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Aminu S, Ascandari A, Laamarti M, Safdi NEH, El Allali A, Daoud R. Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities. Crit Rev Microbiol 2023:1-25. [PMID: 38006569 DOI: 10.1080/1040841x.2023.2282447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/06/2023] [Indexed: 11/27/2023]
Abstract
The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.
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Affiliation(s)
- Suleiman Aminu
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - AbdulAziz Ascandari
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Meriem Laamarti
- Faculty of Medical Sciences, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Nour El Houda Safdi
- AgroBioSciences Program, College for Sustainable Agriculture and Environmental Science, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Rachid Daoud
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
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Dahl SA, Seifert J, Camarinha-Silva A, Hernández-Arriaga A, Windisch W, König A. "Get the best out of what comes in" - adaptation of the microbiota of chamois ( Rupicapra rupicapra) to seasonal forage availability in the Bavarian Alps. Front Microbiol 2023; 14:1238744. [PMID: 37849922 PMCID: PMC10577445 DOI: 10.3389/fmicb.2023.1238744] [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: 06/12/2023] [Accepted: 09/11/2023] [Indexed: 10/19/2023] Open
Abstract
As an inhabitant of the Alps, chamois are exposed to significant climatic changes throughout the year and are also strongly confronted with changing forage availability. Besides horizontal and vertical migratory movements as an adaptation, it undergoes physiological transformations and dynamic changes in the ruminal microbiota. The following study used 48 chamois of different ages and genders to investigate to which extent the ingested food plants, the resulting crude nutrients in the rumen (reticulorumen) contents, and the bacterial microbiota in the rumen and their fermentation products were influenced by the changes over the seasons. Very little is known about the microbiota of wild ruminants, and many bacterial taxa could only be determined to certain taxonomic levels in this study. However, adapted microbiota reflects the significant changes in the ingested forage and the resulting crude nutrients. For some taxa, our results indicated potential functional relationships. In addition, 15 genera were identified, representing almost 90% of the relative abundance, forming the central part of the microbial community throughout the year. The successful and flexible adaptation of chamois is reflected in the chamois rumen's nutrient and microbial profile. This is also the first study that analyzes the microbiota of the chamois using rumen samples and considers the microbiota in a seasonal comparison.
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Affiliation(s)
- Sarah-Alica Dahl
- Wildlife Biology and Management Unit, Chair of Animal Nutrition and Metabolism, Technical University of Munich, Freising, Germany
| | - Jana Seifert
- HoLMiR – Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Amélia Camarinha-Silva
- HoLMiR – Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Angélica Hernández-Arriaga
- HoLMiR – Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Wilhelm Windisch
- TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Andreas König
- Wildlife Biology and Management Unit, Chair of Animal Nutrition and Metabolism, Technical University of Munich, Freising, Germany
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Hsieh JC, Chuang ST, Hsu YT, Ho ST, Li KY, Chou SH, Chen MJ. In vitro ruminal fermentation and cow-to-mouse fecal transplantations verify the inter-relationship of microbiome and metabolome biomarkers: potential to promote health in dairy cows. Front Vet Sci 2023; 10:1228086. [PMID: 37662996 PMCID: PMC10469932 DOI: 10.3389/fvets.2023.1228086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/03/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction There are differences in the gut microbiome and metabolome when the host undergoes different physical or pathological conditions. However, the inter-relationship of microbiome and metabolome biomarkers to potentially promote the health of dairy cows needs to be studied. Further, the development of next-generation probiotics for dairy cattle health promotion has not been demonstrated. Objective In the present study, we identified the microbiome and metabolome biomarkers associated with healthy cows. Methods We analyzed the relationships of the ruminal microorganism profile and metabolites between healthy and mastitis lactating dairy cows. The roles of bacterial biomarker were further verified by in vitro fermentation and cow-to-mouse fecal microbiota transplantation (FMT). Results Two species, Ruminococcus flavefaciens and Bifidobacterium longum subsp. longum, and six rumen metabolites were positively correlated with healthy cows by Spearman's correlation analysis. Through in vitro ruminal fermentation, inoculating R. flavefaciens and B. longum subsp. longum showed the upregulation of the levels of putrescine, xanthurenic acid, and pyridoxal in the mastitis ruminal fluid, which confirmed the inter-relationships between these microbiota and metabolites associated with healthy cows. Further, we verified the role of R. flavefaciens and B. longum subsp. longum in promoting health by FMT. The administration of R. flavefaciens and B. longum subsp. longum reduced the death rate and recovered the bodyweight loss of germ-free mice caused by FMT mastitis feces. Discussion We provided evidence that the bacterial biomarkers alter downstream metabolites. This could indirectly indicate that the two bacterial biomarkers have the potential to be used as next-generation probiotics for dairy cattle, although it needs more evidence to support our hypothesis. Two species, R. flavefaciens and B. longum subsp. longum, with three metabolites, putrescine, xanthurenic acid, and pyridoxal, identified in the ruminal fluid, may point to a new health-promoting and disease-preventing approach for dairy cattle.
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Affiliation(s)
- Jui-Chun Hsieh
- Department of Animal Science and Technology, National Taiwan University, Taipei City, Taiwan
| | - Shih-Te Chuang
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung City, Taiwan
| | - Yu-Ting Hsu
- Department of Animal Science and Technology, National Taiwan University, Taipei City, Taiwan
| | - Shang-Tse Ho
- Department of Wood Based Materials and Design, National Chiayi University, Chiayi City, Taiwan
| | - Kuan-Yi Li
- Department of Animal Science and Technology, National Taiwan University, Taipei City, Taiwan
| | - Shih-Hsuan Chou
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu-Jen Catholic University, New Taipei City, Taiwan
- Biotools Co. Ltd., New Taipei City, Taiwan
| | - Ming-Ju Chen
- Department of Animal Science and Technology, National Taiwan University, Taipei City, Taiwan
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Yang S, Zhang G, Yuan Z, He S, Wang R, Zheng J, Mao H, Chai J, Wu D. Exploring the temporal dynamics of rumen bacterial and fungal communities in yaks ( Bos grunniens) from 5 days after birth to adulthood by full-length 16S and 18S rRNA sequencing. Front Vet Sci 2023; 10:1166015. [PMID: 37415968 PMCID: PMC10321131 DOI: 10.3389/fvets.2023.1166015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
The rumen of ruminants is inhabited by complex and diverse microorganisms. Young animals are exposed to a variety of microorganisms from their mother and the environment, and a few colonize and survive in their digestive tracts, forming specific microflora as the young animals grow and develop. In this study, we conducted full-length sequencing of bacterial and fungal communities in the rumen of pastured yaks of different ages (from 5 days after birth to adulthood) using amplified sequencing technology. The results showed that the rumen microflora of Zhongdian yaks changed gradually from 5 to 180 days after birth and tended to stabilize at 2 years of age. The rumen of adult yaks was the most suitable for the growth and reproduction of most bacteria. Bactria diversity of the yak rumen increased gradually from 5 days after birth to adulthood. With the growth of yaks, different dominated bacteria were enriched in different groups, but Prevotella remained highly abundant in all groups. The yak rumen at 90 days of age was the most suitable for the growth and reproduction of most fungi, and 90 days of age could be a cut-off point for the distribution of fungal communities. Fungal Thelebolus was the firstly reported in yak rumen and was enriched in the yak rumen of 90 days after birth. The most abundant and balanced fungal genera were found in adult yaks, and most of them were only detected in adult yaks. Our study reported on the rumen bacterial and fungal communities of Zhongdian yaks grazed at different ages and provided insights into the dynamic changes of dominant microflora with yak growth.
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Affiliation(s)
- Shuli Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Guangrong Zhang
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Zaimei Yuan
- Kunming Animal Disease Prevention And Control Center, Kunming, China
| | - Shichun He
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Rongjiao Wang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Jieyi Zheng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Huaming Mao
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Jianmin Chai
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Dongwang Wu
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, China
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Lin X, Ju L, Cheng Q, Jiang Y, Hou Q, Hu Z, Wang Y, Wang Z. Comparison of growth performance and rumen metabolic pathways in sheep and goats under the same feeding pattern. Front Vet Sci 2023; 10:1013252. [PMID: 36846256 PMCID: PMC9948245 DOI: 10.3389/fvets.2023.1013252] [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: 08/06/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
Diet and species are important factors affecting the rumen microbiota, with roughage stimulating rumen development and concentrate feeds being broken down by the decomposition of Ruminal flora to provide the organism with a large amount of energy. This study aimed to explore the effects of host and dietary factors on rumen flora composition and diversity, as well as on host metabolism. The study reports the research conducted on 5-month-old male Small-tail Han sheep and 5-month-old male Boer goat, each with an average weight of 33.87 ± 1.70 kg. Five animals of each species were divided into two groups, namely, the S group (Small-tail Han sheep) and the B group (Boer goat). The experiment was carried out in two various periods, namely, X and Y for groups S and B, respectively. The rations were fed with concentrate-to-roughage ratios of 3:7 and 5:5, respectively. Growth performance was measured by the weight increase index. The results showed that, under the same raising conditions, the ratio between body weight increases and the amount of feed was lower in the S group than in the B group, but the differences were not significant. According to the analysis of the apparent digestibility ratio of nutrition ingredients, the XS group had a significantly higher apparent digestibility ratio for acid detergent fiber than the XB group (p < 0.05). Even though the analysis of rumen fermentation parameters showed that the rumen pH has no significant differences between the XS and XB groups, it was significantly lower in the YS group than in the YB group. The XS group contained a significantly lower content of total volatile fatty acids than the XB group (p < 0.05). Analysis of the 16S rDNA sequencing results revealed that, compared to the B group, the S group was highly enriched with the following bacteria: Proteobacteria, γ-proteobacteria, Aeromonadales, and Succinivibrionaceae. Thus, the host species affected the abundance and diversity of rumen bacteria. Feed utilization efficiency of Small-tail Han sheep was higher than Boer goats, which might be specifically associated with Succinivibrionaceae. The results from this study show that animals belonging to the same family but different genera and species can differ in metabolic pathways even when they are provided with the same animal feed.
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Affiliation(s)
| | | | - Qianjin Cheng
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Yue Jiang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Qiuling Hou
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Zhiyong Hu
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
| | - Yun Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China
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Yang X, Fan X, Jiang H, Zhang Q, Basangwangdui, Zhang Q, Dang S, Long R, Huang X. Simulated seasonal diets alter yak rumen microbiota structure and metabolic function. Front Microbiol 2022; 13:1006285. [PMID: 36212853 PMCID: PMC9538157 DOI: 10.3389/fmicb.2022.1006285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Yak is the only ruminant on the Qinghai-Tibetan Plateau that grazes year-round. Although previous research has shown that yak rumen microbiota fluctuates in robust patterns with seasonal foraging, it remains unclear whether these dynamic shifts are driven by changes in environment or nutrient availability. The study examines the response of yak rumen microbiota (bacteria, fungi, and archaea) to simulated seasonal diets, excluding the contribution of environmental factors. A total of 18 adult male yaks were randomly divided into three groups, including a nutrition stress group (NSG, simulating winter pasture), a grazing simulation group (GSG, simulating warm season pasture), and a supplementation group (SG, simulating winter pasture supplemented with feed concentrates). Volatile fatty acids (VFAs) profiling showed that ruminal acetate, propionate and total VFA contents were significantly higher (p < 0.05) in GSG rumen. Metagenomic analysis showed that Bacteroidetes (53.9%) and Firmicutes (37.1%) were the dominant bacterial phyla in yak rumen across dietary treatments. In GSG samples, Actinobacteriota, Succinivibrionaceae_UCG-002, and Ruminococcus albus were the most abundant, while Bacteroides was significantly more abundant in NSG samples (p < 0.05) than that in GSG. The known fiber-degrading fungus, Neocallimastix, was significantly more abundant in NSG and SG samples, while Cyllamyces were more prevalent in NSG rumen than in the SG rumen. These findings imply that a diverse consortium of microbes may cooperate in response to fluctuating nutrient availability, with depletion of known rumen taxa under nutrient deficiency. Archaeal community composition showed less variation between treatments than bacterial and fungal communities. Additionally, Orpinomyces was significantly positively correlated with acetate levels, both of which are prevalent in GSG compared with other groups. Correlation analysis between microbial taxa and VFA production or between specific rumen microbes further illustrated a collective response to nutrient availability by gut microbiota and rumen VFA metabolism. PICRUSt and FUNGuild functional prediction analysis indicated fluctuation response of the function of microbial communities among groups. These results provide a framework for understanding how microbiota participate in seasonal adaptations to forage availability in high-altitude ruminants, and form a basis for future development of probiotic supplements to enhance nutrient utilization in livestock.
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Cheng J, Zhang X, Xu D, Zhang D, Zhang Y, Song Q, Li X, Zhao Y, Zhao L, Li W, Wang J, Zhou B, Lin C, Yang X, Zhai R, Cui P, Zeng X, Huang Y, Ma Z, Liu J, Wang W. Relationship between rumen microbial differences and traits among Hu sheep, Tan sheep, and Dorper sheep. J Anim Sci 2022; 100:skac261. [PMID: 35953151 PMCID: PMC9492252 DOI: 10.1093/jas/skac261] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Rumen microbes play an important role in the growth and development of ruminants. Differences in variety will affect the rumen community structure. The three excellent sheep breeds were selected for this study (Hu sheep, Tan sheep, and Dorper sheep) have different uses and origins. The sheep were raised on the same diet to 180 d of age in a consistent environment. 16S rDNA V3 to V4 region sequencing was used to assess the rumen microbes of 180 individuals (60 per breed). There were differences in microbial diversity among different sheep breeds (P < 0.05). Principal coordinate analysis showed that the three varieties were separated, but also partially overlapped. Linear discriminant analysis effect size identified a total of 19 biomarkers in three breeds. Of these biomarkers, five in Hu sheep were significantly negatively correlated with average feed conversion rate (P < 0.05). Six biomarkers were identified in the rumen of Dorper sheep, among which Ruminococcus was significantly positively correlated with body weight at 80 d (P < 0.05). In Tan sheep, Rikenellaceae_RC9_gut_group was significantly positively correlated with meat fat, and significantly positively correlated with volatile fatty acids (VFAs), such as butyric acid and isobutyric acid (P < 0.05). The Rikenellaceae_RC9_gut_group may regulate Tan mutton fat deposition by affecting the concentration of VFAs. Functional prediction revealed enrichment differences of functional pathways among different sheep breeds were small. All were enriched in functions, such as fermentation and chemoheterotrophy. The results show that there are differences in the rumen microorganisms of the different sheep breeds, and that the microorganisms influence the host.
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Affiliation(s)
- Jiangbo Cheng
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Yukun Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Qizhi Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yuan Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
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