grid.9464.f0000 0001 2290 1502Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Amélia Camarinha-Silva
- grid.9464.f0000 0001 2290 1502HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany ,grid.9464.f0000 0001 2290 1502Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Sven Dänicke
- grid.417834.dInstitute of Animal Nutrition, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Brunswick, Germany
| | - Korinna Huber
- grid.9464.f0000 0001 2290 1502HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany ,grid.9464.f0000 0001 2290 1502Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Jana Frahm
- grid.417834.dInstitute of Animal Nutrition, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Brunswick, Germany
| | - Jana Seifert
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany. .,Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany.
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Mills S, Yang B, Smith GJ, Stanton C, Ross RP. Efficacy of Bifidobacterium longum alone or in multi-strain probiotic formulations during early life and beyond. Gut Microbes 2023; 15:2186098. [PMID: 36896934 PMCID: PMC10012958 DOI: 10.1080/19490976.2023.2186098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/24/2023] [Indexed: 03/11/2023] Open
Abstract
The significance of Bifidobacterium to human health can be appreciated from its early colonization of the neonatal gut, where Bifidobacterium longum represents the most abundant species. While its relative abundance declines with age, it is further reduced in several diseases. Research into the beneficial properties of B. longum has unveiled a range of mechanisms, including the production of bioactive molecules, such as short-chain fatty acids, polysaccharides, and serine protease inhibitors. From its intestinal niche, B. longum can have far-reaching effects in the body influencing immune responses in the lungs and even skin, as well as influencing brain activity. In this review, we present the biological and clinical impacts of this species on a range of human conditions beginning in neonatal life and beyond. The available scientific evidence reveals a strong rationale for continued research and further clinical trials that investigate the ability of B. longum to treat or prevent a range of diseases across the human lifespan.
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Affiliation(s)
- Susan Mills
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | | | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Co Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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5
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Wang Y, Li Z, Jin W, Mao S. Isolation and Characterization of Ruminal Yeast Strain with Probiotic Potential and Its Effects on Growth Performance, Nutrients Digestibility, Rumen Fermentation and Microbiota of Hu Sheep. J Fungi (Basel) 2022; 8:jof8121260. [PMID: 36547593 PMCID: PMC9781649 DOI: 10.3390/jof8121260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022] Open
Abstract
Yeast strains are widely used in ruminant production. However, knowledge about the effects of rumen native yeasts on ruminants is limited. Therefore, this study aimed to obtain a rumen native yeast isolate and investigate its effects on growth performance, nutrient digestibility, rumen fermentation and microbiota in Hu sheep. Yeasts were isolated by picking up colonies from agar plates, and identified by sequencing the ITS sequences. One isolate belonging to Pichia kudriavzevii had the highest optical density among these isolates obtained. This isolate was prepared to perform an animal feeding trial. A randomized block design was used for the animal trial. Sixteen Hu sheep were randomly assigned to the control (CON, fed basal diet, n = 8) and treatment group (LPK, fed basal diet plus P. kudriavzevii, CFU = 8 × 109 head/d, n = 8). Sheep were housed individually and treated for 4 weeks. Compared to CON, LPK increased final body weight, nutrient digestibility and rumen acetate concentration and acetate-to-propionate ratio in sheep. The results of Illumina MiSeq PE 300 sequencing showed that LPK increased the relative abundance of lipolytic bacteria (Anaerovibrio spp. and Pseudomonas spp.) and probiotic bacteria (Faecalibacterium spp. and Bifidobacterium spp.). For rumen eukaryotes, LPK increased the genera associated with fiber degradation, including protozoan Polyplastron and fungus Pichia. Our results discovered that rumen native yeast isolate P. kudriavzevii might promote the digestion of fibers and lipids by modulating specific microbial populations with enhancing acetate-type fermentation.
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Affiliation(s)
- Yao Wang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zihao Li
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Jin
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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6
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Yang B, Ding M, Chen Y, Han F, Yang C, Zhao J, Malard P, Stanton C, Ross RP, Zhang H, Chen W. Development of gut microbiota and bifidobacterial communities of neonates in the first 6 weeks and their inheritance from mother. Gut Microbes 2022; 13:1-13. [PMID: 33847206 PMCID: PMC8049200 DOI: 10.1080/19490976.2021.1908100] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Microbiota especially Bifidobacterium play an important role in adjusting and maintaining homeostatic balance within the infant intestine. The aim of this study was to elucidate the relationship between maternal and infant gut microbiota and identify the Bifidobacterium species that may transfer from mother to infant over the first 42 days of the infant's life. Nineteen mother-infant-pair fecal samples were collected and the diversity and composition of the total bacterial and Bifidobacterium communities were analyzed via 16S rDNA and bifidobacterial groEL gene high throughput sequencing. The results revealed that the relative abundance of Bifidobacterium was significantly higher in the infant gut while Parabacteroides, Blautia, Coprococcus, Lachnospira and Faecalibacterium were at lower relative abundance in 7-day and 42-day infant fecal samples compared to the maternal samples. The maternal gut has more B. pseudocatenulatum. In the infant group, B. breve and B. dentium relative abundance increased while B. animalis subsp. lactis decreased from days 7 to 42. Additionally, B. longum subsp. longum isolated from FGZ16 and FGZ35 may have transferred from mother to infant and colonized the infant gut. The results of the current study provide insight toward the infant gut microbiota composition and structure during the first 42 days and may help guide Bifidobacterium supplementation strategies in mothers and infants.
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Affiliation(s)
- Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China,School of Food Science and Technology, Jiangnan University, Wuxi, China,International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, China
| | - Mengfan Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yingqi Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Fengzhen Han
- Department of Gynaecology and Obsterics, Guangdong Province People’s Hospital, Guangdong Academy of Medical Science, Guangzhou, China
| | - Chunyan Yang
- Department of Gynaecology and Obsterics, Guangdong Province People’s Hospital, Guangdong Academy of Medical Science, Guangzhou, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China,School of Food Science and Technology, Jiangnan University, Wuxi, China,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Patrice Malard
- Biostime (Guangzhou) Health Products Ltd., Guangzhou, China
| | - Catherine Stanton
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, China,Food Bioscience, Teagasc Food Research Centre, Fermoy, Ireland,CONTACT Catherine Stanton Teagasc Food Research Centre, Fermoy, Ireland
| | - R. Paul Ross
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, China,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China,School of Food Science and Technology, Jiangnan University, Wuxi, China,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China,Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China,School of Food Science and Technology, Jiangnan University, Wuxi, China,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China,Wei Chen School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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7
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Li Z, Song Q, Wang M, Ren J, Liu S, Zhao S. Comparative genomics analysis of Pediococcus acidilactici species. J Microbiol 2021; 59:573-583. [PMID: 33990913 DOI: 10.1007/s12275-021-0618-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/05/2021] [Accepted: 02/23/2021] [Indexed: 01/24/2023]
Abstract
Pediococcus acidilactici is a reliable bacteriocin producer and a promising probiotic species with wide application in the food and health industry. However, the underlying genetic features of this species have not been analyzed. In this study, we performed a comprehensive comparative genomic analysis of 41 P. acidilactici strains from various ecological niches. The bacteriocin production of 41 strains were predicted and three kinds of bacteriocin encoding genes were identified in 11 P. acidilactici strains, namely pediocin PA-1, enterolysin A, and colicin-B. Moreover, whole-genome analysis showed a high genetic diversity within the population, mainly related to a large proportion of variable genomes, mobile elements, and hypothetical genes obtained through horizontal gene transfer. In addition, comparative genomics also facilitated the genetic explanation of the adaptation for host environment, which specify the protection mechanism against the invasion of foreign DNA (i.e. CRISPR/Cas locus), as well as carbohydrate fermentation. The 41 strains of P. acidilactici can metabolize a variety of carbon sources, which enhances the adaptability of this species and survival in different environments. This study evaluated the antibacterial ability, genome evolution, and ecological flexibility of P. acidilactici from the perspective of genetics and provides strong supporting evidence for its industrial development and application.
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Affiliation(s)
- Zhenzhen Li
- BGI College, Zhengzhou University, Zhengzhou, 450052, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Qi Song
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
- Key Laboratory of Genomics, Ministry of Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Mingming Wang
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Junli Ren
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Songling Liu
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
- Key Laboratory of Genomics, Ministry of Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Shancen Zhao
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China.
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8
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Virgínio Júnior GF, Coelho MG, de Toledo AF, Montenegro H, Coutinho LL, Bittar CMM. The Liquid Diet Composition Affects the Fecal Bacterial Community in Pre-weaning Dairy Calves. FRONTIERS IN ANIMAL SCIENCE 2021. [DOI: 10.3389/fanim.2021.649468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Feeding a liquid diet to the newborn calf has considerable implications for developing the intestinal microbiota, as its composition can shift the population to a highly adapted microbiota. The present work evaluated 15 Holstein calves individually housed and fed one of the three liquid diets: I – whole milk (n = 5), II – milk replacer (22.9% CP; 16.2% fat; diluted to 14% solids; n = 5) and III – acidified whole milk to pH 4.5 with formic acid (n = 5). All animals received 6 L of liquid diet, divided into two meals, being weaned at week 8 of life. Calves also had free access to water and starter concentrate. After weaning, all calves were grouped on pasture, fed with starter concentrate, and hay ad libitum. The fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8, and 10 of life. The bacterial community was assessed the through sequencing of the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform and analyzed using the DADA2 pipeline. Diversity indices were not affected by the liquid diets, but by age (P < 0.001) with weeks 1 and 2 presenting lower diversity, evenness, and richness values. The bacterial community structure was affected by diet, age, and the interaction of these factors (P < 0.01). Twenty-eight bacterial phyla were identified in the fecal samples, and the most predominant phyla were Firmicutes (42.35%), Bacteroidota (39.37%), and Proteobacteria (9.36%). The most prevalent genera were Bacteroides (10.71%), Lactobacillus (8.11%), Alloprevotella (6.20%). Over the weeks, different genera were predominant, with some showing significant differences among treatments. The different liquid diets altered the fecal bacterial community during the pre-weaning period. However, differences in the initial colonization due to different liquid diets are alleviated after weaning, when animals share a common environment and solid diet composition.
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Berger K, Burleigh S, Lindahl M, Bhattacharya A, Patil P, Stålbrand H, Nordberg Karlsson E, Hållenius F, Nyman M, Adlercreutz P. Xylooligosaccharides Increase Bifidobacteria and Lachnospiraceae in Mice on a High-Fat Diet, with a Concomitant Increase in Short-Chain Fatty Acids, Especially Butyric Acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3617-3625. [PMID: 33724030 PMCID: PMC8041301 DOI: 10.1021/acs.jafc.0c06279] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Effects of xylooligosaccharides (XOSs) as well as a mixture of XOS, inulin, oligofructose, and partially hydrolyzed guar gum (MIX) in mice fed a high-fat diet (HFD) were studied. Control groups were fed an HFD or a low-fat diet. Special attention was paid to the cecal composition of the gut microbiota and formation of short-chain fatty acids, but metabolic parameters were also documented. The XOS group had significantly higher cecum levels of acetic, propionic, and butyric acids than the HFD group, and the butyric acid content was higher in the XOS than in the MIX group. The cecum microbiota of the XOS group contained more Bifidobacteria, Lachnospiraceae, and S24-7 bacteria than the HFD group. A tendency of lower body weight gain was observed on comparing the XOS and HFD groups. In conclusion, the XOS was shown to be a promising prebiotic candidate. The fiber diversity in the MIX diet did not provide any advantages compared to the XOS diet.
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Affiliation(s)
- Karin Berger
- Department
of Experimental Medical Science, Lund University, P.O. Box 188, SE-221 00 Lund, Sweden
| | - Stephen Burleigh
- Department
of Food Technology, Engineering and Nutrition, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Maria Lindahl
- Department
of Experimental Medical Science, Lund University, P.O. Box 188, SE-221 00 Lund, Sweden
| | - Abhishek Bhattacharya
- Division
of Biochemistry and Structural Biology, Department of Chemistry, Lund University, P.O.
Box 124, SE-221 00 Lund, Sweden
| | - Prachiti Patil
- Department
of Food Technology, Engineering and Nutrition, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Henrik Stålbrand
- Division
of Biochemistry and Structural Biology, Department of Chemistry, Lund University, P.O.
Box 124, SE-221 00 Lund, Sweden
| | - Eva Nordberg Karlsson
- Division
of Biotechnology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Frida Hållenius
- Department
of Food Technology, Engineering and Nutrition, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Margareta Nyman
- Department
of Food Technology, Engineering and Nutrition, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Patrick Adlercreutz
- Division
of Biotechnology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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Inulin Fermentation by Lactobacilli and Bifidobacteria from Dairy Calves. Appl Environ Microbiol 2020; 87:AEM.01738-20. [PMID: 33008824 DOI: 10.1128/aem.01738-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022] Open
Abstract
Prebiotics are increasingly examined for their ability to modulate the neonate gut microbiota of livestock, and products such as inulin are commonly added to milk replacer used in calving. However, the ability of specific members of the bovine neonate microbiota to respond to inulin remains to be determined, particularly among indigenous lactobacilli and bifidobacteria, beneficial genera commonly enriched by inulin. Screening of Bifidobacterium and Lactobacillus isolates obtained from fresh feces of dairy calves revealed that lactobacilli had a higher prevalence of inulin fermentation capacity (58%) than bifidobacteria (17%). Several Ligilactobacillus agilis (synonym Lactobacillus agilis) isolates exhibited vigorous growth on, and complete degradation of, inulin; however, the phenotype was strain specific. The most vigorous inulin-fermenting strain, L. agilis YZ050, readily degraded long-chain inulin not consumed by bifidobacterial isolates. Comparative genomic analysis of both L. agilis fermenter and nonfermenter strains indicated that strain YZ050 encodes an inulinase homolog, previously linked to extracellular degradation of long-chain inulin in Lacticaseibacillus paracasei, that was strongly induced during growth on inulin. Inulin catabolism by YZ050 also generates extracellular fructose, which can cross-feed other non-inulin-fermenting lactic acid bacteria isolated from the same bovine feces. The presence of specific inulin-responsive bacterial strains within calf gut microbiome provides a mechanistic rationale for enrichment of specific lactobacilli and creates a foundation for future synbiotic applications in dairy calves aimed at improving health in early life.IMPORTANCE The gut microbiome plays an important role in animal health and is increasingly recognized as a target for diet-based manipulation. Inulin is a common prebiotic routinely added to animal feeds; however, the mechanism of inulin consumption by specific beneficial taxa in livestock is ill defined. In this study, we examined Lactobacillus and Bifidobacterium isolates from calves fed inulin-containing milk replacer and characterized specific strains that robustly consume long-chain inulin. In particular, novel Ligilactobacillus agilis strain YZ050 consumed inulin via an extracellular fructosidase, resulting in complete consumption of all long-chain inulin. Inulin catabolism resulted in temporal release of extracellular fructose, which can promote growth of other non-inulin-consuming strains of lactic acid bacteria. This work provides the mechanistic insight needed to purposely modulate the calf gut microbiome via the establishment of networks of beneficial microbes linked to specific prebiotics.
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Silva N, Phythian CJ, Currie C, Tassi R, Ballingall KT, Magro G, McNeilly TN, Zadoks RN. Antimicrobial resistance in ovine bacteria: A sheep in wolf's clothing? PLoS One 2020; 15:e0238708. [PMID: 32881949 PMCID: PMC7470381 DOI: 10.1371/journal.pone.0238708] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/21/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND To monitor the prevalence of antimicrobial resistance (AMR), methods for interpretation of susceptibility phenotypes of bacteria are needed. Reference limits to declare resistance are generally based on or dominated by data from human bacterial isolates and may not reflect clinical relevance or wild type (WT) populations in livestock or other hosts. METHODS We compared the observed prevalence of AMR using standard and bespoke interpretations based on clinical breakpoints or epidemiological cut-offs (ECOFF) using gram positive (Staphylococcus aureus) and gram negative (Escherichia coli) bacteria from sheep as exemplars. Isolates were obtained from a cross-sectional study in three lowland sheep flocks in Scotland, and from a longitudinal study in one flock in Norway. S. aureus (n = 101) was predominantly isolated from milk or mammary glands whilst E. coli (n = 103) was mostly isolated from faecal samples. Disc diffusion testing was used to determine inhibition zone diameters, which were interpreted using either clinical breakpoints or ECOFF, which distinguish the bacterial wild type population from bacteria with acquired or mutational resistance to the compound of interest (non-wild type). Standard ECOFF values were considered as well as sheep-specific values calculated from the data using Normalized Resistance Interpretation (NRI) methodology. RESULTS The prevalence of AMR as measured based on clinical breakpoints was low, e.g. 4.0% for penicillin resistance in S. aureus. Estimation of AMR prevalence based on standard ECOFFs was hampered by lack of relevant reference values. In addition, standard ECOFFS, which are predominantly based on human data, bisected the normal distribution of inhibition zone diameters for several compounds in our analysis of sheep isolates. This contravenes recommendations for ECOFF setting based on NRI methodology and may lead to high apparent AMR prevalence. Using bespoke ECOFF values based on NRI, S. aureus showed non-wild type for less than 4% of isolates across 13 compounds, and ca. 13% non-wild type for amoxicillin and ampicillin, while E. coli showed non-wild type for less than 3% of isolates across 12 compounds, and ca. 13% non-wild type for tetracyclines and sulfamethoxazole-trimethoprim. CONCLUSION The apparent prevalence of AMR in bacteria isolated from sheep is highly dependent on interpretation criteria. The sheep industry may want to establish bespoke cut-off values for AMR monitoring to avoid the use of cut-offs developed for other host species. The latter could lead to high apparent prevalence of resistance, including to critically important antimicrobial classes such as 4th generation cephalosporins and carbapenems, suggesting an AMR problem that may not actually exist.
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Affiliation(s)
- Nuno Silva
- Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom
| | - Clare J. Phythian
- Institute for Production Animal Clinical Science, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Sandnes, Norway
| | - Carol Currie
- Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom
| | - Riccardo Tassi
- Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom
| | - Keith T. Ballingall
- Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom
| | - Giada Magro
- Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom
| | - Tom N. McNeilly
- Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom
| | - Ruth N. Zadoks
- Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, Australia
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12
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Jaglan N, Kumar S, Choudhury PK, Tyagi B, Tyagi AK. Isolation, characterization and conjugated linoleic acid production potential of bifidobacterial isolates from ruminal fluid samples of Murrah buffaloes. Anaerobe 2019; 56:40-45. [PMID: 30738138 DOI: 10.1016/j.anaerobe.2019.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/24/2019] [Accepted: 02/05/2019] [Indexed: 12/12/2022]
Abstract
In the present study, we investigated the potential of Bifidobacterium spp., isolated from ruminal fluid samples from buffaloes (Bubalus bubalis) for conjugated linoleic acid (CLA) production. A total of 294 isolates were obtained from 86 ruminal fluid samples using Bifidus Selective Medium (BSM) medium, and based on phospoketolase assay, 24 isolates were presumptively confirmed to be Bifidobacterium species. Further, the isolates were confirmed morphologically, biochemically and by PCR assays for genus specific (16s rDNA) and transaldolase genes. All 24 strains were positive for conversion of linoleic acid (LA) to CLA by spectrophotometric screening. Gas chromatographic analysis showed that the strains produced cis9, trans11 and tran10, cis12 CLA isomers in LA-supplemented deMan-Rogosa-Sharpe (MRS) broth. The strains were identified as B. thermophilum (n = 21) and B. pseudolongum (n = 3) based on 16 rDNA sequence analysis. The study shows that Bifidobacterium spp., present in the rumens of buffaloes produce CLA from LA and the strains may have the potential to be used as probiotics to enhance the nutraceutical value of ruminant food products.
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Affiliation(s)
- Neeru Jaglan
- Animal Nutrition Division, Indian Council of Agricultural Research - National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Sachin Kumar
- Animal Nutrition Division, Indian Council of Agricultural Research - National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Prasanta Kumar Choudhury
- Animal Nutrition Division, Indian Council of Agricultural Research - National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Bhawna Tyagi
- Animal Nutrition Division, Indian Council of Agricultural Research - National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Amrish Kumar Tyagi
- Animal Nutrition Division, Indian Council of Agricultural Research - National Dairy Research Institute, Karnal, 132001, Haryana, India.
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14
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Seddik H, Xu L, Wang Y, Mao SY. A rapid shift to high-grain diet results in dynamic changes in rumen epimural microbiome in sheep. Animal 2018; 13:1614-1622. [PMID: 30560755 DOI: 10.1017/s1751731118003269] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The rapid shift to high-grain (HG) diets in ruminants can affect the function of the rumen epithelium, but the dynamic changes in the composition of the epithelium-associated (epimural) bacterial community in sheep still needs further investigation. Twenty male lambs were randomly allocated to four groups (n = 5). Animals of the first group received hay diet and represented a control group (CON). Simultaneously, animals in the other three groups (HG groups) were rapidly shifted to an HG diet (60% concentrate)which continued for 7 (HG7), 14 (HG14) and 28 (HG28) days, correspondingly. Results showed that ruminal pH dramatically decreased due to the rapid shift to the HG diet (P <0.001), while, the concentrations of butyrate (P <0.001), lactate (P = 0.001), valerate (P = 0.008) and total volatile fatty acids (P = 0.001) increased. Diversity estimators showed a dramatic decrease after the shift without recovering as the HG feeding continued. The principal coordinates analysis showed that CON group clustered separately from all HG groups with the presence of significant difference only between HG7 and HG28 (P = 0.034). The non-parametric multivariate analysis (npmv R-package) deduced that the primary significant differences in phyla and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt)-predicted Kyoto Encyclopedia of Genes and Genomes (KEGGs) was attributed mainly to the diet composition (P <0.001, P = 0.001) compared to its application period (P = 0.140, 0.545) which showed a significant effect only on the genus (P = 0.001) and the operational taxonomic units (OTUs) level (P = 0.011). The Kruskal-Wallis test deduced that six phyla showed a significant effect due to the shift in diet composition. At the genus level, HG feeding altered the abundance of 12 taxa, four of which showed a significant variation due to the duration of the HG diet application. Similarly, we found that 21 OTUs showed significant variations due to the duration of the HG diet application. Furthermore, the genes abundance predicted by PICRUSt revealed that the HG feeding significantly affected seven metabolic pathways identified in the KEGG. Particularly, the abundance of gene families associated with carbohydrates metabolism were significantly higher in HG feeding groups (P = 0.027). Collectively, these results revealed that the rapid transition to an HG diet causes dramatic alterations in ruminal fermentation and the composition and function of ruminal epithelium-associated microbiome in sheep, while, the duration of the HG diet application causes drastic alterations to the abundance of some species.
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Affiliation(s)
- H Seddik
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health,Laboratory of Gastrointestinal Microbiology,College of Animal Science and Technology,Nanjing Agricultural University,Nanjing 210095,Jiangsu Province,China
| | - L Xu
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health,Laboratory of Gastrointestinal Microbiology,College of Animal Science and Technology,Nanjing Agricultural University,Nanjing 210095,Jiangsu Province,China
| | - Y Wang
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health,Laboratory of Gastrointestinal Microbiology,College of Animal Science and Technology,Nanjing Agricultural University,Nanjing 210095,Jiangsu Province,China
| | - S Y Mao
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health,Laboratory of Gastrointestinal Microbiology,College of Animal Science and Technology,Nanjing Agricultural University,Nanjing 210095,Jiangsu Province,China
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15
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Ru X, Zhang CC, Yuan YH, Yue TL, Guo CF. Bile salt hydrolase activity is present in nonintestinal lactic acid bacteria at an intermediate level. Appl Microbiol Biotechnol 2018; 103:893-902. [PMID: 30421106 DOI: 10.1007/s00253-018-9492-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 09/05/2018] [Accepted: 10/29/2018] [Indexed: 01/04/2023]
Abstract
It is generally considered that bile salt hydrolase (BSH) activity is hardly detected in nonintestinal lactic acid bacteria (LAB). The aim of this study was to investigate the distribution and intensity of BSH activity in LAB isolated from naturally fermented vegetables and milk. A total of 624 lactic acid bacterial strains classified into 6 genera and 50 species were isolated from 144 naturally fermented vegetable samples and 103 naturally fermented milk samples, and their BSH activity was screened by gas chromatography with electron capture detection. The BSH-positive strains were further analyzed quantitatively for their deconjugation ability against six human-conjugated bile salts by HPLC based on the disappearance of the conjugated bile salts from the reaction mixture. The results showed that 39% of the strains possessed BSH activity distributed in 24 lactic acid bacterial species. The strains of the fermented vegetable origin showed a 0.5-fold higher incidence of BSH-positive strains than those of the fermented milk origin, and the lactic acid bacilli exhibited 2.5-fold higher incidence of BSH-positive strains than the lactic acid cocci in general. The strains of the fermented vegetable origin generally had greater bile salt deconjugation ability than those of the fermented milk origin. More than 97% and 93% of the BSH-positive strains exhibited a greater substrate preference for glycoconjugated bile salts than tauroconjugated bile salts and for dihydroxy bile salts than trihydroxy bile salts, respectively. This study demonstrated that BSH activity was also present in nonintestinal LAB.
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Affiliation(s)
- Xiao Ru
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China
| | - Chuang-Chuang Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China
| | - Ya-Hong Yuan
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China
| | - Tian-Li Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China
| | - Chun-Feng Guo
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China.
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16
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Mathew S, Aronsson A, Karlsson EN, Adlercreutz P. Xylo- and arabinoxylooligosaccharides from wheat bran by endoxylanases, utilisation by probiotic bacteria, and structural studies of the enzymes. Appl Microbiol Biotechnol 2018; 102:3105-3120. [DOI: 10.1007/s00253-018-8823-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/16/2018] [Accepted: 01/20/2018] [Indexed: 01/02/2023]
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17
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Arboleya S, Bottacini F, O'Connell-Motherway M, Ryan CA, Ross RP, van Sinderen D, Stanton C. Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains. BMC Genomics 2018; 19:33. [PMID: 29310579 PMCID: PMC5759876 DOI: 10.1186/s12864-017-4388-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 12/15/2017] [Indexed: 12/15/2022] Open
Abstract
Background Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B. longum strains, most of which had previously been isolated from infants, by performing whole genome sequencing and comparative analysis, and to analyse their carbohydrate utilization abilities using a gene-trait matching approach. Results We analysed their pan-genome and their phylogenetic relatedness. All strains clustered in the B. longum ssp. longum phylogenetic subgroup, except for one individual strain which was found to cluster in the B. longum ssp. suis phylogenetic group. The examined strains exhibit genomic diversity, while they also varied in their sugar utilization profiles. This allowed us to perform a gene-trait matching exercise enabling the identification of five gene clusters involved in the utilization of xylo-oligosaccharides, arabinan, arabinoxylan, galactan and fucosyllactose, the latter of which is an abundant human milk oligosaccharide (HMO). Conclusions The results showed high diversity in terms of genes and predicted glycosyl-hydrolases, as well as the ability to metabolize a large range of sugars. Moreover, we corroborate the capability of B. longum ssp. longum to metabolise HMOs. Ultimately, their intraspecific genomic diversity and the ability to consume a wide assortment of carbohydrates, ranging from plant-derived carbohydrates to HMOs, may provide an explanation for the competitive advantage and persistence of B. longum in the human gut microbiome. Electronic supplementary material The online version of this article (10.1186/s12864-017-4388-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Silvia Arboleya
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.,Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares, Villaviciosa, Asturias, Spain
| | - Francesca Bottacini
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Mary O'Connell-Motherway
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - C Anthony Ryan
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Institute, University College Cork, Cork, Ireland. .,Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.
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18
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Hidalgo-Cantabrana C, Crawley AB, Sanchez B, Barrangou R. Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum. Front Microbiol 2017; 8:1851. [PMID: 29033911 PMCID: PMC5626976 DOI: 10.3389/fmicb.2017.01851] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/11/2017] [Indexed: 12/18/2022] Open
Abstract
Diverse CRISPR-Cas systems provide adaptive immunity in many bacteria and most archaea, via a DNA-encoded, RNA-mediated, nucleic-acid targeting mechanism. Over time, CRISPR loci expand via iterative uptake of invasive DNA sequences into the CRISPR array during the adaptation process. These genetic vaccination cards thus provide insights into the exposure of strains to phages and plasmids in space and time, revealing the historical predatory exposure of a strain. These genetic loci thus constitute a unique basis for genotyping of strains, with potential of resolution at the strain-level. Here, we investigate the occurrence and diversity of CRISPR-Cas systems in the genomes of various Bifidobacterium longum strains across three sub-species. Specifically, we analyzed the genomic content of 66 genomes belonging to B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis, and identified 25 strains that carry 29 total CRISPR-Cas systems. We identify various Type I and Type II CRISPR-Cas systems that are widespread in this species, notably I-C, I-E, and II-C. Noteworthy, Type I-C systems showed extended CRISPR arrays, with extensive spacer diversity. We show how these hypervariable loci can be used to gain insights into strain origin, evolution and phylogeny, and can provide discriminatory sequences to distinguish even clonal isolates. By investigating CRISPR spacer sequences, we reveal their origin and implicate phages and prophages as drivers of CRISPR immunity expansion in this species, with redundant targeting of select prophages. Analysis of CRISPR spacer origin also revealed novel PAM sequences. Our results suggest that CRISPR-Cas immune systems are instrumental in mounting diversified viral resistance in B. longum, and show that these sequences are useful for typing across three subspecies.
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Affiliation(s)
- Claudio Hidalgo-Cantabrana
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, IPLA-CSIC, Villaviciosa, Spain
| | - Alexandra B. Crawley
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Borja Sanchez
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, IPLA-CSIC, Villaviciosa, Spain
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
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20
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Cookson AL, Biggs PJ, Marshall JC, Reynolds A, Collis RM, French NP, Brightwell G. Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure. Sci Rep 2017; 7:841. [PMID: 28404985 PMCID: PMC5429811 DOI: 10.1038/s41598-017-00890-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/16/2017] [Indexed: 01/09/2023] Open
Abstract
Current culture methods to investigate changes in Escherichia coli community structure are often slow and laborious. Genes such as gnd (6-phosphogluconate dehydrogenase) have a highly variable nucleotide sequence and may provide a target for E. coli microbiome analysis using culture-independent methods. Metabarcoded PCR primers were used to generate separate libraries from calf faecal samples for high throughput sequencing. Although a total of 348 separate gnd sequence types (gSTs) were identified, 188 were likely to be due to sequencing errors. Of the remaining 160 gSTs, 92 did not match those in a database of 319 separate gnd sequences. ‘Animal’ was the main determinant of E. coli diversity with limited impact of sample type or DNA extraction method on intra-host E. coli community variation from faeces and recto-anal mucosal swab samples. This culture-independent study has addressed the difficulties of quantifying bacterial intra-species diversity and revealed that, whilst individual animals may harbour >50 separate E. coli strains, communities are dominated by <10 strains alongside a large pool of subdominant strains present at low abundances. This method will be useful for characterising the diversity and population structure of E. coli in experimental studies designed to assess the impact of interventions on the gut microbiome.
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Affiliation(s)
- Adrian L Cookson
- AgResearch Limited, Hopkirk Research Institute, Palmerston North, New Zealand. .,mEpiLab, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand.
| | - Patrick J Biggs
- mEpiLab, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand.,Massey Genome Service, New Zealand Genomics Limited, Massey University, Palmerston North, New Zealand
| | - Jonathan C Marshall
- mEpiLab, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand.,Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Angela Reynolds
- AgResearch Limited, Hopkirk Research Institute, Palmerston North, New Zealand
| | - Rose M Collis
- AgResearch Limited, Hopkirk Research Institute, Palmerston North, New Zealand
| | - Nigel P French
- mEpiLab, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Gale Brightwell
- AgResearch Limited, Hopkirk Research Institute, Palmerston North, New Zealand
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