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Meene A, Gierse L, Schwaiger T, Karte C, Schröder C, Höper D, Wang H, Groß V, Wünsche C, Mücke P, Kreikemeyer B, Beer M, Becher D, Mettenleiter TC, Riedel K, Urich T. Archaeome structure and function of the intestinal tract in healthy and H1N1 infected swine. Front Microbiol 2023; 14:1250140. [PMID: 37779690 PMCID: PMC10534045 DOI: 10.3389/fmicb.2023.1250140] [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: 06/29/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
Background Methanogenic archaea represent a less investigated and likely underestimated part of the intestinal tract microbiome in swine. Aims/Methods This study aims to elucidate the archaeome structure and function in the porcine intestinal tract of healthy and H1N1 infected swine. We performed multi-omics analysis consisting of 16S rRNA gene profiling, metatranscriptomics and metaproteomics. Results and discussion We observed a significant increase from 0.48 to 4.50% of archaea in the intestinal tract microbiome along the ileum and colon, dominated by genera Methanobrevibacter and Methanosphaera. Furthermore, in feces of naïve and H1N1 infected swine, we observed significant but minor differences in the occurrence of archaeal phylotypes over the course of an infection experiment. Metatranscriptomic analysis of archaeal mRNAs revealed the major methanogenesis pathways of Methanobrevibacter and Methanosphaera to be hydrogenotrophic and methyl-reducing, respectively. Metaproteomics of archaeal peptides indicated some effects of the H1N1 infection on central metabolism of the gut archaea. Conclusions/Take home message Finally, this study provides the first multi-omics analysis and high-resolution insights into the structure and function of the porcine intestinal tract archaeome during a non-lethal Influenza A virus infection of the respiratory tract, demonstrating significant alterations in archaeal community composition and central metabolic functions.
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Affiliation(s)
- Alexander Meene
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Laurin Gierse
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | | | | | - Dirk Höper
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Haitao Wang
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Verena Groß
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christine Wünsche
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Pierre Mücke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Bernd Kreikemeyer
- Institute for Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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2
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Feehan B, Ran Q, Dorman V, Rumback K, Pogranichniy S, Ward K, Goodband R, Niederwerder MC, Lee STM. Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea. Anim Microbiome 2023; 5:35. [PMID: 37461084 DOI: 10.1186/s42523-023-00256-6] [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: 01/16/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination. RESULTS We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.
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Affiliation(s)
- Brandi Feehan
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Qinghong Ran
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Victoria Dorman
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kourtney Rumback
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Sophia Pogranichniy
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kaitlyn Ward
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Robert Goodband
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Sonny T M Lee
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA.
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3
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Metzler-Zebeli BU, Lerch F, Yosi F, Vötterl J, Ehmig J, Koger S, Verhovsek D. Temporal Microbial Dynamics in Feces Discriminate by Nutrition, Fecal Color, Consistency and Sample Type in Suckling and Newly Weaned Piglets. Animals (Basel) 2023; 13:2251. [PMID: 37508029 PMCID: PMC10376145 DOI: 10.3390/ani13142251] [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: 06/06/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Feces enable frequent samplings for the same animal, which is valuable in studies investigating the development of the gut microbiome in piglets. Creep feed should prepare the piglet's gut for the postweaning period and shape the microbiome accordingly. Little is known about the variation that is caused by differences in fecal color and consistency and different sample types (feces versus swab samples). Therefore, this study evaluated the age-related alterations in the microbiome composition (16S rRNA gene) in feces of suckling and newly weaned piglets in the context of nutrition and fecal consistency, color and sample type from day 2 to 34 of life. Feces from 40 healthy piglets (2 each from 20 litters) were collected on days 2, 6, 13, 20, 27, 30 and 34. Weaning occurred on day 28. Half of the litters only drank sow milk during the suckling phase, whereas the other half had access to creep feed from day 10. Creep feeding during the suckling phase influenced the age-related total bacterial and archaeal abundances but had less of an influence on the relative bacterial composition. Results further showed different taxonomic compositions in feces of different consistency, color and sample type, emphasizing the need to consider these characteristics in comprehensive microbiome studies.
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Affiliation(s)
- Barbara U Metzler-Zebeli
- Unit Nutritional Physiology, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
- Christian-Doppler Laboratory for Innovative Gut Health Concepts of Livestock, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Frederike Lerch
- Unit Nutritional Physiology, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
- Christian-Doppler Laboratory for Innovative Gut Health Concepts of Livestock, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Fitra Yosi
- Unit Nutritional Physiology, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
- Christian-Doppler Laboratory for Innovative Gut Health Concepts of Livestock, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
- Department of Animal Science, Faculty of Agriculture, University of Sriwijaya, Palembang 30662, Indonesia
| | - Julia Vötterl
- Unit Nutritional Physiology, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
- Christian-Doppler Laboratory for Innovative Gut Health Concepts of Livestock, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Juliane Ehmig
- Unit Nutritional Physiology, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
- Christian-Doppler Laboratory for Innovative Gut Health Concepts of Livestock, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Simone Koger
- Christian-Doppler Laboratory for Innovative Gut Health Concepts of Livestock, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Doris Verhovsek
- University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
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4
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Feehan B, Ran Q, Dorman V, Rumback K, Pogranichniy S, Ward K, Goodband R, Niederwerder MC, Summers KL, Lee STM. Stability and volatility shape the gut bacteriome and Kazachstania slooffiae dynamics in preweaning, nursery and adult pigs. Sci Rep 2022; 12:15080. [PMID: 36064754 PMCID: PMC9445069 DOI: 10.1038/s41598-022-19093-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
The gut microbiome plays important roles in the maintenance of health and pathogenesis of diseases in the growing host. In order to fully comprehend the interplay of the gut microbiome and host, a foundational understanding of longitudinal microbiome, including bacteria and fungi, development is necessary. In this study, we evaluated enteric microbiome and host dynamics throughout the lifetime of commercial swine. We collected a total of 234 fecal samples from ten pigs across 31 time points in three developmental stages (5 preweaning, 15 nursery, and 11 growth adult). We then performed 16S rRNA gene amplicon sequencing for bacterial profiles and qPCR for the fungus Kazachstania slooffiae. We identified distinct bacteriome clustering according to the host developmental stage, with the preweaning stage exhibiting low bacterial diversity and high volatility amongst samples. We further identified clusters of bacteria that were considered core, increasing, decreasing or stage-associated throughout the host lifetime. Kazachstania slooffiae was absent in the preweaning stage but peaked during the nursery stage of the host. We determined that all host growth stages contained negative correlations between K. slooffiae and bacterial genera, with only the growth adult stage containing positive correlates. Our stage-associated bacteriome results suggested the neonate contained a volatile gut microbiome. Upon weaning, the microbiome became relatively established with comparatively fewer perturbations in microbiome composition. Differential analysis indicated bacteria might play distinct stage-associated roles in metabolism and pathogenesis. The lack of positive correlates and shared K. slooffiae-bacteria interactions between stages warranted future research into the interactions amongst these kingdoms for host health. This research is foundational for understanding how bacteria and fungi develop singularly, as well as within a complex ecosystem in the host's gut environment.
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Affiliation(s)
- Brandi Feehan
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Qinghong Ran
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Victoria Dorman
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kourtney Rumback
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Sophia Pogranichniy
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kaitlyn Ward
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Robert Goodband
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, 66506, USA
| | - Megan C Niederwerder
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.,Swine Health Information Center, Ames, IA, 50010, USA
| | - Katie Lynn Summers
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Center, United States Department of Agriculture, Beltsville, MD, 20705, USA
| | - Sonny T M Lee
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA.
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5
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Xiong X, Rao Y, Tu X, Wang Z, Gong J, Yang Y, Wu H, Liu X. Gut archaea associated with bacteria colonization and succession during piglet weaning transitions. BMC Vet Res 2022; 18:243. [PMID: 35751084 PMCID: PMC9229118 DOI: 10.1186/s12917-022-03330-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/27/2022] [Indexed: 11/10/2022] Open
Abstract
Background Host-associated gut microbial communities are key players in shaping the fitness and health of animals. However, most current studies have focused on the gut bacteria, neglecting important gut fungal and archaeal components of these communities. Here, we investigated the gut fungi and archaea community composition in Large White piglets using shotgun metagenomic sequencing, and systematically evaluated how community composition association with gut microbiome, functional capacity, and serum metabolites varied across three weaning periods. Results We found that Mucoromycota, Ascomycota and Basidiomycota were the most common fungi phyla and Euryarchaeota was the most common archaea phyla across individuals. We identified that Methanosarcina siciliae was the most significantly different archaea species among three weaning periods, while Parasitella parasitica, the only differential fungi species, was significantly and positively correlated with Methanosarcina siciliae enriched in day 28 group. The random forest analysis also identified Methanosarcina siciliae and Parasitella parasitica as weaning-biased archaea and fungi at the species level. Additionally, Methanosarcina siciliae was significantly correlated with P. copri and the shifts of functional capacities of the gut microbiome and several CAZymes in day 28 group. Furthermore, characteristic successional alterations in gut archaea, fungi, bacteria, and serum metabolites with each weaning step revealed a weaning transition coexpression network, e.g., Methanosarcina siciliae and P. copri were positively and significantly correlated with 15-HEPE, 8-O-Methyloblongine, and Troxilin B3. Conclusion Our findings provide a deep insight into the interactions among gut archaea, fungi, bacteria, and serum metabolites and will present a theoretical framework for understanding gut bacterial colonization and succession association with archaea during piglet weaning transitions. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03330-4.
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Affiliation(s)
- Xinwei Xiong
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China.
| | - Yousheng Rao
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Xutang Tu
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Zhangfeng Wang
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Jishang Gong
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Yanbei Yang
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Haobin Wu
- Institute of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, 330032, People's Republic of China
| | - Xianxian Liu
- Key Laboratory of Women's Reproductive Health of Jiangxi, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi, 330006, People's Republic of China.
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6
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Deng F, Peng Y, Zhang Z, Howe S, Wu Z, Dou J, Li Y, Wei X, Wang X, Liang Y, Zhao J, Li Y. Weaning Time Affects the Archaeal Community Structure and Functional Potential in Pigs. Front Microbiol 2022; 13:845621. [PMID: 35387077 PMCID: PMC8979004 DOI: 10.3389/fmicb.2022.845621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/28/2022] [Indexed: 12/02/2022] Open
Abstract
Archaea are considered a “keystone” of the gut microbiome and are linked with the host’s energy harvest and health. Although a few studies have investigated the gut archaea in pigs, especially piglets, little is known about the effects of weaning on archaeal structure and function. In this study, we explored the effects of weaning on the longitudinal changes of archaeal composition, diversity, and functional potential in pigs overtime by re-analyzing a recently published metagenomic dataset that included 176 fecal samples collected from commercial pigs on days 7, 14, 21, 28, 35, 70, and 140 after birth. Overall, the richness and diversity of archaeal species showed an increasing trend, and weaning significantly affected the richness of archaeal species. Methanobrevibacter A smithii significantly decreased and was replaced by Methanobrevibacter A sp900769095 within 2 weeks after weaning. For the functional potential, the richness of KEGG KOs increased over time. LEfSe analysis identified 18 KOs, including for example, ko04623 (cytosolic DNA-sensing pathway), ko00500 (starch and sucrose metabolism), and so on, significantly enriched in the weaning pigs, suggesting the involvement of archaea in the piglets’ adaptation to the new diet after weaning. Correlation analysis based on Random Forest regression and Pearson correlation showed that archaeal species richness was significantly associated with pig bodyweight on both days 70 and 140. Methanobrevibacter A sp900769095 (R = 0.405, p = 0.040) and Methanobrevibacter A smithii (R = 0.535, p = 0.004) were positively linked with pigs’ bodyweight on days 70 and 140, respectively. Our results revealed the dynamic changes of archaeal diversity and functions and demonstrated the effects of weaning on the gut archaea of pigs, suggesting archaea might play essential roles in swine nutrition, metabolism, and growth performance, especially during the critical weaning process.
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Affiliation(s)
- Feilong Deng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,School of Life Science and Engineering, Foshan University, Foshan, China
| | - Yunjuan Peng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,School of Life Science and Engineering, Foshan University, Foshan, China
| | - Zhihao Zhang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,School of Life Science and Engineering, Foshan University, Foshan, China
| | - Samantha Howe
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Zhuosui Wu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,School of Life Science and Engineering, Foshan University, Foshan, China
| | - Jieying Dou
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,School of Life Science and Engineering, Foshan University, Foshan, China
| | - Yuling Li
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Xiaoyuan Wei
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Xiaofan Wang
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Yong Liang
- Institute of Systems Engineering, Macau University of Science and Technology, Macau, China.,The Peng Cheng Laboratory, Shenzhen, China
| | - Jiangchao Zhao
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,School of Life Science and Engineering, Foshan University, Foshan, China
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7
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The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs. Animals (Basel) 2021; 11:ani11072139. [PMID: 34359268 PMCID: PMC8300674 DOI: 10.3390/ani11072139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Archaea is identified as the key link in the interaction between gut microbiota and host metabo-lism. Studies on human and mice have reported archaea, especially methanogenic archaea, makes an important impact on the energy harvesting capacity of the host by improving fermentation. But, in pigs, the metabolic potential of archaea at different production stages are still largely unknown. Herein, we re-analyzed 276 metagenomic samples to explore the diversity, composi-tion, and potential functions of archaea in pigs. The results showed significant regional variations in archaeal composition. Furthermore, the Metacyc pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, and archaea may be involved in carbohydrate metabolism and de novo synthesis of some kinds of essential amino acid. Overall, metagenomic re-analysis revealed that the composition and functional potential of archaea in the swine gut and suggested that archaea may make an important function in pigs. Abstract Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (p < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray–Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32, 11.67, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.
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8
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Misiukiewicz A, Gao M, Filipiak W, Cieslak A, Patra AK, Szumacher-Strabel M. Review: Methanogens and methane production in the digestive systems of nonruminant farm animals. Animal 2020; 15:100060. [PMID: 33516013 DOI: 10.1016/j.animal.2020.100060] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 08/25/2020] [Accepted: 08/25/2020] [Indexed: 11/30/2022] Open
Abstract
The greenhouse gases (GHGs) derived from agriculture include carbon dioxide, nitrous oxide, and methane (CH4). Of these GHGs, CH4, in particular, constitutes a major component of the GHG emitted by the agricultural sector. Along with environmental concerns, CH4 emission also leads to losses in gross energy intake with economic implications. While ruminants are considered the main source of CH4 from agriculture, nonruminant animals also contribute substantially, and the CH4 emission intensity of nonruminants remains comparable to that of ruminants. Means of mitigating CH4 emissions from enteric fermentation have therefore been sought. Methane is produced by methanogens-archaeal microorganisms that inhabit the digestive tracts of animals and participate in fermentation processes. As the diversity of methanogen communities is thought to be responsible for the differences in CH4 production among nonruminant animals, it is necessary to investigate the archaeal composition of specific animal species. Methanogens play an important role in energy metabolism and adipose tissue deposition in animals. Higher abundances of methanogens, along with their higher diversity, have been reported to contribute to lean phenotype in pigs. In particular, a greater abundance of Methanosphaera spp. and early dominance of Methanobrevibacter smithii have been reported to correlate with lower body fat formation in pigs. Besides the contribution of methanogens to the metabolic phenotype of their hosts, CH4 release reduces the productivity that could be achieved through other hydrogen (H2) disposal pathways. Enhanced participation of acetogenesis in H2 disposal, leading to acetate formation, could be a more favorable direction for animal production and the environment. Better knowledge and understanding of the archaeal communities of the gastrointestinal tract (GIT), including their metabolism and interactions with other microorganisms, would thus allow the development of new strategies for inhibiting methanogens and shifting toward acetogenesis. There are a variety of approaches to inhibiting methanogens and mitigating methanogenesis in ruminants, which can find an application for nonruminants, such as nutritional changes through supplementation with biologically active compounds and management changes. We summarize the available reports and provide a comprehensive review of methanogens living in the GIT of various nonruminants, such as swine, horses, donkeys, rabbits, and poultry. This review will help in a better understanding of the populations and diversity of methanogens and the implications of their presence in nonruminant animals.
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Affiliation(s)
- A Misiukiewicz
- Department of Animal Nutrition, Poznań University of Life Sciences, Wołyńska 33, 60-637 Poznań, Poland
| | - M Gao
- Department of Animal Nutrition, Poznań University of Life Sciences, Wołyńska 33, 60-637 Poznań, Poland
| | - W Filipiak
- Department of Animal Nutrition, Poznań University of Life Sciences, Wołyńska 33, 60-637 Poznań, Poland
| | - A Cieslak
- Department of Animal Nutrition, Poznań University of Life Sciences, Wołyńska 33, 60-637 Poznań, Poland
| | - A K Patra
- Department of Animal Nutrition, West Bengal University of Animal and Fishery Sciences, Kolkata 700037, India
| | - M Szumacher-Strabel
- Department of Animal Nutrition, Poznań University of Life Sciences, Wołyńska 33, 60-637 Poznań, Poland.
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9
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Zeng Z, Zhang M, Kang D, Li Y, Yu T, Li W, Xu D, Zhang W, Shan S, Zheng P. Enhanced anaerobic treatment of swine wastewater with exogenous granular sludge: Performance and mechanism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 697:134180. [PMID: 32380626 DOI: 10.1016/j.scitotenv.2019.134180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 06/11/2023]
Abstract
Anaerobic biotechnology has been widely used to the treatment of swine wastewater, but its organic loading rate is far lower than the expected. In this study, the fatigue effect was observed for indigenous anaerobic sludge (IAS) of anaerobic digestion system treating swine wastewater. On the contrary, the enhancement effect was demonstrated for exogenous granular sludge (EGS) originated from the internal circulation reactor treating pulping wastewater. The results showed the anaerobic digestion of swine wastewater with acclimatized EGS was much better than with IAS, 10th-day COD removal efficiency of 85% and 37% respectively. The better performance of acclimatized EGS was attributed to the more efficient degradation of volatile fatty acids (VFAs) as well as a stronger tolerance to the ammonia inhibition of swine wastewater. Revealed by molecular techniques, the acclimatized EGS contained more abundant syntrophic bacteria and methanogens than IAS. These functional microbes colonized in the acclimatized EGS could overcome the fatigue effect of IAS which contained a similar microbial community to pig gastrointestinal tract microbes. This study provides a feasible and promising way to enhance the efficiency of anaerobic digestion of swine wastewater.
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Affiliation(s)
- Zhuo Zeng
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Meng Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China; Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore
| | - Da Kang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Yiyu Li
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Tao Yu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Wenji Li
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Dongdong Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Wudi Zhang
- School of Energy & Environmental Science, Yunnan Normal University, Kunming 650500, Yunnan, PR China
| | - Shengdao Shan
- School of Environmental and Natural Resources, Zhejiang University of Science & Technology, 318 Liuhe Rd, Hangzhou 310023, Zhejiang, PR China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China.
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10
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Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets. Microorganisms 2019; 7:microorganisms7090343. [PMID: 31547478 PMCID: PMC6780805 DOI: 10.3390/microorganisms7090343] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/13/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022] Open
Abstract
Dietary, environmental, and social stresses induced by weaning transition in pig production are associated with alterations of gut microbiota, diarrhea, and enteric infections. With the boom of -omic technologies, numerous studies have investigated the dynamics of fecal bacterial communities of piglets throughout weaning but much less research has been focused on the composition and functional properties of microbial communities inhabiting other gastrointestinal segments. The objective of the present study was to bring additional information about the piglet bacterial and archaeal microbiota throughout the entire digestive tract, both at the structural level by using quantitative PCR and high-throughput sequencing, and on functionality by measurement of short-chain fatty acids and predictions using Tax4Fun tool. Our results highlighted strong structural and functional differences between microbial communities inhabiting the fore and the lower gut as well as a quantitatively important archaeal community in the hindgut. The presence of opportunistic pathogens was also noticed throughout the entire digestive tract and could trigger infection emergence. Understanding the role of the intestinal piglet microbiota at weaning could provide further information about the etiology of post-weaning infections and lead to the development of effective preventive solutions.
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11
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Zwirzitz B, Pinior B, Metzler-Zebeli B, Handler M, Gense K, Knecht C, Ladinig A, Dzieciol M, Wetzels SU, Wagner M, Schmitz-Esser S, Mann E. Microbiota of the Gut-Lymph Node Axis: Depletion of Mucosa-Associated Segmented Filamentous Bacteria and Enrichment of Methanobrevibacter by Colistin Sulfate and Linco-Spectin in Pigs. Front Microbiol 2019; 10:599. [PMID: 31031713 PMCID: PMC6470194 DOI: 10.3389/fmicb.2019.00599] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 03/08/2019] [Indexed: 12/11/2022] Open
Abstract
Microorganisms are translocated from the gut to lymphatic tissues via immune cells, thereby challenging and training the mammalian immune system. Antibiotics alter the gut microbiome and consecutively might also affect the corresponding translocation processes, resulting in an imbalanced state between the intestinal microbiota and the host. Hence, understanding the variant effects of antibiotics on the microbiome of gut-associated tissues is of vital importance for maintaining metabolic homeostasis and animal health. In the present study, we analyzed the microbiome of (i) pig feces, ileum, and ileocecal lymph nodes under the influence of antibiotics (Linco-Spectin and Colistin sulfate) using 16S rRNA gene sequencing for high-resolution community profiling and (ii) ileocecal lymph nodes in more detail with two additional methodological approaches, i.e., cultivation of ileocecal lymph node samples and (iii) metatranscriptome sequencing of a single lymph node sample. Supplementation of medicated feed showed a local effect on feces and ileal mucosa-associated microbiomes. Pigs that received antibiotics harbored significantly reduced amounts of segmented filamentous bacteria (SFB) along the ileal mucosa (p = 0.048; 199.17-fold change) and increased amounts of Methanobrevibacter, a methanogenic Euryarchaeote in fecal samples (p = 0.005; 20.17-fold change) compared to the control group. Analysis of the porcine ileocecal lymph node microbiome exposed large differences between the viable and the dead fraction of microorganisms and the microbiome was altered to a lesser extent by antibiotics compared with feces and ileum. The core microbiome of lymph nodes was constituted mainly of Proteobacteria. RNA-sequencing of a single lymph node sample unveiled transcripts responsible for amino acid and carbohydrate metabolism as well as protein turnover, DNA replication and signal transduction. The study presented here is the first comparative study of microbial communities in feces, ileum, and its associated ileocecal lymph nodes. In each analyzed site, we identified specific phylotypes susceptible to antibiotic treatment that can have profound impacts on the host physiological and immunological state, or even on global biogeochemical cycles. Our results indicate that pathogenic bacteria, e.g., enteropathogenic Escherichia coli, could escape antibiotic treatment by translocating to lymph nodes. In general ileocecal lymph nodes harbor a more diverse and active community of microorganisms than previously assumed.
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Affiliation(s)
- Benjamin Zwirzitz
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
| | - Beate Pinior
- Institute for Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Barbara Metzler-Zebeli
- University Clinic for Swine, University of Veterinary Medicine, Vienna, Austria.,Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Vienna, Austria
| | - Monika Handler
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria
| | - Kristina Gense
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria
| | - Christian Knecht
- University Clinic for Swine, University of Veterinary Medicine, Vienna, Austria
| | - Andrea Ladinig
- University Clinic for Swine, University of Veterinary Medicine, Vienna, Austria
| | - Monika Dzieciol
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria
| | - Stefanie U Wetzels
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
| | - Martin Wagner
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
| | | | - Evelyne Mann
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
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12
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Eger M, Graz M, Riede S, Breves G. Application of Mootral TM Reduces Methane Production by Altering the Archaea Community in the Rumen Simulation Technique. Front Microbiol 2018; 9:2094. [PMID: 30233557 PMCID: PMC6132076 DOI: 10.3389/fmicb.2018.02094] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/16/2018] [Indexed: 11/28/2022] Open
Abstract
The reduction of methane emissions by ruminants is a highly desirable goal to mitigate greenhouse gas emissions. Various feed additives have already been tested for their ability to decrease methane production; however, practical use is often limited due to negative effects on rumen fermentation or high costs. Organosulphur compounds from garlic (Allium sativum) and flavonoids have been identified as promising plant-derived compounds which are able to reduce methane production. Here, we evaluated the effects of a combination of garlic powder and bitter orange (Citrus aurantium) extracts, Mootral, on ruminal methane production, ruminal fermentation and the community of methanogenic Archaea by using the rumen simulation technique as ex vivo model. The experiment consisted of an equilibration period of 7 days, an experimental period of 8 days and a withdrawal period of 4 days. During the experimental period three fermenters each were either treated as controls (CON), received a low dose of Mootral (LD), a high dose of Mootral (HD), or monensin (MON) as positive control. Application of Mootral strongly reduced the proportion of methane in the fermentation gas and the production rate of methane. Moreover, the experimental mixture induced a dose-dependent increase in the production rate of short chain fatty acids and in the molar proportion of butyrate. Some effects persisted during the withdrawal period. Both, single strand conformation polymorphism and Illumina MiSeq 16S rRNA amplicon sequencing indicated an archaeal community distinct from CON and MON samples in the LD and HD samples. Among archaeal families the percentage of Methanobacteriaceae was reduced during application of both doses of Mootral. Moreover, several significant differences were observed on OTU level among treatment groups and after withdrawal of the additives for LD and HD group. At day 14, 4 OTUs were positively correlated with methane production. In conclusion this mixture of garlic and citrus compounds appears to effectively reduce methane production by alteration of the archaeal community without exhibiting negative side effects on rumen fermentation.
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Affiliation(s)
- Melanie Eger
- Institute for Physiology, University of Veterinary Medicine Hanover, Hanover, Germany
| | | | - Susanne Riede
- Institute for Physiology, University of Veterinary Medicine Hanover, Hanover, Germany
| | - Gerhard Breves
- Institute for Physiology, University of Veterinary Medicine Hanover, Hanover, Germany
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13
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Comparative Genomic Analysis of Members of the Genera Methanosphaera and Methanobrevibacter Reveals Distinct Clades with Specific Potential Metabolic Functions. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2018; 2018:7609847. [PMID: 30210264 PMCID: PMC6120340 DOI: 10.1155/2018/7609847] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/02/2018] [Indexed: 12/11/2022]
Abstract
Methanobrevibacter and Methanosphaera species represent some of the most prevalent methanogenic archaea in the gastrointestinal tract of animals and humans and play an important role in this environment. The aim of this study was to identify genomic features that are shared or specific for members of each genus with a special emphasis of the analysis on the assimilation of nitrogen and acetate and the utilization of methanol and ethanol for methanogenesis. Here, draft genome sequences of Methanobrevibacter thaueri strain DSM 11995T, Methanobrevibacter woesei strain DSM 11979T, and Methanosphaera cuniculi strain 4103T are reported and compared to those of 16 other Methanobrevibacter and Methanosphaera genomes, including genomes of the 13 currently available types of strains of the two genera. The comparative genome analyses indicate that among other genes, the absence of molybdopterin cofactor biosynthesis is conserved in Methanosphaera species but reveals also that the three species share a core set of more than 300 genes that distinguishes the genus Methanosphaera from the genus Methanobrevibacter. Multilocus sequence analysis shows that the genus Methanobrevibacter can be subdivided into clades, potentially new genera, which may display characteristic specific metabolic features. These features include not only the potential ability of nitrogen fixation and acetate assimilation in a clade comprised of Methanobrevibacter species from the termite gut and Methanobrevibacter arboriphilus strains but also the potential capability to utilize ethanol and methanol in a clade comprising Methanobrevibacter wolinii strain DSM 11976T, Mbb. sp. AbM4, and Mbb. boviskoreani strain DSM 25824T.
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14
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Niu L, Zhang X, Li Y, Wang P, Zhang W, Wang C, Wang Q. Elevational characteristics of the archaeal community in full-scale activated sludge wastewater treatment plants at a 3,660-meter elevational scale. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2017; 76:531-541. [PMID: 28759436 DOI: 10.2166/wst.2017.215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Due to the important roles of archaea in wastewater treatment processes, archaeal communities have been studied extensively in various anaerobic reactors, but the knowledge of archaeal communities in full-scale activated sludge wastewater treatment plants (WWTPs) remains quite poor. In this study, 454-pyrosequencing was for the first time employed to investigate archaeal communities from 20 full-scale activated sludge WWTPs distributed at a 3,660-meter elevational scale in China. Results showed that archaeal communities from WWTPs were dominated by Methanosarcinales (84.6%). A core archaeal population (94.5%) composed of Methanosaeta, Methanosarcina, Methanogenium and Methanobrevibacter was shared among WWTPs. The elevational pattern of archaeal communities was observed in WWTPs, with an elevational threshold associated with archaeal community richness and structures at approximately 1,500 meters above sea level (masl). A declining trend in community richness with increasing elevation was observed at higher elevations, whereas no trend was presented at lower elevations. Spearman correlation analysis indicated that the archaeal community richness at higher elevations was associated with more environmental variables than that at lower elevations. Redundancy analysis indicated that wastewater variables were the dominant contributors to the variation of community structures at higher elevations, followed by operational variables and elevation.
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Affiliation(s)
- Lihua Niu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China E-mail:
| | - Xue Zhang
- Collaborative Innovation Center for Advanced Nuclear Energy Technology, Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084, China
| | - Yi Li
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China E-mail:
| | - Peifang Wang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China E-mail:
| | - Wenlong Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China E-mail:
| | - Chao Wang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China E-mail:
| | - Qing Wang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China E-mail:
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15
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Luo Y, Chen H, Yu B, He J, Zheng P, Mao X, Tian G, Yu J, Huang Z, Luo J, Chen D. Dietary pea fiber increases diversity of colonic methanogens of pigs with a shift from Methanobrevibacter to Methanomassiliicoccus-like genus and change in numbers of three hydrogenotrophs. BMC Microbiol 2017; 17:17. [PMID: 28095773 PMCID: PMC5240297 DOI: 10.1186/s12866-016-0919-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/20/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pea fiber (PF) is a potential fibrous supplement in swine production. The influence of dietary PF on microbial community in the colon of pigs remains largely unexplored. Methanogens in the hindgut of monogastric animals play important roles in degradation of dietary fibers and efficient removal of microbial metabolic end product H2. Understanding the impact of dietary PF on the structure of colonic methanogens may help understand the mechanisms of microbe-mediated physiological functions of PF. This study investigated the influence of PF on the diversity and quantity and/or activity of colonic methanongens of piglets and finishing pigs. Four archaeal 16S rRNA clone libraries were constructed for piglets and finishers fed with control (Piglet-C and Finisher-C) or PF diet (Piglet-P and Finisher-P). RESULTS There were 195, 190, 194 and 196 clones obtained from the library Piglet-C, Piglet-P, Finisher-C and Finisher-P, respectively, with corresponding 12, 11, 11 and 16 OTUs (operational taxonomic units). Significant differences of Shannon Index among the four libraries were found (P < 0.05). Libshuff analysis showed that the archaeal community structure among the four libraries were significantly different (P < 0.0001). The predominant methanogens shifted from Methanobrevibacter to Methanobrevibacter and Methanomassiliicoccus-like genus as a result of dietary PF. Supplementation of PF significantly increased the copy numbers of mcrA and dsrA genes (P < 0.05). CONCLUSIONS Alteration of methanogenic community structure may lead to functional transition from utilization of H2/CO2 to employment of both H2/CO2 and methanol/CO2. Quantification of three functional genes (mcrA, dsrA and fhs) of methanogens, sulfate-reducing bacteria (SRB) and acetogens revealed that dietary PF also increased the activity of methanogens and SRB,probably associated with increased proportion of Methanomassiliicoccus luminyensis-species. Further study is required to examine the interaction between specific methanogens and SRB during fermentation of dietary PF.
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Affiliation(s)
- Yuheng Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Hong Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Bing Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jun He
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Ping Zheng
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiangbing Mao
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Gang Tian
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jie Yu
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhiqing Huang
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Junqiu Luo
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Daiwen Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
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16
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Miragoli F, Federici S, Ferrari S, Minuti A, Rebecchi A, Bruzzese E, Buccigrossi V, Guarino A, Callegari ML. Impact of cystic fibrosis disease on archaea and bacteria composition of gut microbiota. FEMS Microbiol Ecol 2016; 93:fiw230. [PMID: 27810876 PMCID: PMC5155554 DOI: 10.1093/femsec/fiw230] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/08/2016] [Accepted: 11/02/2016] [Indexed: 12/21/2022] Open
Abstract
Cystic fibrosis is often associated with intestinal inflammation due to several factors, including altered gut microbiota composition. In this study, we analyzed the fecal microbiota among patients with cystic fibrosis of 10–22 years of age, and compared the findings with age-matched healthy subjects. The participating patients included 14 homozygotes and 14 heterozygotes with the delF508 mutation, and 2 heterozygotes presenting non-delF508 mutations. We used PCR-DGGE and qPCR to analyze the presence of bacteria, archaea and sulfate-reducing bacteria. Overall, our findings confirmed disruption of the cystic fibrosis gut microbiota. Principal component analysis of the qPCR data revealed no differences between homozygotes and heterozygotes, while both groups were distinct from healthy subjects who showed higher biodiversity. Archaea were under the detection limit in all homozygotes subjects, whereas methanogens were detected in 62% of both cystic fibrosis heterozygotes and healthy subjects. Our qPCR results revealed a low frequency of sulfate-reducing bacteria in the homozygote (13%) and heterozygote (13%) patients with cystic fibrosis compared with healthy subjects (87.5%). This is a pioneer study showing that patients with cystic fibrosis exhibit significant reduction of H2-consuming microorganisms, which could increase hydrogen accumulation in the colon and the expulsion of this gas through non-microbial routes.
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Affiliation(s)
- Francesco Miragoli
- Centro Ricerche Biotecnologiche, Università Cattolica del Sacro Cuore, Cremona 26100, Italy
| | - Sara Federici
- Centro Ricerche Biotecnologiche, Università Cattolica del Sacro Cuore, Cremona 26100, Italy
| | - Susanna Ferrari
- Centro Ricerche Biotecnologiche, Università Cattolica del Sacro Cuore, Cremona 26100, Italy
| | - Andrea Minuti
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza 29122, Italy
| | - Annalisa Rebecchi
- Centro Ricerche Biotecnologiche, Università Cattolica del Sacro Cuore, Cremona 26100, Italy
| | - Eugenia Bruzzese
- Department of Translational Medical Sciences, Section of Pediatrics, University Federico II, Naples 80131, Italy
| | - Vittoria Buccigrossi
- Department of Translational Medical Sciences, Section of Pediatrics, University Federico II, Naples 80131, Italy
| | - Alfredo Guarino
- Department of Translational Medical Sciences, Section of Pediatrics, University Federico II, Naples 80131, Italy
| | - Maria Luisa Callegari
- Centro Ricerche Biotecnologiche, Università Cattolica del Sacro Cuore, Cremona 26100, Italy
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17
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Sweeney T, O'Doherty JV. Marine macroalgal extracts to maintain gut homeostasis in the weaning piglet. Domest Anim Endocrinol 2016; 56 Suppl:S84-9. [PMID: 27345326 DOI: 10.1016/j.domaniend.2016.02.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 02/12/2016] [Accepted: 02/15/2016] [Indexed: 11/26/2022]
Abstract
The mammalian gastrointestinal tract (GIT) is a dynamic environment, where a symbiotic relationship exists between the resident microbiota and the digestive and immune systems of the host. The development of the immune system begins in-utero and is further developed after the colonization of the GIT with microbiota during birth and postnatal life. The early establishment of this relationship is fundamental to the development and long-term maintenance of gut homeostasis. Regulatory mechanisms ensure an appropriate level of immune reactivity in the gut to accommodate the presence of beneficial and dietary microorganisms, whereas allowing effective immune responses to clear pathogens. However, unfavorable alterations in the composition of the microbiota, known as dysbiosis, have been implicated in many conditions including post-weaning diarrhea in pigs. Weaning is a major critical period in pig husbandry. It involves complex dietary, social, and environmental stresses that interfere with gut development. Post-weaning complications in piglets are characterized by a reduction in-feed intake and growth, atrophy of small intestine architecture, upregulation of intestinal inflammatory cytokines, alterations in GIT microflora, diarrhea, and heightened susceptibility to infection. These challenges have been controlled with in-feed prophylactic antibiotics and dietary minerals. However, these strategies are under scrutiny because of their role in promoting multidrug resistant bacteria and the accumulation of minerals in the environment, respectively. Therefore, significant efforts are being made to identify natural alternatives to support homeostasis in the piglet GIT, in particular during the weaning period. Chemodiversity in nature; including microorganisms, terrestrial plants, seaweeds, and marine organisms, offers a valuable source for novel bioactives. In this review, we discuss the advances in our understanding of the immune mechanisms by which the dynamic interplay of the intestinal microbiota and its host normally favors a homeostatic, symbiotic relationship, and how feeding macroalgal bioactives in both the maternal diet and the piglet diet, can be used to support this symbiotic relationship in times of challenge.
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Affiliation(s)
- T Sweeney
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireleand.
| | - J V O'Doherty
- School of Agriculture, University College Dublin, Belfield, Dublin 4, Ireleand
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