1
|
Wang R, He S, Huang D, He S, Guo T, Chen T, Peng H, Jiaka L, He M, Chen C, Song D, Huang X, Wu D, Mao H. Differences in composition and diversity of rumen fungi in buffalo fed different diets. Anim Biotechnol 2023; 34:5075-5086. [PMID: 37946542 DOI: 10.1080/10495398.2023.2276974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The rumen is a complex ecosystem containing a variety of fungi, which are crucial for the digestive activities of ruminants. Previous research on rumen fungi has mainly focused on anaerobic fungi, given the rumen's reputation as a mainly anaerobic environment. The objective of this study was to investigate rumen fungal diversity and the presence of aerobic fungi in buffalo fed on different diets. Three adult buffaloes were used as experimental animals. Alfalfa hay, oat hay, whole corn silage, sugarcane shoot silage, fresh king grass, dried rice straw, and five kinds of mixed diets with concentrate to roughage ratios of 20:80, 35:65, 50:50, 65:35, and 80:20 were used as the experimental diets. The experimental animals were fed different diets for 22 days. Rumen fluid was collected from the rumen fistula for ITS (Internal Transcribed Spacer) sequencing 2 h after feeding on the morning of day 22. The results indicate the presence of large quantities of aerobic fungi in the rumen of the buffaloes 2 h after feeding and suggest that Ascomycota and Basidiomycota are the dominant fungal groups under different feeding conditions. The study also identified 62 different fungal types, which showed significant differences among the 11 experimental diets.
Collapse
Affiliation(s)
- Rongjiao Wang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Shichun He
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Dan Huang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Shaoying He
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Taiqing Guo
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Tao Chen
- Animal Husbandry Station, Mangshi, Yunnan, China
| | - Hongen Peng
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Latie Jiaka
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Min He
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Changguo Chen
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Dingzhou Song
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Xiujun Huang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Dongwang Wu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Huaming Mao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| |
Collapse
|
2
|
Sun X, Tiffany DG, Urriola PE, Shurson GG, Hu B. Nutrition upgrading of corn-ethanol co-product by fungal fermentation: Amino acids enrichment and anti-nutritional factors degradation. FOOD AND BIOPRODUCTS PROCESSING 2021. [DOI: 10.1016/j.fbp.2021.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
3
|
Wilken SE, Seppälä S, Lankiewicz TS, Saxena M, Henske JK, Salamov AA, Grigoriev IV, O'Malley MA. Genomic and proteomic biases inform metabolic engineering strategies for anaerobic fungi. Metab Eng Commun 2019; 10:e00107. [PMID: 31799118 PMCID: PMC6883316 DOI: 10.1016/j.mec.2019.e00107] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/24/2019] [Accepted: 11/04/2019] [Indexed: 12/22/2022] Open
Abstract
Anaerobic fungi (Neocallimastigomycota) are emerging non-model hosts for biotechnology due to their wealth of biomass-degrading enzymes, yet tools to engineer these fungi have not yet been established. Here, we show that the anaerobic gut fungi have the most GC depleted genomes among 443 sequenced organisms in the fungal kingdom, which has ramifications for heterologous expression of genes as well as for emerging CRISPR-based genome engineering approaches. Comparative genomic analyses suggest that anaerobic fungi may contain cellular machinery to aid in sexual reproduction, yet a complete mating pathway was not identified. Predicted proteomes of the anaerobic fungi also contain an unusually large fraction of proteins with homopolymeric amino acid runs consisting of five or more identical consecutive amino acids. In particular, threonine runs are especially enriched in anaerobic fungal carbohydrate active enzymes (CAZymes) and this, together with a high abundance of predicted N-glycosylation motifs, suggests that gut fungal CAZymes are heavily glycosylated, which may impact heterologous production of these biotechnologically useful enzymes. Finally, we present a codon optimization strategy to aid in the development of genetic engineering tools tailored to these early-branching anaerobic fungi.
Collapse
Affiliation(s)
- St Elmo Wilken
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Thomas S Lankiewicz
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA.,Department of Evolution Ecology and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Mohan Saxena
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - John K Henske
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Asaf A Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| |
Collapse
|
4
|
Gao W, Zhang B, Lv B, Liu C, Chen D. Ruminal degradability and intestinal digestibility of individual amino acids in mixed diets with different crude protein levels measured by the modified in vitro three-step and mobile nylon bag technique. Anim Sci J 2015; 87:547-56. [PMID: 26559908 DOI: 10.1111/asj.12464] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 04/27/2015] [Indexed: 11/28/2022]
Abstract
The ruminal degradability and intestinal digestibility of dry matter (DM), crude protein (CP) and amino acids (AA) in three total mixed rations with different CP levels were estimated using the modified in vitro three-step procedure (TSP) and mobile nylon bag (MNB) technique on growing lambs. The ruminal effective degradability of DM and CP did not respond with increasing dietary CP level. However, the intestinal digestibility of DM was significantly increased with increasing dietary CP level estimated by TSP (P < 0.05) or MNB method (P < 0.01). Intestinal digestibility coefficients of CP determined by TSP were lower than those of the MNB method. Histidine was extensively degraded by rumen micro-organisms, while tyrosine was the most anti-degradable AA among the samples. The ruminal AA degradability exhibited no significant differences except for threonine, tryptophan, alanine, aspartic acid and proline for the three diets. Similarly, only a few AAs (i.e. histidine, methionine, tryptophan, aspartic acid and cysteine in TSP; histidine, tryptophan, aspartic acid and serine in MNB) had significant differences in their intestinal digestibility; in addition, values of MNB were lower than that of the TSP method, indicating that intestinal digestibility of DM seems to be overestimated in TSP, while that of CP might be overestimated in the MNB method.
Collapse
Affiliation(s)
| | | | | | - Chenli Liu
- College of Animal Science and Technology, Shihezi University, Shihezi City, China
| | | |
Collapse
|
5
|
Gruninger RJ, Puniya AK, Callaghan TM, Edwards JE, Youssef N, Dagar SS, Fliegerova K, Griffith GW, Forster R, Tsang A, McAllister T, Elshahed MS. Anaerobic fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential. FEMS Microbiol Ecol 2014; 90:1-17. [PMID: 25046344 DOI: 10.1111/1574-6941.12383] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 07/03/2014] [Accepted: 07/07/2014] [Indexed: 02/05/2023] Open
Abstract
Anaerobic fungi (phylum Neocallimastigomycota) inhabit the gastrointestinal tract of mammalian herbivores, where they play an important role in the degradation of plant material. The Neocallimastigomycota represent the earliest diverging lineage of the zoosporic fungi; however, understanding of the relationships of the different taxa (both genera and species) within this phylum is in need of revision. Issues exist with the current approaches used for their identification and classification, and recent evidence suggests the presence of several novel taxa (potential candidate genera) that remain to be characterised. The life cycle and role of anaerobic fungi has been well characterised in the rumen, but not elsewhere in the ruminant alimentary tract. Greater understanding of the 'resistant' phase(s) of their life cycle is needed, as is study of their role and significance in other herbivores. Biotechnological application of anaerobic fungi, and their highly active cellulolytic and hemi-cellulolytic enzymes, has been a rapidly increasing area of research and development in the last decade. The move towards understanding of anaerobic fungi using -omics based (genomic, transcriptomic and proteomic) approaches is starting to yield valuable insights into the unique cellular processes, evolutionary history, metabolic capabilities and adaptations that exist within the Neocallimastigomycota.
Collapse
|
6
|
Giannoutsou EP, Katsifas EA, Geli A, Karagouni AD. Protein increase and lysine production by a Paecilomyces variotii strain grown on two-phase olive mill waste. World J Microbiol Biotechnol 2011; 28:849-56. [DOI: 10.1007/s11274-011-0881-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 09/05/2011] [Indexed: 11/28/2022]
|
7
|
Guliye AY, Wallace RJ. Effects of aromatic amino acids, phenylacetate and phenylpropionate on fermentation of xylan by the rumen anaerobic fungi, Neocallimastix frontalis and Piromyces communis. J Appl Microbiol 2007; 103:924-9. [PMID: 17897195 DOI: 10.1111/j.1365-2672.2007.03327.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS Anaerobic fungi are important members of the fibrolytic community of the rumen. The aim of this study was to study their requirement for aromatic amino acids (AA) and related phenyl acids (phenylpropionic and phenylacetic acids) for optimal xylan fermentation. METHODS AND RESULTS Neocallimastix frontalis RE1 and Piromyces communis P were grown in a defined medium containing oat spelts xylan as the sole energy source, plus one of the following N sources: ammonia; ammonia plus a complete mixture of 20 AA commonly found in protein; ammonia plus complete AA mixture minus aromatic AA; ammonia plus phenyl acids; ammonia plus complete AA mixture without aromatic AA plus phenyl acids. Both species grew in all the media, indicating no absolute requirement for AA. The complete AA mixture increased (P<0.05) acetate concentration by 18% and 15%, sugar utilization by 33% and 22% and microbial yield by about 22% and 15% in N. frontalis and P. communis, respectively, in comparison with the treatments that had ammonia as the only N source. Neither the supply of aromatic AA or phenol acids, nor their deletion from the complete AA mixture, affected the fermentation rate, products or yield of either species. CONCLUSIONS AA were not essential for N. frontalis and P. communis, but their growth on xylan was stimulated. The effects could not be explained in terms of aromatic AA alone. SIGNIFICANCE AND IMPACT OF THE STUDY Ruminant diets should contain sufficient protein to sustain optimal fibre digestion by ruminal fungi. Aromatic AA or phenyl acids alone cannot replace the complete AA mixture.
Collapse
Affiliation(s)
- A Y Guliye
- Rowett Research Institute, Bucksburn, Aberdeen, UK
| | | |
Collapse
|