1
|
Meili CH, TagElDein MA, Jones AL, Moon CD, Andrews C, Kirk MR, Janssen PH, J. Yeoman C, Grace S, Borgogna JLC, Foote AP, Nagy YI, Kashef MT, Yassin AS, Elshahed MS, Youssef NH. Diversity and community structure of anaerobic gut fungi in the rumen of wild and domesticated herbivores. Appl Environ Microbiol 2024; 90:e0149223. [PMID: 38299813 PMCID: PMC10880628 DOI: 10.1128/aem.01492-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
The rumen houses a diverse community that plays a major role in the digestion process in ruminants. Anaerobic gut fungi (AGF) are key contributors to plant digestion in the rumen. Here, we present a global amplicon-based survey of the rumen AGF mycobiome by examining 206 samples from 15 animal species, 15 countries, and 6 continents. The rumen AGF mycobiome was highly diverse, with 81 out of 88 currently recognized AGF genera or candidate genera identified. However, only six genera (Neocallimastix, Orpinomyces, Caecomyces, Cyllamyces, NY9, and Piromyces) were present at >4% relative abundance. AGF diversity was higher in members of the families Antilocapridae and Cervidae compared to Bovidae. Community structure analysis identified a pattern of phylosymbiosis, where host family (10% of total variance) and species (13.5%) partially explained the rumen mycobiome composition. As well, diet composition (9%-19%), domestication (11.14%), and biogeography (14.1%) also partially explained AGF community structure; although sampling limitation, geographic range restrictions, and direct association between different factors hindered accurate elucidation of the relative contribution of each factor. Pairwise comparison of rumen and fecal samples obtained from the same subject (n = 13) demonstrated greater diversity and inter-sample variability in rumen versus fecal samples. The genera Neocallimastix and Orpinomyces were present in higher abundance in rumen samples, while Cyllamyces and Caecomyces were enriched in fecal samples. Comparative analysis of global rumen and feces data sets revealed a similar pattern. Our results provide a global view of AGF community in the rumen and identify patterns of AGF variability between rumen and feces in herbivores Gastrointestinal (GI) tract.IMPORTANCERuminants are highly successful and economically important mammalian suborder. Ruminants are herbivores that digest plant material with the aid of microorganisms residing in their GI tract. In ruminants, the rumen compartment represents the most important location where microbially mediated plant digestion occurs, and is known to house a bewildering array of microbial diversity. An important component of the rumen microbiome is the anaerobic gut fungi (AGF), members of the phylum Neocallimastigomycota. So far, studies examining AGF diversity have mostly employed fecal samples, and little is currently known regarding the identity of AGF residing in the rumen compartment, factors that impact the observed patterns of diversity and community structure of AGF in the rumen, and how AGF communities in the rumen compare to AGF communities in feces. Here, we examined the rumen AGF diversity using an amplicon-based survey targeting a wide range of wild and domesticated ruminants (n = 206, 15 different animal species) obtained from 15 different countries. Our results demonstrate that while highly diverse, no new AGF genera were identified in the rumen mycobiome samples examined. Our analysis also indicate that animal host phylogeny, diet, biogeography, and domestication status could play a role in shaping AGF community structure. Finally, we demonstrate that a greater level of diversity and higher inter-sample variability was observed in rumen compared to fecal samples, with two genera (Neocallimastix and Orpinomyces) present in higher abundance in rumen samples, and two others (Cyllamyces and Caecomyces) enriched in fecal samples. Our results provide a global view of the identity, diversity, and community structure of AGF in ruminants, elucidate factors impacting diversity and community structure of the rumen mycobiome, and identify patterns of AGF community variability between the rumen and feces in the herbivorous GI tract.
Collapse
Affiliation(s)
- Casey H. Meili
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Moustafa A. TagElDein
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Adrienne L. Jones
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Christina D. Moon
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Catherine Andrews
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Michelle R. Kirk
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Peter H. Janssen
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Carl J. Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, USA
| | - Savannah Grace
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, USA
| | | | - Andrew P. Foote
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Yosra I. Nagy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Mona T. Kashef
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Aymen S. Yassin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| |
Collapse
|
2
|
Jones AL, Pratt CJ, Meili CH, Soo RM, Hugenholtz P, Elshahed MS, Youssef NH. Anaerobic gut fungal communities in marsupial hosts. mBio 2024; 15:e0337023. [PMID: 38259066 PMCID: PMC10865811 DOI: 10.1128/mbio.03370-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
The anaerobic gut fungi (AGF) inhabit the alimentary tracts of herbivores. In contrast to placental mammals, information regarding the identity, diversity, and community structure of AGF in marsupials is extremely sparse. Here, we characterized AGF communities in 61 fecal samples from 10 marsupial species belonging to four families in the order Diprotodontia: Vombatidae (wombats), Phascolarctidae (koalas), Phalangeridae (possums), and Macropodidae (kangaroos, wallabies, and pademelons). An amplicon-based diversity survey using the D2 region of the large ribosomal subunit as a phylogenetic marker indicated that marsupial AGF communities were dominated by eight genera commonly encountered in placental herbivores (Neocallimastix, Caecomyces, Cyllamyces, Anaeromyces, Orpinomyces, Piromyces, Pecoramyces, and Khoyollomyces). Community structure analysis revealed a high level of stochasticity, and ordination approaches did not reveal a significant role for the animal host, gut type, dietary preferences, or lifestyle in structuring marsupial AGF communities. Marsupial foregut and hindgut communities displayed diversity and community structure patterns comparable to AGF communities typically encountered in placental foregut hosts while exhibiting a higher level of diversity and a distinct community structure compared to placental hindgut communities. Quantification of AGF load using quantitative PCR indicated a significantly smaller load in marsupial hosts compared to their placental counterparts. Isolation efforts were only successful from a single red kangaroo fecal sample and yielded a Khoyollomyces ramosus isolate closely related to strains previously isolated from placental hosts. Our results suggest that AGF communities in marsupials are in low abundance and show little signs of selection based on ecological and evolutionary factors.IMPORTANCEThe AGF are integral part of the microbiome of herbivores. They play a crucial role in breaking down plant biomass in hindgut and foregut fermenters. The majority of research has been conducted on the AGF community in placental mammalian hosts. However, it is important to note that many marsupial mammals are also herbivores and employ a hindgut or foregut fermentation strategy for breaking down plant biomass. So far, very little is known regarding the AGF diversity and community structure in marsupial mammals. To fill this knowledge gap, we conducted an amplicon-based diversity survey targeting AGF in 61 fecal samples from 10 marsupial species. We hypothesize that, given the distinct evolutionary history and alimentary tract architecture, novel and unique AGF communities would be encountered in marsupials. Our results indicate that marsupial AGF communities are highly stochastic, present in relatively low loads, and display community structure patterns comparable to AGF communities typically encountered in placental foregut hosts. Our results indicate that marsupial hosts harbor AGF communities; however, in contrast to the strong pattern of phylosymbiosis typically observed between AGF and placental herbivores, the identity and gut architecture appear to play a minor role in structuring AGF communities in marsupials.
Collapse
Affiliation(s)
- Adrienne L. Jones
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Carrie J. Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Casey H. Meili
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Rochelle M. Soo
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| |
Collapse
|
3
|
Wu Y, Jiao C, Diao Q, Tu Y. Effect of Dietary and Age Changes on Ruminal Microbial Diversity in Holstein Calves. Microorganisms 2023; 12:12. [PMID: 38276181 PMCID: PMC10818949 DOI: 10.3390/microorganisms12010012] [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: 11/02/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 01/27/2024] Open
Abstract
Ruminal microorganisms play a crucial role in the energy supply of ruminants and animal performance. We analyzed the variations in rumen bacteria and fungi at 45 d, 75 d, and 105 d by using 16SrRNA and ITS sequencing data and investigated their correlation with rumen fermentation. According to the results, rumen microflora tended to gradually mature with age, and bacterial and fungal establishment gradually stabilized. Upon comparing the three periods, the concentration of propionic acid increased significantly (p < 0.05) after weaning, and weaning accompanied by a transition in diet remarkably decreased (p < 0.05) rumen diversity in the short term and induced a corresponding change in the rumen microbiota composition. Bacteroidota, Actinobacteriota, and Firmicutes were the core bacterial phyla for all age periods. Ruminococcus, NK4A214_group, Sharpea, Rikenellaceae_RC9_gut_group, and norank_f__Butyricicoccaceae were the markedly abundant bacterial genera in pre-weaning. After weaning, the relative abundance of Erysipelotrichaceae_ UCG-002, Eubacterium_ruminantium_group, and Solobacterium significantly increased (p < 0.05). The relative abundance of Acetitomaculum increased with age with the greatest abundance noted at 105 d (37%). The dominant fungal phyla were Ascomycota and Basidiomycota, and Aspergillus and Xeromyces were the most abundant fungal genera after weaning. Trichomonascus, Phialosimplex, and Talaromyces were enriched at 105 d. However, the low abundance of Neocallimastigomycota was not detected throughout the study, which is worthy of further investigation. In addition, correlations were observed between age-related abundances of specific genera and microbiota functions and rumen fermentation-related parameters. This study revealed that rumen microbiota and rumen fermentation capacity are correlated, which contributed to a better understanding of the effects of age and diet on rumen microbiology and fermentation in calves.
Collapse
Affiliation(s)
| | | | | | - Yan Tu
- Key Laboratory for Dairy Cow Nutrition, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (C.J.); (Q.D.)
| |
Collapse
|
4
|
Liang Z, Zhang J, Ahmad AA, Han J, Gharechahi J, Du M, Zheng J, Wang P, Yan P, Salekdeh GH, Ding X. Forage lignocellulose is an important factor in driving the seasonal dynamics of rumen anaerobic fungi in grazing yak and cattle. Microbiol Spectr 2023; 11:e0078823. [PMID: 37707448 PMCID: PMC10581131 DOI: 10.1128/spectrum.00788-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/20/2023] [Indexed: 09/15/2023] Open
Abstract
Anaerobic fungi (AF) inhabit the gastrointestinal tract of ruminants and play an important role in the degradation of fiber feed. However, limited knowledge is available on seasonal dynamics and inter-species differences in rumen AF community in yak and cattle under natural grazing systems. Using the random forests model, the null model, and structural equation model, we investigated the seasonal dynamics and key driving factors of fiber-associated rumen AF in grazing yak and cattle throughout the year on the Qinghai-Tibet Plateau (QTP). We found that the richness and diversity of rumen AF of grazing yak and cattle in cold season were significantly higher than those in warm season (P < 0.05). We identified 12 rumen AF genera, among which , Cyllamyces, and Orpinomyces were predominant in the rumen of both grazing yak and cattle. LEfSe and random forest analysis showed that Feramyces, Tahromyces, and Buwchfawromyces were important seasonal indicator of rumen AF in grazing yak (P < 0.05), and Caecomyces, Cyllamyces, and Piromyces in grazing cattle (P < 0.05). Null model analysis revealed that the dynamic changes of rumen AF community structure were mainly affected by deterministic factors. Notably, mantel test and structural equation model revealed that forage physical-chemical properties, including dry matter (DM), neutral detergent fiber (NDF), and hemicellulose contents (HC) were the key factors driving the seasonal variations of the rumen AF community (P < 0.05). The results revealed that forage lignocellulose was probably an important factor affecting the seasonal dynamics and inter-species differences of the rumen AF community under natural grazing conditions. IMPORTANCE The seasonal dynamics of rumen anaerobic fungi in nature grazing yak and cattle were determined during cold and warm seasons based on pasture nutritional quality and environmental data sets. The main driving factors of anaerobic fungi in yak and cattle rumen were explored by combining random forest and structural equation models. In addition, the dynamic differences in the composition of the anaerobic fungi community in the yak and cattle in different seasons were characterized. It was found that some rumen anaerobic fungi have contributed to high fiber degradation rate in yak. These novel findings improve our understanding of the association of environmental and dietary seasonal variations with anaerobic fungal community, facilitating yak adaptation to high altitude.
Collapse
Affiliation(s)
- Zeyi Liang
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianbo Zhang
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Anum Ali Ahmad
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianlin Han
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mei Du
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Juanshan Zheng
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Peng Wang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
- Department of Molecular Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Xuezhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| |
Collapse
|
5
|
Zhao Y, Ren X, Wu H, Hu H, Cheng C, Du M, Huang Y, Zhao X, Wang L, Yi L, Tao J, Li Y, Lin Y, Su S, Dugarjaviin M. Diversity and functional prediction of fungal communities in different segments of mongolian horse gastrointestinal tracts. BMC Microbiol 2023; 23:253. [PMID: 37689675 PMCID: PMC10492400 DOI: 10.1186/s12866-023-03001-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 08/29/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND Anaerobic fungi are effective fibre-degrading microorganisms in the digestive tract of horses. However, our understanding of their diversity and community structure is limited, especially in different parts of the gastrointestinal tract. RESULTS For the first time, high-throughput sequencing technology was used to analyse and predict fungal microbial diversity in different parts of the gastrointestinal tract of Mongolian horses. The results revealed that the richness and diversity of fungi in the hindgut of Mongolian horses were much higher than those in the foregut. The foregut was dominated by Basidiomycota and Ascomycota, whereas the hindgut was dominated by Neocallimastigomycota and Basidiomycota. At the genus level, the relative abundance of many pathogenic fungi (Cryptococcus, Cladosporium, Alternaria, and Sarocladium) in the foregut was significantly higher than that in the posterior gut, indicating that Mongolian horses have strong disease resistance. The prediction of fungal function also showed significant differences in the fungal flora between the foregut and the hindgut. The fungi in Mongolian horses' foreguts were mainly pathologically nutritive and contained many animal and plant pathogens, particularly in the small intestine (jejunum and ileum). This indicates that the foregut may be the most important immune site in the digestive system of Mongolian horses, which explains the high disease resistance of Mongolian horses. The number of unassigned functional groups in the posterior gut was significantly higher than that in the anterior gut, indicating that the functions of fungal groups in the posterior gut have not been fully explored, and further studies are required in the future. CONCLUSIONS Analysis of high-throughput sequencing results revealed that the fungal composition varied greatly among different gastrointestinal tract segments in Mongolian horses, whose hindgut contains many anaerobic fungi involved in plant cellulose degradation. This provides important basic data for studying fungal diversity in the digestive system of healthy horses, which can be used for the health assessment of horses and provides clues for further research on the disease resistance and digestive capacity of horses, as well as a reference for the early diagnosis of intestinal diseases and innovative treatment methods.
Collapse
Affiliation(s)
- Yiping Zhao
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Xiujuan Ren
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Haiqing Wu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Biotechnology Research Centre, Hohhot, 010031, China
| | - He Hu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Biotechnology Research Centre, Hohhot, 010031, China
| | - Chao Cheng
- College of Life Science and Technology, Jining Normal University, Ulanqab, 012000, China
| | - Ming Du
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yao Huang
- Education Department, Baotou Light Industry Vocational Technical College, Baotou, China
| | - Xiaoqing Zhao
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Biotechnology Research Centre, Hohhot, 010031, China
| | - Liwei Wang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Biotechnology Research Centre, Hohhot, 010031, China
| | - Liuxi Yi
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Jinshan Tao
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yajing Li
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yanan Lin
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Shaofeng Su
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, 010018, China.
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Biotechnology Research Centre, Hohhot, 010031, China.
| | - Manglai Dugarjaviin
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Scientific Observing and Experimental Station of Equine Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Equine Research Centre, Inner Mongolia Agricultural University, Hohhot, 010018, China.
| |
Collapse
|
6
|
Li L, Qu L, Li T. The effects of Selenohomolanthionine supplementation on the rumen eukaryotic diversity of Shaanbei white cashmere wether goats. Sci Rep 2023; 13:13134. [PMID: 37573461 PMCID: PMC10423290 DOI: 10.1038/s41598-023-39953-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 08/02/2023] [Indexed: 08/14/2023] Open
Abstract
Selenium (Se) is an important microelement for animal health. However, the knowledge about the effects of Se supplementation on rumen eukaryotic community remains less explored. In this study, the ruminal eukaryotic diversity in three months old Shaanbei white cashmere wether goats, with body weight (26.18 ± 2.71) kg, fed a basal diet [0.016 mg/kg Se dry matter (DM), control group (CG)] were compared to those animals given basal diet supplemented with different levels of organic Se in the form of Selenohomolanthionine (SeHLan), namely low Se group (LSE, 0.3 mg/kg DM), medium Se group (MSE, 0.6 mg/kg Se DM) and high Se group (HSE, 1.2 mg/kg DM) using 18S rRNA amplicon sequencing. Illumina sequencing generated 2,623,541 reads corresponding to 3123 operational taxonomic units (OTUs). Taxonomic analysis revealed that Eukaryota (77.95%) and Fungi (14.10%) were the dominant eukaryotic kingdom in all samples. The predominant rumen eukaryotic phylum was found to be Ciliophora (92.14%), while fungal phyla were dominated by Ascomycota (40.77%), Basidiomycota (23.77%), Mucoromycota (18.32%) and unidentified_Fungi (13.89%). The dominant eukaryotic genera were found to be Entodinium (55.44%), Ophryoscolex (10.51%) and Polyplastron (10.19%), while the fungal genera were dominanted by Mucor (15.39%), Pichia (9.88%), Aspergillu (8.24%), Malassezia (7.73%) and unidentified_Neocallimastigaceae (7.72%). The relative abundance of eukaryotic genera Ophryoscolex, Enoploplastron and fungal genus Mucor were found to differ significantly among the four treatment groups (P < 0.05). Moreover, Spearman correlation analysis revealed that the ciliate protozoa and fungi were negatively correlated with each other. The results of this study provided newer information about the effects of Se on rumen eukaryotic diversity patterns using 18s rRNA high-throughput sequencing technology.
Collapse
Affiliation(s)
- Longping Li
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, 719000, China.
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, 719000, China
| | - Tuo Li
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, 719000, China
- College of Life Sciences, Yulin University, Yulin, 719000, China
| |
Collapse
|
7
|
Meili CH, Jones AL, Arreola AX, Habel J, Pratt CJ, Hanafy RA, Wang Y, Yassin AS, TagElDein MA, Moon CD, Janssen PH, Shrestha M, Rajbhandari P, Nagler M, Vinzelj JM, Podmirseg SM, Stajich JE, Goetsch AL, Hayes J, Young D, Fliegerova K, Grilli DJ, Vodička R, Moniello G, Mattiello S, Kashef MT, Nagy YI, Edwards JA, Dagar SS, Foote AP, Youssef NH, Elshahed MS. Patterns and determinants of the global herbivorous mycobiome. Nat Commun 2023; 14:3798. [PMID: 37365172 PMCID: PMC10293281 DOI: 10.1038/s41467-023-39508-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
Despite their role in host nutrition, the anaerobic gut fungal (AGF) component of the herbivorous gut microbiome remains poorly characterized. Here, to examine global patterns and determinants of AGF diversity, we generate and analyze an amplicon dataset from 661 fecal samples from 34 mammalian species, 9 families, and 6 continents. We identify 56 novel genera, greatly expanding AGF diversity beyond current estimates (31 genera and candidate genera). Community structure analysis indicates that host phylogenetic affiliation, not domestication status and biogeography, shapes the community rather than. Fungal-host associations are stronger and more specific in hindgut fermenters than in foregut fermenters. Transcriptomics-enabled phylogenomic and molecular clock analyses of 52 strains from 14 genera indicate that most genera with preferences for hindgut hosts evolved earlier (44-58 Mya) than those with preferences for foregut hosts (22-32 Mya). Our results greatly expand the documented scope of AGF diversity and provide an ecologically and evolutionary-grounded model to explain the observed patterns of AGF diversity in extant animal hosts.
Collapse
Affiliation(s)
- Casey H Meili
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Adrienne L Jones
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Alex X Arreola
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Jeffrey Habel
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Carrie J Pratt
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Radwa A Hanafy
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Yan Wang
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Aymen S Yassin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Moustafa A TagElDein
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Christina D Moon
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Peter H Janssen
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Mitesh Shrestha
- Department of Applied Microbiology and Food Technology, Research Institute for Bioscience and Biotechnology (RIBB), Kathmandu, Nepal
| | - Prajwal Rajbhandari
- Department of Applied Microbiology and Food Technology, Research Institute for Bioscience and Biotechnology (RIBB), Kathmandu, Nepal
| | - Magdalena Nagler
- Universität Innsbruck, Faculty of Biology, Department of Microbiology, Innsbruck, Austria
| | - Julia M Vinzelj
- Universität Innsbruck, Faculty of Biology, Department of Microbiology, Innsbruck, Austria
| | - Sabine M Podmirseg
- Universität Innsbruck, Faculty of Biology, Department of Microbiology, Innsbruck, Austria
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, USA
| | | | | | - Diana Young
- Bavarian State Research Center for Agriculture, Freising, Germany
| | - Katerina Fliegerova
- Institute of Animal Physiology and Genetics Czech Academy of Sciences, Prague, Czechia
| | - Diego Javier Grilli
- Área de Microbiología, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina
| | | | - Giuseppe Moniello
- Department of Veterinary Medicine, University of Sassari, Sardinia, Italy
| | - Silvana Mattiello
- University of Milan, Dept. of Agricultural and Environmental Sciences, Milan, Italy
| | - Mona T Kashef
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Yosra I Nagy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | | | | | - Andrew P Foote
- Oklahoma State University, Department of Animal and Food Sciences, Stillwater, OK, USA
| | - Noha H Youssef
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA.
| | - Mostafa S Elshahed
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA.
| |
Collapse
|
8
|
Du Y, Gao Y, Hu M, Hou J, Yang L, Wang X, Du W, Liu J, Xu Q. Colonization and development of the gut microbiome in calves. J Anim Sci Biotechnol 2023; 14:46. [PMID: 37031166 PMCID: PMC10082981 DOI: 10.1186/s40104-023-00856-x] [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: 10/14/2022] [Accepted: 02/16/2023] [Indexed: 04/10/2023] Open
Abstract
Colonization and development of the gut microbiome are crucial for the growth and health of calves. In this review, we summarized the colonization, beneficial nutrition, immune function of gut microbiota, function of the gut barrier, and the evolution of core microbiota in the gut of calves of different ages. Homeostasis of gut microbiome is beneficial for nutritional and immune system development of calves. Disruption of the gut microbiome leads to digestive diseases in calves, such as diarrhea and intestinal inflammation. Microbiota already exists in the gut of calf fetuses, and the colonization of microbiota continues to change dynamically under the influence of various factors, which include probiotics, diet, age, and genotype. Colonization depends on the interaction between the gut microbiota and the immune system of calves. The abundance and diversity of these commensal microbiota stabilize and play a critical role in the health of calves.
Collapse
Affiliation(s)
- Yufeng Du
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ya Gao
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingyang Hu
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiu Hou
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Linhai Yang
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianghuang Wang
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenjuan Du
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianxin Liu
- MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qingbiao Xu
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
9
|
The impact of polyphenolic compounds on the in vitro growth of oak-associated foliar endophytic and saprotrophic fungi. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2023.101226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
|
10
|
Patel J, Grab S, De Maayer P. Distinct microbial communities across a climatically versatile summit in the Lesotho highlands. Ecol Evol 2023; 13:e9891. [PMID: 36937054 PMCID: PMC10015361 DOI: 10.1002/ece3.9891] [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: 11/14/2022] [Revised: 02/14/2023] [Accepted: 02/24/2023] [Indexed: 03/17/2023] Open
Abstract
Most studies investigating the effects of climatological factors on microbial community composition and diversity focus on comparisons of geographically distinct environments (e.g., cold vs hot deserts) or across various temporal scales. Mountain regions provide unique environments to explore relationships between various environmental factors and soil microorganisms given their range of microclimatic conditions and vegetation types. This study investigated micro-topographically (i.e., north-/south-facing slope aspects and flat plateau between them) controlled microbial diversity and community structures across a Lesotho mountain summit. Amplicon sequence analysis revealed that the north- and south-facing slopes were dominated by more Proteobacteria and Bacteroidetes, while the plateau was dominated by more Acidobacteria. Fungi from the phylum Chytridiomycota more strongly dominated the plateau and the north-facing slope than the south-facing slope. Slope aspect, through its direct influence on air and soil micro-climatology and plant diversity, significantly affects bacterial and fungal community structures at this location. These results provide original insight into soil microbial diversity in the Lesotho highlands and offer an opportunity to project the likely response of soil microorganisms to future climate warming in highly variable mountain environments such as the Lesotho highlands.
Collapse
Affiliation(s)
- Jasmin Patel
- School of Molecular and Cell Biology, Faculty of ScienceUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Stefan Grab
- School of Geography, Archaeology and Environmental Studies, Faculty of ScienceUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Pieter De Maayer
- School of Molecular and Cell Biology, Faculty of ScienceUniversity of the WitwatersrandJohannesburgSouth Africa
| |
Collapse
|
11
|
Hu J, Chen J, Hou Q, Xu X, Ren J, Ma L, Yan X. Core-predominant gut fungus Kazachstania slooffiae promotes intestinal epithelial glycolysis via lysine desuccinylation in pigs. MICROBIOME 2023; 11:31. [PMID: 36814349 PMCID: PMC9948344 DOI: 10.1186/s40168-023-01468-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Gut fungi are increasingly recognized as important contributors to host physiology, although most studies have focused on gut bacteria. Post-translational modifications (PTMs) of proteins play vital roles in cell metabolism. However, the contribution of gut fungi to host protein PTMs remains unclear. Mining gut fungi that mediate host protein PTMs and dissecting their mechanism are urgently needed. RESULTS We studied the gut fungal communities of 56 weaned piglets and 56 finishing pigs from seven pig breeds using internal transcribed spacer (ITS) gene amplicon sequencing and metagenomics. The results showed that Kazachstania slooffiae was the most abundant gut fungal species in the seven breeds of weaned piglets. K. slooffiae decreased intestinal epithelial lysine succinylation levels, and these proteins were especially enriched in the glycolysis pathway. We demonstrated that K. slooffiae promoted intestinal epithelial glycolysis by decreasing lysine succinylation by activating sirtuin 5 (SIRT5). Furthermore, K. slooffiae-derived 5'-methylthioadenosine metabolite promoted the SIRT5 activity. CONCLUSIONS These findings provide a landscape of gut fungal communities of pigs and suggest that K. slooffiae plays a crucial role in intestinal glycolysis metabolism through lysine desuccinylation. Our data also suggest a potential protective strategy for pigs with an insufficient intestinal energy supply. Video Abstract.
Collapse
Affiliation(s)
- Jun Hu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Jianwei Chen
- BGI Research-Qingdao, BGI, Qingdao, 266555, China
| | - Qiliang Hou
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Xiaojian Xu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Jing Ren
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Libao Ma
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Xianghua Yan
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China.
| |
Collapse
|
12
|
Lv QB, Meng JX, Ma H, Liu R, Qin Y, Qin YF, Geng HL, Ni HB, Zhang XX. Description of Gut Mycobiota Composition and Diversity of Caprinae Animals. Microbiol Spectr 2023; 11:e0242422. [PMID: 36625628 PMCID: PMC9927506 DOI: 10.1128/spectrum.02424-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
The fungal community, also known as mycobiota, plays pivotal roles in host nutrition and metabolism and has potential to cause disease. However, knowledge of the gut fungal structure in Caprinae is quite limited. In this study, the composition and diversity of the gut mycobiota of Caprinae animals from different geographical locations (Anhui, Jilin, Guangxi, Shandong, Shanxi, and Tibet) were comprehensively characterized by analyzing the internal transcribed spacer 2 (ITS-2) sequences of the fungal community. The results showed that Ascomycota and Basidiomycota were the dominant phyla, which, respectively, accounted for 90.86 to 95.27% and 2.58 to 7.62% of sequences in samples from each region. Nonetheless, the structure of the gut mycobiota was largely different in Caprinae animals in the different provinces. Therein, Sporormiaceae and Thelebolaceae were the dominant fungal families in the samples from Tibet, whereas their abundance was generally low in other regions. The intestinal diversity of individuals from Guangxi was higher than that in other regions. In addition, there were 114 differential genera among all regions. Finally, the co-occurrence network revealed 285 significant correlations in cross-family pairs in the guts of Caprinae animals, which contained 149 positive and 136 negative relationships, with 96 bacterial and 86 fungal participants at the family level. This study has improved the understanding of the mycobiota of ruminants and provided support for the improvement in animal health and productivity. IMPORTANCE In this study, we elucidated and analyzed the structure of the gut mycobiota of Caprinae animals from different regions. This study revealed differences in the structure of the gut mycobiota among Caprinae animals from different geographical environments. Based on previous findings, correlations between fungal and bacterial communities were analyzed. This study adds to previous research that has expanded the present understanding of the gut microbiome of Caprinae animals.
Collapse
Affiliation(s)
- Qing-Bo Lv
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jin-Xin Meng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - He Ma
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Rui Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Ya Qin
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province, People’s Republic of China
| | - Yi-Feng Qin
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province, People’s Republic of China
| | - Hong-Li Geng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin Province, People’s Republic of China
| | - Hong-Bo Ni
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xiao-Xuan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, People’s Republic of China
| |
Collapse
|
13
|
Zhang Z, Huang B, Gao X, Shi X, Wang X, Wang T, Wang Y, Liu G, Wang C. Dynamic changes in fecal microbiota in donkey foals during weaning: From pre-weaning to post-weaning. Front Microbiol 2023; 14:1105330. [PMID: 36778861 PMCID: PMC9915154 DOI: 10.3389/fmicb.2023.1105330] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/12/2023] [Indexed: 01/28/2023] Open
Abstract
Introduction A better understanding of the microbiota community in donkey foals during the weaning transition is a prerequisite to optimize gut function and improve feed efficiency. The objective of the present study was to investigate the dynamic changes in fecal microbiota in donkey foals from pre-to post-weaning period. Methods A total of 27 fecal samples of donkey foals were collected in the rectum before morning feeding at pre-weaning (30 days of age, PreW group, n = 9), dur-weaning (100 days of age, DurW group, n = 9) and post-weaning (170 days of age, PostW group, n = 9) period. The 16S rRNA amplicon sequencing were employed to indicate the microbial changes during the weaning period. Results In the present study, the cessation of breastfeeding gradually and weaning onto plant-based feeds increased the microbial diversity and richness, with a higher Shannon, Ace, Chao and Sobs index in DurW and PostW than in PreW (p < 0.05). The predominant bacterial phyla in donkey foal feces were Firmicutes (>50.5%) and Bacteroidota (>29.5%), and the predominant anaerobic fungi and archaea were Neocallimastigomycota and Euryarchaeota. The cellulolytic related bacteria including phylum Firmicutes, Spirochaetota and Fibrobacterota and genus norank_f_F082, Treponema, NK4A214_group, Lachnospiraceae_AC2044_group and Streptococcus were increased from pre-to post-weaning donkey foals (p < 0.05). Meanwhile, the functions related to the fatty acid biosynthesis, carbohydrate metabolism and amino acid biosynthesis were significantly enriched in the fecal microbiome in the DurW and PostW donkeys. Furthermore, the present study provided the first direct evidence that the initial colonization and establishment of anaerobic fungi and archaea in donkey foals began prior to weaning. The relative abundance of Orpinomyces were the highest in DurW donkey foals among the three groups (p < 0.01). In terms of archaea, the abundance of Methanobrevibacter were higher in PreW than in DurW and PostW (p < 0.01), but the abundance of Methanocorpusculum were significantly increased in DurW and PostW compared to PreW donkey foals (p < 0.01). Discussion Altogether, the current study contributes to a comprehensive understanding of the development of the microbiota community in donkey foals from pre-to post-weaning period, which may eventually result in an improvement of the digestion and feed efficiency in donkeys.
Collapse
|
14
|
Lin L, Lai Z, Zhang J, Zhu W, Mao S. The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet. MICROBIOME 2023; 11:10. [PMID: 36670455 PMCID: PMC9863278 DOI: 10.1186/s40168-022-01453-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 12/19/2022] [Indexed: 05/10/2023]
Abstract
BACKGROUND Dairy cattle (Bos taurus), especially Holstein cows, which are the highest-producing dairy animals and are widely bred to provide milk products to humans, rely critically on their associated gastrointestinal tract (GIT) microbiota to digest plant feed. However, the region-specific taxonomic composition and function of the GIT microbiome in dairy cattle and the mechanistic basis for the diet-induced effects remain to be elucidated. RESULTS: We collected 120 digesta samples from 10 GIT regions of 12 Holstein cows fed forage- and grain-based diets and characterized their GIT microbiome via functional shotgun metagenomics and the resolution of metagenome-assembled genomes. Our results demonstrated that the GIT microbiome was mainly partitioned into three distinct clusters, four-chambered stomach, small intestine, and large intestine. Moreover, we found that the four-chambered stomach microbiome with the highest diversity had a strong ability to degrade recalcitrant polysaccharide substrates, underpinned by the prevalence of potential cellulosome--producing and plant-derived polysaccharide utilization loci-encoding consortia. In contrast, the post-gastric intestinal microbiome orchestrated alternative fermentation pathways to adapt to nutrient availability and energy acquisition. Diet shifts selectively modified the metabolic cascades of the microbiome in specific GIT regions, evidenced by the loss of fiber-degrading taxa and increased hydrogen sinks in propionate after grain introduction. CONCLUSIONS Our findings provide new insights into GIT microbial organization and function in dairy cattle by GIT regions and diet regimes, which offers clues for improving animal production and health in the future. Video Abstract.
Collapse
Affiliation(s)
- Limei Lin
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research On Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zheng Lai
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research On Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiyou Zhang
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research On Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research On Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shengyong Mao
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research On Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
15
|
Wunderlich G, Bull M, Ross T, Rose M, Chapman B. Understanding the microbial fibre degrading communities & processes in the equine gut. Anim Microbiome 2023; 5:3. [PMID: 36635784 PMCID: PMC9837927 DOI: 10.1186/s42523-022-00224-6] [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: 07/29/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023] Open
Abstract
The equine gastrointestinal tract is a self-sufficient fermentation system, housing a complex microbial consortium that acts synergistically and independently to break down complex lignocellulolytic material that enters the equine gut. Despite being strict herbivores, equids such as horses and zebras lack the diversity of enzymes needed to completely break down plant tissue, instead relying on their resident microbes to carry out fibrolysis to yield vital energy sources such as short chain fatty acids. The bulk of equine digestion occurs in the large intestine, where digesta is fermented for 36-48 h through the synergistic activities of bacteria, fungi, and methanogenic archaea. Anaerobic gut dwelling bacteria and fungi break down complex plant polysaccharides through combined mechanical and enzymatic strategies, and notably possess some of the greatest diversity and repertoire of carbohydrate active enzymes among characterized microbes. In addition to the production of enzymes, some equid-isolated anaerobic fungi and bacteria have been shown to possess cellulosomes, powerful multi-enzyme complexes that further enhance break down. The activities of both anaerobic fungi and bacteria are further facilitated by facultatively aerobic yeasts and methanogenic archaea, who maintain an optimal environment for fibrolytic organisms, ultimately leading to increased fibrolytic microbial counts and heightened enzymatic activity. The unique interactions within the equine gut as well as the novel species and powerful mechanisms employed by these microbes makes the equine gut a valuable ecosystem to study fibrolytic functions within complex communities. This review outlines the primary taxa involved in fibre break down within the equine gut and further illuminates the enzymatic strategies and metabolic pathways used by these microbes. We discuss current methods used in analysing fibrolytic functions in complex microbial communities and propose a shift towards the development of functional assays to deepen our understanding of this unique ecosystem.
Collapse
Affiliation(s)
- Georgia Wunderlich
- grid.1009.80000 0004 1936 826XTasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia ,Quantal Bioscience Pty Ltd, Castle Hill, Australia
| | - Michelle Bull
- grid.1009.80000 0004 1936 826XTasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia ,Quantal Bioscience Pty Ltd, Castle Hill, Australia
| | - Tom Ross
- grid.1009.80000 0004 1936 826XTasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
| | - Michael Rose
- grid.1009.80000 0004 1936 826XTasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
| | - Belinda Chapman
- grid.1009.80000 0004 1936 826XTasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia ,Quantal Bioscience Pty Ltd, Castle Hill, Australia
| |
Collapse
|
16
|
Tang Q, He R, Huang F, Liang Q, Zhou Z, Zhou J, Wang Q, Zou C, Gu Q. Effects of ensiling sugarcane tops with bacteria-enzyme inoculants on growth performance, nutrient digestibility, and the associated rumen microbiome in beef cattle. J Anim Sci 2023; 101:skad326. [PMID: 37813104 PMCID: PMC10636847 DOI: 10.1093/jas/skad326] [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] [Received: 04/12/2023] [Accepted: 10/07/2023] [Indexed: 10/11/2023] Open
Abstract
Major challenges when ensiling sugarcane tops include fermentation that results in high quantities of alcohol and decrease in nutrient digestibility due to the accumulation of fiber components. Increased efforts to apply bacteria-enzyme inoculants in silage have the potential to improve nutrient digestibility. This study aimed to evaluate the effects of ensiling sugarcane tops with bacteria-enzyme inoculants or mixed bacterial inoculants on growth performance, nutrient digestibility, and rumen microbiome in beef cattle. Chopped sugarcane tops were ensiled in plastic bags for 60 d after application of 1) no inoculant (control check, CK); 2) bacteria-enzyme inoculants containing Pediococcus acidilactici, Saccharomyces cerevisiae, cellulase, and xylanase (T1, viable colony-forming units of each bacterial strain ≥108 CFU/g; enzyme activity of each enzyme ≥200 U/g); or 3) mixed bacterial inoculants containing Lactobacillus plantarum, Bacillus subtilis, and Aspergillus oryzae (T2, viable colony-forming units of each bacterial strain ≥107 CFU/g). Silages were fed to eighteen Holstein bull calves (n = 6/treatment) weighing 163.83 ± 7.13 kg to determine intake in a 49-d experimental period. The results showed that beef cattle-fed T1 silage or T2 silage had a significantly higher (P < 0.05) average daily gain than those fed CK silage, but the difference in dry matter intake was not significant (P > 0.05). The apparent digestibility of crude protein (CP) and acid detergent fiber (ADF) were higher (P < 0.05) for beef cattle-fed T1 silage or T2 silage than for those fed CK silage. The rumen bacterial community of beef cattle-fed T1 silage or T2 silage had a tendency to increase (P > 0.05) abundance of Firmicutes and Rikenellaceae_RC9_gut_group than those fed CK silage. Rumen fungal communities of beef cattle-fed T1 or T2 silage had a tendency to increase (P > 0.05) abundance of Mortierellomycota and of Mortierella than those fed CK silage. Spearman's rank correlation coefficient showed that the apparent digestibility of ADF for beef cattle was positively correlated with unclassified_p_Ascomycota of the fungal genera (P < 0.05). Neocalimastigomycota of the fungal phyla was strongly positively correlated with the apparent digestibility of neutral detergent fiber (NDF) (P < 0.05). Ruminococcus was positively correlated with the apparent digestibility of CP (P < 0.05). It was concluded that both T1 and T2 improved the growth performance of beef cattle by improving the ruminal apparent digestibility of CP and ADF, and had no significant impact on major rumen microbial communities in beef cattle.
Collapse
Affiliation(s)
- Qingfeng Tang
- Collegeof Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Renchun He
- The Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning, Guangxi 530000, China
| | - Feng Huang
- Collegeof Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Qimei Liang
- The Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning, Guangxi 530000, China
| | - Zhiyang Zhou
- The Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning, Guangxi 530000, China
| | - Junhua Zhou
- The Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning, Guangxi 530000, China
| | - Qizhi Wang
- The Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning, Guangxi 530000, China
| | - Caixia Zou
- Collegeof Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Qichao Gu
- Collegeof Animal Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| |
Collapse
|
17
|
Joshi A, Young D, Huang L, Mosberger L, Munk B, Vinzelj J, Flad V, Sczyrba A, Griffith GW, Podmirseg SM, Warthmann R, Lebuhn M, Insam H. Effect of Growth Media on the Diversity of Neocallimastigomycetes from Non-Rumen Habitats. Microorganisms 2022; 10:1972. [PMID: 36296248 PMCID: PMC9612151 DOI: 10.3390/microorganisms10101972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/25/2022] [Accepted: 10/01/2022] [Indexed: 12/02/2022] Open
Abstract
Anaerobic fungi (AF), belonging to the phylum Neocallimastigomycota, are a pivotal component of the digestive tract microbiome of various herbivorous animals. In the last decade, the diversity of AF has rapidly expanded due to the exploration of numerous (novel) habitats. Studies aiming at understanding the role of AF require robust and reliable isolation and cultivation techniques, many of which remained unchanged for decades. Using amplicon sequencing, we compared three different media: medium with rumen fluid (RF), depleted rumen fluid (DRF), and no rumen fluid (NRF) to enrich the AF from the feces of yak, as a rumen control; and Przewalski's horse, llama, guanaco, and elephant, as a non-rumen habitats. The results revealed the selective enrichment of Piromyces and Neocallimastix from the feces of elephant and llama, respectively, in the RF medium. Similarly, the enrichment culture in DRF medium explicitly manifested Piromyces-related sequences from elephant feces. Five new clades (MM1-5) were defined from llama, guanaco, yak, and elephant feces that could as well be enriched from llama and elephant samples using non-conventional DRF and NRF media. This study presents evidence for the selective enrichment of certain genera in medium with RF and DRF from rumen as well as from non-rumen samples. NRF medium is suggested for the isolation of AF from non-rumen environments.
Collapse
Affiliation(s)
- Akshay Joshi
- Biocatalysis, Environment and Process Technology Unit, Life Science and Facility Management, Zurich University of Applied Sciences (ZHAW), 8820 Wadenswil, Switzerland
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Diana Young
- Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany
| | - Liren Huang
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Lona Mosberger
- Biocatalysis, Environment and Process Technology Unit, Life Science and Facility Management, Zurich University of Applied Sciences (ZHAW), 8820 Wadenswil, Switzerland
| | - Bernhard Munk
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Julia Vinzelj
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Veronika Flad
- Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany
| | - Alexander Sczyrba
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Gareth W. Griffith
- Department of Life Sciences, Cledwyn Building, Aberystwyth University, Aberystwyth SY23 3DD, UK
| | - Sabine Marie Podmirseg
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Rolf Warthmann
- Biocatalysis, Environment and Process Technology Unit, Life Science and Facility Management, Zurich University of Applied Sciences (ZHAW), 8820 Wadenswil, Switzerland
| | - Michael Lebuhn
- Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| |
Collapse
|
18
|
Young D, Joshi A, Huang L, Munk B, Wurzbacher C, Youssef NH, Elshahed MS, Moon CD, Ochsenreither K, Griffith GW, Callaghan TM, Sczyrba A, Lebuhn M, Flad V. Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages. Microorganisms 2022; 10:1749. [PMID: 36144352 PMCID: PMC9504928 DOI: 10.3390/microorganisms10091749] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/16/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022] Open
Abstract
Anaerobic fungi from the herbivore digestive tract (Neocallimastigomycetes) are primary lignocellulose modifiers and hold promise for biotechnological applications. Their molecular detection is currently difficult due to the non-specificity of published primer pairs, which impairs evolutionary and ecological research with environmental samples. We developed and validated a Neocallimastigomycetes-specific PCR primer pair targeting the D2 region of the ribosomal large subunit suitable for screening, quantifying, and sequencing. We evaluated this primer pair in silico on sequences from all known genera, in vitro with pure cultures covering 16 of the 20 known genera, and on environmental samples with highly diverse microbiomes. The amplified region allowed phylogenetic differentiation of all known genera and most species. The amplicon is about 350 bp long, suitable for short-read high-throughput sequencing as well as qPCR assays. Sequencing of herbivore fecal samples verified the specificity of the primer pair and recovered highly diverse and so far unknown anaerobic gut fungal taxa. As the chosen barcoding region can be easily aligned and is taxonomically informative, the sequences can be used for classification and phylogenetic inferences. Several new Neocallimastigomycetes clades were obtained, some of which represent putative novel lineages such as a clade from feces of the rodent Dolichotis patagonum (mara).
Collapse
Affiliation(s)
- Diana Young
- Micro and Molecular Biology, Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, 85354 Freising, Germany
| | - Akshay Joshi
- Biocatalysis, Environment and Process Technology Unit, Life Science and Facility Management, ZHAW, 8820 Wadenswil, Switzerland
- Department of Microbiology, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Liren Huang
- Center for Biotechnology (CeBiTec), University of Bielefeld, 33615 Bielefeld, Germany
| | - Bernhard Munk
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics (OSU), Oklahoma State University, Stillwater, OK 74074, USA
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics (OSU), Oklahoma State University, Stillwater, OK 74074, USA
| | - Christina D. Moon
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Katrin Ochsenreither
- Process Engineering in Life Sciences 2: Technical Biology (KIT), Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Gareth W. Griffith
- Department of Life Sciences (DoLS), Aberystwyth University, Aberystwyth SY23 3DD, Wales, UK
| | | | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), University of Bielefeld, 33615 Bielefeld, Germany
| | - Michael Lebuhn
- Micro and Molecular Biology, Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, 85354 Freising, Germany
| | - Veronika Flad
- Micro and Molecular Biology, Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, 85354 Freising, Germany
| |
Collapse
|
19
|
Hanafy RA, Dagar SS, Griffith GW, Pratt CJ, Youssef NH, Elshahed MS. Taxonomy of the anaerobic gut fungi ( Neocallimastigomycota): a review of classification criteria and description of current taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 35776761 DOI: 10.1099/ijsem.0.005322] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Members of the anaerobic gut fungi (Neocallimastigomycota) reside in the rumen and alimentary tract of larger mammalian and some reptilian, marsupial and avian herbivores. The recent decade has witnessed a significant expansion in the number of described Neocallimastigomycota genera and species. However, the difficulties associated with the isolation and maintenance of Neocallimastigomycota strains has greatly complicated comparative studies to resolve inter- and intra-genus relationships. Here, we provide an updated outline of Neocallimastigomycota taxonomy. We critically evaluate various morphological, microscopic and phylogenetic traits previously and currently utilized in Neocallimastigomycota taxonomy, and provide an updated key for quick characterization of all genera. We then synthesize data from taxa description manuscripts, prior comparative efforts and molecular sequence data to present an updated list of Neocallimastigomycota genera and species, with an emphasis on resolving relationships and identifying synonymy between recent and historic strains. We supplement data from published manuscripts with information and illustrations from strains in the authors' collections. Twenty genera and 36 species are recognized, but the status of 10 species in the genera Caecomyces, Piromyces, Anaeromyces and Cyllamyces remains uncertain due to the unavailability of culture and conferre (cf.) strains, lack of sequence data, and/or inadequacy of available microscopic and phenotypic data. Six cases of synonymy are identified in the genera Neocallimastix and Caecomyces, and two names in the genus Piromyces are rejected based on apparent misclassification.
Collapse
Affiliation(s)
- Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Sumit S Dagar
- Bioenergy Group, Agharkar Research Institute, Pune, India
| | - Gareth W Griffith
- Institute of Biological, Environmental, and Rural Sciences (IBERS) Aberystwyth University, Aberystwyth, Wales, UK
| | - Carrie J Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| |
Collapse
|
20
|
Zhang Z, Gao X, Dong W, Huang B, Wang Y, Zhu M, Wang C. Plant cell wall breakdown by hindgut microorganisms: can we get scientific insights from rumen microorganisms? J Equine Vet Sci 2022; 115:104027. [PMID: 35661771 DOI: 10.1016/j.jevs.2022.104027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 01/20/2023]
Abstract
Equines and ruminants have evolved as grazing herbivores with specialized gastrointestinal tracts capable of utilizing a wide range of fibrous feeds. In China, agricultural by-products, including corn straw, wheat straw, peanut vine, wheat husk, rice husk, and grass hay, have been extensively included in both equine and ruminant diets. These plant materials, which are composed predominantly of cellulose, hemicellulose, noncellulosic polysaccharides, and lignin, are largely undegradable by equines and ruminants themselves. Their breakdown is accomplished by communities of resident microorganisms that live in symbiotic or mutualistic associations with the host. Information relating to microbial composition in the hindgut and rumen has become increasingly available. Rumen fermentation is unique in that plant cell wall breakdown relies on the cooperation between microorganisms that produce fibrolytic enzymes and that ruminant animals provide an anaerobic fermentation chamber. Similar to the rumen, the equine hindgut is also an immensely enlarged fermentative chamber that includes an extremely abundant and highly complex community of microorganisms. However, few studies have characterized the microbial functions and their utilization process of lignocellulosic feeds within the equine hindgut. The process of understanding and describing plant cell wall degradation mechanisms in the equine hindgut ecosystem is important for providing information for proper feeding practices to be implemented. In the present study, we gather existing information on the rumen and equine ecosystem and provide scientific insights for understanding the process of plant cell wall breakdown within the hindgut.
Collapse
Affiliation(s)
- Zhenwei Zhang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Xu Gao
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Wanting Dong
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Bingjian Huang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Yonghui Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Mingxia Zhu
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China.
| |
Collapse
|
21
|
Abstract
The utilization of dietary cellulose by resident bacteria in the large intestine of mammals, both herbivores and omnivores (including humans), has been a subject of interest since the nineteenth century. Cellulolytic bacteria are key participants in this breakdown process of cellulose, which is otherwise indigestible by the host. They critically contribute to host nutrition and health through the production of short-chain fatty acids, in addition to maintaining the balance of intestinal microbiota. Despite this key role, cellulolytic bacteria have not been well studied. In this review, we first retrace the history of the discovery of cellulolytic bacteria in the large intestine. We then focus on the current knowledge of cellulolytic bacteria isolated from the large intestine of various animal species and humans and discuss the methods used for isolating these bacteria. Moreover, we summarize the enzymes and the mechanisms involved in cellulose degradation. Finally, we present the contribution of these bacteria to the host.
Collapse
Affiliation(s)
- Alicia Froidurot
- Université Bourgogne Franche–Comté, Institut Agro Dijon, PAM UMR A 02.102, Dijon, France,CONTACT Alicia Froidurot Université Bourgogne Franche–Comté, Institut Agro Dijon, PAM UMR A 02.102Dijon, France
| | - Véronique Julliand
- Université Bourgogne Franche–Comté, Institut Agro Dijon, PAM UMR A 02.102, Dijon, France
| |
Collapse
|
22
|
Weinstein SB, Stephens WZ, Greenhalgh R, Round JL, Dearing MD. Wild herbivorous mammals (genus Neotoma) host a diverse but transient assemblage of fungi. Symbiosis 2022; 87:45-58. [PMID: 37915425 PMCID: PMC10619970 DOI: 10.1007/s13199-022-00853-0] [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: 04/30/2022] [Accepted: 06/14/2022] [Indexed: 10/16/2022]
Abstract
Fungi are often overlooked in microbiome research and, as a result, little is known about the mammalian mycobiome. Although frequently detected in vertebrate guts and known to contribute to digestion in some herbivores, whether these eukaryotes are a persistent part of the mammalian gut microbiome remains contentious. To address this question, we sampled fungi from wild woodrats (Neotoma spp.) collected from 25 populations across the southwestern United States. For each animal, we collected a fecal sample in the wild, and then re-sampled the same individual after a month in captivity on a controlled diet. We characterized and quantified fungi using three techniques: ITS metabarcoding, shotgun metagenomics and qPCR. Wild individuals contained diverse fungal assemblages dominated by plant pathogens, widespread molds, and coprophilous taxa primarily in Ascomycota and Mucoromycota. Fungal abundance, diversity and composition differed between individuals, and was primarily influenced by animal geographic origin. Fungal abundance and diversity significantly declined in captivity, indicating that most fungi in wild hosts came from diet and environmental exposure. While this suggests that these mammals lack a persistent gut mycobiome, natural fungal exposure may still impact fungal dispersal and animal health.
Collapse
Affiliation(s)
- Sara B. Weinstein
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - W. Zac Stephens
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT, USA
| | - Robert Greenhalgh
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - June L. Round
- University of Utah School of Medicine, Department of Pathology, Division of Microbiology and Immunology, Salt Lake City, UT, USA
| | - M. Denise Dearing
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| |
Collapse
|
23
|
Robinson K, Yang Q, Stewart S, Whitmore MA, Zhang G. Biogeography, succession, and origin of the chicken intestinal mycobiome. MICROBIOME 2022; 10:55. [PMID: 35365230 PMCID: PMC8976367 DOI: 10.1186/s40168-022-01252-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 02/24/2022] [Indexed: 05/15/2023]
Abstract
BACKGROUND Extensive work has been accomplished to characterize the intestinal bacterial community, known as the microbiota, and its association with host health and disease. However, very little is known about the spatiotemporal development and the origin of a minor intestinal fungal community, known as the mycobiota, in humans and animals, particularly in avian species. RESULTS In this study, we comprehensively characterized the biogeography and succession of the gastrointestinal (GI) mycobiota of broiler chickens and further revealed the fungal sources that are responsible for initial and long-term establishment of the mycobiota in the GI tract. Using Illumina sequencing of the internal transcribed spacer 2 (ITS2) region of fungal rRNA genes, we detected significant spatial and temporal differences in the mycobiota along the GI tract. In contrary to the microbiota, the mycobiota was more diverse in the upper than the lower GI tract with no apparent trend of succession up to 42 days of age. The intestinal mycobiota was dominated by the phyla Ascomycota and Basidiomycota with Gibberella, Aspergillus, and Candida being the most abundant genera. Although the chicken mycobiota was highly dynamic, Fusarium pseudonygamai was dominant throughout the GI tract regardless of age in this study. The core chicken mycobiome consisted of 26 fungal taxa accounting for greater than 85% of the fungal population in each GI location. However, we observed high variations of the intestinal mycobiota among different studies. We also showed that the total fungal population varied greatly from 1.0 × 104 to 1.1 × 106 /g digesta along the GI tract and only accounted for less than 0.06% of the bacteria in day-42 broilers. Finally, we revealed that the mycobiota from the hatchery environment was responsible for initial colonization in the GI tract of newly hatched chickens, but was quickly replaced by the fungi in the diet within 3 days. CONCLUSIONS Relative to the intestinal microbiota that consists of trillions of bacteria in hundreds of different species and becomes relatively stabilized as animals age, the chicken intestinal mycobiota is a minor microbial community that is temporally dynamic with limited diversity and no obvious pattern of successive changes. However, similar to the microbiota, the chicken mycobiota is spatially different along the GI tract, although it is more diverse in the upper than the lower GI tract. Dietary fungi are the major source of the intestinal mycobiota in growing chickens. Video abstract.
Collapse
Affiliation(s)
- Kelsy Robinson
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma USA
- Present Address: Poultry Research Unit, USDA–Agricultural Research Service, Mississippi State, MS USA
| | - Qing Yang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma USA
| | - Sydney Stewart
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma USA
- Present Address: Safety and Security Division, Institute for Public Research, CNA, Arlington, VA USA
| | - Melanie A. Whitmore
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma USA
| | - Guolong Zhang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma USA
| |
Collapse
|
24
|
Sharma AK, Davison S, Pafco B, Clayton JB, Rothman JM, McLennan MR, Cibot M, Fuh T, Vodicka R, Robinson CJ, Petrzelkova K, Gomez A. The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors. NPJ Biofilms Microbiomes 2022; 8:12. [PMID: 35301322 PMCID: PMC8930997 DOI: 10.1038/s41522-022-00274-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/31/2022] [Indexed: 11/29/2022] Open
Abstract
The gut microbiome of primates is known to be influenced by both host genetic background and subsistence strategy. However, these inferences have been made mainly based on adaptations in bacterial composition - the bacteriome and have commonly overlooked the fungal fraction - the mycobiome. To further understand the factors that shape the gut mycobiome of primates and mycobiome-bacteriome interactions, we sequenced 16 S rRNA and ITS2 markers in fecal samples of four different nonhuman primate species and three human groups under different subsistence patterns (n = 149). The results show that gut mycobiome composition in primates is still largely unknown but highly plastic and weakly structured by primate phylogeny, compared with the bacteriome. We find significant gut mycobiome overlap between captive apes and human populations living under industrialized subsistence contexts; this is in contrast with contemporary hunter-gatherers and agriculturalists, who share more mycobiome traits with diverse wild-ranging nonhuman primates. In addition, mycobiome-bacteriome interactions were specific to each population, revealing that individual, lifestyle and intrinsic ecological factors affect structural correspondence, number, and kind of interactions between gut bacteria and fungi in primates. Our findings indicate a dominant effect of ecological niche, environmental factors, and diet over the phylogenetic background of the host, in shaping gut mycobiome composition and mycobiome-bacteriome interactions in primates.
Collapse
Affiliation(s)
- Ashok K Sharma
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA.,Department of Gastroenterology, Inflammatory Bowel & Immunology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Sam Davison
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA
| | - Barbora Pafco
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jonathan B Clayton
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA.,Callitrichid Research Center (CRC, Marmoset Colony) at the University of Nebraska at Omaha, Omaha, NE, USA.,Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.,Primate Microbiome Project, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jessica M Rothman
- Department of Anthropology, Hunter College of the City University of New York, 695 Park Avenue, New York, NY, USA.,New York Consortium in Evolutionary Primatology, New York, NY, USA
| | - Matthew R McLennan
- Department of Social Sciences, Faculty of Humanities and Social Sciences, Oxford Brookes University, Oxford, UK.,Bulindi Chimpanzee & Community Project, Hoima, Uganda
| | - Marie Cibot
- Department of Social Sciences, Faculty of Humanities and Social Sciences, Oxford Brookes University, Oxford, UK.,Bulindi Chimpanzee & Community Project, Hoima, Uganda.,Anicoon Vétérinaires, Ploemeur, France
| | - Terence Fuh
- WWF Central African Republic, Bayanga, Central African Republic
| | | | | | - Klara Petrzelkova
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Brno, Czech Republic
| | - Andres Gomez
- Department of Animal Science, University of Minnesota, St. Paul, MN, USA. .,Primate Microbiome Project, University of Nebraska-Lincoln, Lincoln, NE, USA. .,Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, USA.
| |
Collapse
|
25
|
Liu N, Yu W, Guo X, Chen J, Xia D, Yu J, Li D. Oxidative cleavage of cellulose in the horse gut. Microb Cell Fact 2022; 21:38. [PMID: 35279161 PMCID: PMC8917663 DOI: 10.1186/s12934-022-01767-8] [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: 10/28/2021] [Accepted: 03/01/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Lytic polysaccharide monooxygenases (LPMOs) belonging to the auxiliary activity 9 family (AA9) are widely found in aerobic fungi. These enzymes are O2-dependent copper oxidoreductases that catalyze the oxidative cleavage of cellulose. However, studies that have investigated AA9 LPMOs of aerobic fungi in the herbivore gut are scare. To date, whether oxidative cleavage of cellulose occurs in the herbivore gut is unknown.
Results
We report for the first time experimental evidence that AA9 LPMOs from aerobic thermophilic fungi catalyze the oxidative cleavage of cellulose present in the horse gut to C1-oxidized cellulose and C1- and C4-oxidized cello-oligosaccharides. We isolated and identified three thermophilic fungi and measured their growth and AA9 LPMO expression at 37 °C in vitro. We also assessed the expression and the presence of AA9 LPMOs from thermophilic fungi in situ. Finally, we used two recombinant AA9 LPMOs and a native AA9 LPMO from thermophilic fungi to cleave cellulose to yield C1-oxidized products at 37 °C in vitro.
Conclusions
The oxidative cleavage of cellulose occurs in the horse gut. This finding will broaden the known the biological functions of the ubiquitous LPMOs and aid in determining biological significance of aerobic thermophilic fungi.
Collapse
|
26
|
Schulz D, Pšenková-Profousová I, Červená B, Procter M, Neba TF, Modrý D, Petrželková KJ, Qablan MA. Occurrence and diversity of anaerobic gut fungi in wild forest elephants and buffaloes inhabiting two separated forest ecosystems in Central West Africa. JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.21033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Doreen Schulz
- Department of Pathology and Parasitology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Ilona Pšenková-Profousová
- Department of Pathology and Parasitology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Barbora Červená
- Department of Pathology and Parasitology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Miranda Procter
- Department of Veterinary Medicine, United Arab Emirates University, College of Agriculture and Veterinary Medicine, Al Ain, Abu Dhabi, United Arab Emirates; e-mail: ,
| | - Terence Fuh Neba
- World Wildlife Fund, Primate Habituation Project, Dzanga-Sangha Protected Areas, Bangui, Central African Republic; e-mail:
| | - David Modrý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic; e-mail: ,
| | - Klára J. Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic; e-mail: ,
| | - Moneeb A. Qablan
- Department of Veterinary Medicine, United Arab Emirates University, College of Agriculture and Veterinary Medicine, Al Ain, Abu Dhabi, United Arab Emirates; e-mail: ,
| |
Collapse
|
27
|
Houshyar Y, Massimino L, Lamparelli LA, Danese S, Ungaro F. Going Beyond Bacteria: Uncovering the Role of Archaeome and Mycobiome in Inflammatory Bowel Disease. Front Physiol 2021; 12:783295. [PMID: 34938203 PMCID: PMC8685520 DOI: 10.3389/fphys.2021.783295] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 11/09/2021] [Indexed: 12/15/2022] Open
Abstract
Inflammatory Bowel Disease (IBD) is a multifaceted class of relapsing-remitting chronic inflammatory conditions where microbiota dysbiosis plays a key role during its onset and progression. The human microbiota is a rich community of bacteria, viruses, fungi, protists, and archaea, and is an integral part of the body influencing its overall homeostasis. Emerging evidence highlights dysbiosis of the archaeome and mycobiome to influence the overall intestinal microbiota composition in health and disease, including IBD, although they remain some of the least understood components of the gut microbiota. Nonetheless, their ability to directly impact the other commensals, or the host, reasonably makes them important contributors to either the maintenance of the mucosal tissue physiology or to chronic intestinal inflammation development. Therefore, the full understanding of the archaeome and mycobiome dysbiosis during IBD pathogenesis may pave the way to the discovery of novel mechanisms, finally providing innovative therapeutic targets that can soon implement the currently available treatments for IBD patients.
Collapse
Affiliation(s)
| | - Luca Massimino
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Silvio Danese
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
- Faculty of Medicine, Università Vita-Salute San Raffaele, Milan, Italy
| | - Federica Ungaro
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| |
Collapse
|
28
|
Kar B, Özköse E, Ekinci MS. The Comparisons of Fatty Acid Composition in Some Anaerobic Gut Fungi Neocallimastix, Orpinomyces, Piromyces, and Caecomyces. AN ACAD BRAS CIENC 2021; 93:e20200896. [PMID: 34705941 DOI: 10.1590/0001-3765202120200896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/03/2020] [Indexed: 11/22/2022] Open
Abstract
The objective of this study were to identify the fatty acid composition for decanoic (C10:0), tridecanoic (C13:0), myristic (C14:0), pentadecanoic (C15:0), palmitic (C16:0), stearic (C18:0), oleic (C18:1n9c), linoleic (C18:2n6c), arachidic (C20:0), arachidonic (C20:4n6), heneicosanoic (C21:0), erucic (C22:1n9) and Cis-4,7,10,13,16,19-docosahexaenoic (C22:6n3) acids by Neocallimastix, Orpinomyces, Caecomyces and Piromyces species of rumen fungus during in vitro culture. Fatty acid (FA) profi le of anaerobic fungi comprises carbon chains of length ranging from 10 to 22 were analyzed as methyl esters. Analysis of fatty acids was performed using Gas Chromatography-Mass Spectrophotometer (GC-MS). FA measures are presented as proportions of relative amounts (% total fatty acid). The highest amounts of fatty acids for all samples were found as myristic (C14:0) acid. The tridecanoic (C13:0) acid represented the second abundant FA in the fungi in all experimental groups. Stearic acid (C18:0) was the third major fatty acid for isolates investigated in the current study. In addition, another fatty acid was palmitic (C16:0) acid with relative amount representing >20 % of total FA in all samples. Pentadecanoic (C15:0) acid could not be found in any other samples except Orpinomyces sp. (GMLF5). It is concluded that biohydrogenation of fatty acid composition by anaerobic gut fungi are very variable.
Collapse
Affiliation(s)
- Bülent Kar
- Munzur University, Tunceli Vocational School, Department of Organic Agriculture, Aktuluk Street, University Campus, Postal 62000, Tunceli Center/ Tunceli, Turkey
| | - Emin Özköse
- Kahramanmaras Sutcu Imam University, Faculty of Agriculture, Department of Animal Science, Avsar Campus, Postal 46000, Avsar Village/Kahramanmaras, Turkey
| | - Mehmet Sait Ekinci
- Kahramanmaras Sutcu Imam University, Faculty of Agriculture, Department of Animal Science, Avsar Campus, Postal 46000, Avsar Village/Kahramanmaras, Turkey
| |
Collapse
|
29
|
Early-diverging fungal phyla: taxonomy, species concept, ecology, distribution, anthropogenic impact, and novel phylogenetic proposals. FUNGAL DIVERS 2021; 109:59-98. [PMID: 34608378 PMCID: PMC8480134 DOI: 10.1007/s13225-021-00480-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/19/2021] [Indexed: 01/02/2023]
Abstract
The increasing number of new fungal species described from all over the world along with the use of genetics to define taxa, has dramatically changed the classification system of early-diverging fungi over the past several decades. The number of phyla established for non-Dikarya fungi has increased from 2 to 17. However, to date, both the classification and phylogeny of the basal fungi are still unresolved. In this article, we review the recent taxonomy of the basal fungi and re-evaluate the relationships among early-diverging lineages of fungal phyla. We also provide information on the ecology and distribution in Mucoromycota and highlight the impact of chytrids on amphibian populations. Species concepts in Chytridiomycota, Aphelidiomycota, Rozellomycota, Neocallimastigomycota are discussed in this paper. To preserve the current application of the genus Nephridiophaga (Chytridiomycota: Nephridiophagales), a new type species, Nephridiophaga blattellae, is proposed.
Collapse
|
30
|
Harrison XA, McDevitt AD, Dunn JC, Griffiths SM, Benvenuto C, Birtles R, Boubli JP, Bown K, Bridson C, Brooks DR, Browett SS, Carden RF, Chantrey J, Clever F, Coscia I, Edwards KL, Ferry N, Goodhead I, Highlands A, Hopper J, Jackson J, Jehle R, da Cruz Kaizer M, King T, Lea JMD, Lenka JL, McCubbin A, McKenzie J, de Moraes BLC, O'Meara DB, Pescod P, Preziosi RF, Rowntree JK, Shultz S, Silk MJ, Stockdale JE, Symondson WOC, de la Pena MV, Walker SL, Wood MD, Antwis RE. Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome. Proc Biol Sci 2021; 288:20210552. [PMID: 34403636 PMCID: PMC8370808 DOI: 10.1098/rspb.2021.0552] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/14/2021] [Indexed: 12/30/2022] Open
Abstract
Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, comparative evidence for fungi is lacking, especially in natural populations. Using data from 49 species, we present novel evidence of strong covariation between fungal and bacterial communities across the host phylogeny, indicative of recruitment by hosts for specific suites of microbes. Using co-occurrence networks, we demonstrate marked variation across host taxonomy in patterns of covariation between bacterial and fungal abundances. Host phylogeny drives differences in the overall richness of bacterial and fungal communities, but the effect of diet on richness was only evident in the mammalian gut microbiome. Sample type, tissue storage and DNA extraction method also affected bacterial and fungal community composition, and future studies would benefit from standardized approaches to sample processing. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.
Collapse
Affiliation(s)
| | - Allan D. McDevitt
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jenny C. Dunn
- School of Life Sciences, Joseph Banks Laboratories, University of Lincoln, UK
| | - Sarah M. Griffiths
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Chiara Benvenuto
- School of Science, Engineering and Environment, University of Salford, UK
| | - Richard Birtles
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jean P. Boubli
- School of Science, Engineering and Environment, University of Salford, UK
| | - Kevin Bown
- School of Science, Engineering and Environment, University of Salford, UK
| | - Calum Bridson
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | - Darren R. Brooks
- School of Science, Engineering and Environment, University of Salford, UK
| | - Samuel S. Browett
- School of Science, Engineering and Environment, University of Salford, UK
| | - Ruth F. Carden
- School of Archaeology, University College Dublin, Ireland
- Wildlife Ecological and Osteological Consultancy, Wicklow, Ireland
| | - Julian Chantrey
- Institute of Veterinary Science, University of Liverpool, UK
| | - Friederike Clever
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
- Smithsonian Tropical Research Institute, Ancon, Republic of Panama
| | - Ilaria Coscia
- School of Science, Engineering and Environment, University of Salford, UK
| | - Katie L. Edwards
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, UK
| | - Natalie Ferry
- School of Science, Engineering and Environment, University of Salford, UK
| | - Ian Goodhead
- School of Science, Engineering and Environment, University of Salford, UK
| | - Andrew Highlands
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jane Hopper
- The Aspinall Foundation, Port Lympne Reserve, Hythe, Kent, UK
| | - Joseph Jackson
- School of Science, Engineering and Environment, University of Salford, UK
| | - Robert Jehle
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Tony King
- The Aspinall Foundation, Port Lympne Reserve, Hythe, Kent, UK
- School of Anthropology and Conservation, University of Kent, UK
| | - Jessica M. D. Lea
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | - Jessica L. Lenka
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Jack McKenzie
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Denise B. O'Meara
- School of Science and Computing, Waterford Institute of Technology, Ireland
| | - Poppy Pescod
- School of Science, Engineering and Environment, University of Salford, UK
| | - Richard F. Preziosi
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Jennifer K. Rowntree
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Susanne Shultz
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | | | - Jennifer E. Stockdale
- School of Biosciences, University of Cardiff, UK
- School of Life Sciences, University of Nottingham, UK
| | | | | | - Susan L. Walker
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, UK
| | - Michael D. Wood
- School of Science, Engineering and Environment, University of Salford, UK
| | - Rachael E. Antwis
- School of Science, Engineering and Environment, University of Salford, UK
| |
Collapse
|
31
|
Musumeci S, Coen M, Leidi A, Schrenzel J. The human gut mycobiome and the specific role of Candida albicans: where do we stand, as clinicians? Clin Microbiol Infect 2021; 28:58-63. [PMID: 34363944 DOI: 10.1016/j.cmi.2021.07.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/08/2021] [Accepted: 07/22/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND The so-called 'mycobiome' has progressively acquired interest and increased the complexity of our understanding of the human gut microbiota. Several questions are arising concerning the role of fungi (and in particular of Candida albicans), the so-called 'mycobiome', that has been neglected for a long time and only recently gained interest within the scientific community. There is no consensus on mycobiome normobiosis because of its instability and variability. This review aims to raise awareness about this interesting topic and provide a framework to guide physicians faced with such questions. OBJECTIVES To summarize current knowledge and discuss current and potential implications of the mycobiome in clinical practice. SOURCES We performed a review of the existing literature in Medline Pubmed. CONTENT This review identifies several studies showing associations between specific mycobiome profiles and health. Fungi represent a significant biomass within the microbiota and several factors, such as diet, sex, age, co-morbidities, medications, immune status and inter-kingdom interactions, can influence its structure and population. The human gut mycobiota is indeed a key factor for several physiological processes (e.g. training of the immune system against infections) and pathological processes (e.g. immunological/inflammatory disorders, inflammatory bowel diseases, metabolic syndromes). Moreover, the mycobiome (and C. albicans in particular) could influence an even broader spectrum of conditions such as psychiatric diseases (depression, schizophrenia, bipolar disorder) or chronic viral infections (human immunodeficiency virus, hepatitis B virus); moreover, it could be implicated in tumorigenesis. IMPLICATIONS Candida albicans is a well-known opportunistic pathogen and a major component of the mycobiome but its role in the gastrointestinal tract is still poorly understood. From a potential screening biomarker to a key factor for several pathological processes, its presence could influence or even modify our clinical practice.
Collapse
Affiliation(s)
- Stefano Musumeci
- Service of Internal Medicine, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Matteo Coen
- Service of Internal Medicine, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland; Unit of Development and Research in Medical Education (UDREM), Faculty of Medicine, Geneva, Switzerland.
| | - Antonio Leidi
- Service of Internal Medicine, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Jacques Schrenzel
- Bacteriology Laboratory, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland; Genomic Research Laboratory, Department of Medicine, Geneva University Hospitals and University of Geneva, Geneva, Switzerland; Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| |
Collapse
|
32
|
Wang Y, Fu Y, He Y, Kulyar MFEA, Iqbal M, Li K, Liu J. Longitudinal Characterization of the Gut Bacterial and Fungal Communities in Yaks. J Fungi (Basel) 2021; 7:jof7070559. [PMID: 34356938 PMCID: PMC8304987 DOI: 10.3390/jof7070559] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/28/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Development phases are important in maturing immune systems, intestinal functions, and metabolism for the construction, structure, and diversity of microbiome in the intestine during the entire life. Characterizing the gut microbiota colonization and succession based on age-dependent effects might be crucial if a microbiota-based therapeutic or disease prevention strategy is adopted. The purpose of this study was to reveal the dynamic distribution of intestinal bacterial and fungal communities across all development stages in yaks. Dynamic changes (a substantial difference) in the structure and composition ratio of the microbial community were observed in yaks that matched the natural aging process from juvenile to natural aging. This study included a significant shift in the abundance and proportion of bacterial phyla (Planctomycetes, Firmicutes, Bacteroidetes, Spirochaetes, Tenericutes, Proteobacteria, and Cyanobacteria) and fungal phyla (Chytridiomycota, Mortierellomycota, Neocallimastigomycota, Ascomycota, and Basidiomycota) across all development stages in yaks. As yaks grew older, variation reduced, and diversity increased as compared to young yaks. In addition, the intestine was colonized by a succession of microbiomes that coalesced into a more mature adult, including Ruminococcaceae_UCG-005, Romboutsia, Prevotellaceae_UCG-004, Blautia, Clostridium_sensu_stricto_1, Ruminococcus_1, Ruminiclostridium_5, Rikenellaceae_RC9_gut_group, Alloprevotella, Acetitomaculum, Lachnospiraceae_NK3A20_group, Bacteroides, Treponema_2, Olsenella, Escherichia-Shigella, Candidatus_Saccharimonas, and fungal communities Mortierella, Lomentospora, Orpinomyces, and Saccharomyces. In addition, microorganisms that threaten health, such as Escherichia-Shigella, Mortierella, Lomentospora and Hydrogenoanaerobacterium, Corynebacterium_1, Trichosporon, and Coprinellus, were enriched in young and old yaks, respectively, although all yaks were healthy. The significant shifts in microflora composition and structure might reflect adaptation of gut microbiome, which is associated with physicochemical conditions changes and substrate availability in the gut across all development periods of yaks.
Collapse
Affiliation(s)
- Yaping Wang
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.H.); (M.F.-e.-A.K.); (M.I.)
| | - Yuhang Fu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.H.); (M.F.-e.-A.K.); (M.I.)
| | - Yuanyuan He
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.H.); (M.F.-e.-A.K.); (M.I.)
| | - Muhammad Fakhar-e-Alam Kulyar
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.H.); (M.F.-e.-A.K.); (M.I.)
| | - Mudassar Iqbal
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.H.); (M.F.-e.-A.K.); (M.I.)
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (K.L.); (J.L.)
| | - Jiaguo Liu
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (K.L.); (J.L.)
| |
Collapse
|
33
|
Hanafy RA, Youssef NH, Elshahed MS. Paucimyces polynucleatus gen. nov, sp. nov., a novel polycentric genus of anaerobic gut fungi from the faeces of a wild blackbuck antelope. Int J Syst Evol Microbiol 2021; 71. [PMID: 34161217 DOI: 10.1099/ijsem.0.004832] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The anaerobic gut fungi (AGF; phylum Neocallimastigomycota) reside in the alimentary tracts of herbivores. Multiple novel, yet-uncultured AGF taxa have recently been identified in culture-independent diversity surveys. Here, we report on the isolation and characterization of the first representative of the RH5 lineage from faecal samples of a wild blackbuck (Indian Antelope, Antilope cervicapra) from Sutton County, Texas, USA. The isolates displayed medium sized (2-4 mm) compact circular colonies on agar roll tubes and thin loose biofilm-like growth in liquid medium. Microscopic examination revealed monoflagellated zoospores and polycentric thalli with highly branched nucleated filamentous rhizomycelium, a growth pattern encountered in a minority of described AGF genera so far. The obtained isolates are characterized by formation of spherical vesicles at the hyphal tips from which multiple sporangia formed either directly on the spherical vesicles or at the end of sporangiophores. Phylogenetic analysis using the D1/D2 regions of the large ribosomal subunit (D1/D2 LSU) and the ribosomal internal transcribed spacer 1 (ITS1) revealed sequence similarities of 93.5 and 81.3%, respectively, to the closest cultured relatives (Orpinomyces joyonii strain D3A (D1/D2 LSU) and Joblinomyces apicalis strain GFH681 (ITS1). Substrate utilization experiments using the type strain (BB-3T) demonstrated growth capabilities on a wide range of mono-, oligo- and polysaccharides, including glucose, xylose, mannose, fructose, cellobiose, sucrose, maltose, trehalose, lactose, cellulose, xylan, starch and raffinose. We propose accommodating these novel isolates in a new genus and species, for which the name Paucimyces polynucleatus gen. nov., sp. nov. is proposed.
Collapse
Affiliation(s)
- Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA
| |
Collapse
|
34
|
Abstract
Anaerobic fungi (Neocallimastigomycota) isolated from the guts of herbivores are powerful biomass-degrading organisms that enhance their degradative ability through the formation of cellulosomes, multienzyme complexes that synergistically colocalize enzymes to extract sugars from recalcitrant plant matter. However, a functional understanding of how fungal cellulosomes are deployed in vivo to orchestrate plant matter degradation is lacking, as is knowledge of how cellulosome production and function vary throughout the morphologically diverse life cycle of anaerobic fungi. In this work, we generated antibodies against three major fungal cellulosome protein domains, a dockerin, scaffoldin, and glycoside hydrolase (GH) 48 protein, and used them in conjunction with helium ion and immunofluorescence microscopy to characterize cellulosome localization patterns throughout the life cycle of Piromyces finnis when grown on simple sugars and complex cellulosic carbon sources. Our analyses reveal that fungal cellulosomes are cell-localized entities specifically targeted to the rhizoids of mature fungal cells and bodies of zoospores. Examination of cellulosome localization patterns across life stages also revealed that cellulosome production is independent of growth substrate in zoospores but repressed by simple sugars in mature cells. This suggests that further exploration of gene regulation patterns in zoospores is needed and can inform potential strategies for derepressing cellulosome expression and boosting hydrolytic enzyme yields from fungal cultures. Collectively, these findings underscore how life cycle-dependent cell morphology and regulation of cellulosome production impact biomass degradation by anaerobic fungi, insights that will benefit ongoing efforts to develop these organisms and their cellulosomes into platforms for converting waste biomass into valuable bioproducts.
Collapse
|
35
|
Rajeswari G, Jacob S, Chandel AK, Kumar V. Unlocking the potential of insect and ruminant host symbionts for recycling of lignocellulosic carbon with a biorefinery approach: a review. Microb Cell Fact 2021; 20:107. [PMID: 34044834 PMCID: PMC8161579 DOI: 10.1186/s12934-021-01597-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/17/2021] [Indexed: 12/02/2022] Open
Abstract
Uprising fossil fuel depletion and deterioration of ecological reserves supply have led to the search for alternative renewable and sustainable energy sources and chemicals. Although first generation biorefinery is quite successful commercially in generating bulk of biofuels globally, the food versus fuel debate has necessitated the use of non-edible feedstocks, majorly waste biomass, for second generation production of biofuels and chemicals. A diverse class of microbes and enzymes are being exploited for biofuels production for a series of treatment process, however, the conversion efficiency of wide range of lignocellulosic biomass (LCB) and consolidated way of processing remains challenging. There were lot of research efforts in the past decade to scour for potential microbial candidate. In this context, evolution has developed the gut microbiota of several insects and ruminants that are potential LCB degraders host eco-system to overcome its host nutritional constraints, where LCB processed by microbiomes pretends to be a promising candidate. Synergistic microbial symbionts could make a significant contribution towards recycling the renewable carbon from distinctly abundant recalcitrant LCB. Several studies have assessed the bioprospection of innumerable gut symbionts and their lignocellulolytic enzymes for LCB degradation. Though, some reviews exist on molecular characterization of gut microbes, but none of them has enlightened the microbial community design coupled with various LCB valorization which intensifies the microbial diversity in biofuels application. This review provides a deep insight into the significant breakthroughs attained in enrichment strategy of gut microbial community and its molecular characterization techniques which aids in understanding the holistic microbial community dynamics. Special emphasis is placed on gut microbial role in LCB depolymerization strategies to lignocellulolytic enzymes production and its functional metagenomic data mining eventually generating the sugar platform for biofuels and renewable chemicals production.
Collapse
Affiliation(s)
- Gunasekaran Rajeswari
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Chengalpattu Dist. , Kattankulathur, 603203, Tamil Nadu, India
| | - Samuel Jacob
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Chengalpattu Dist. , Kattankulathur, 603203, Tamil Nadu, India.
| | - Anuj Kumar Chandel
- Department of Biotechnology, Engineering School of Lorena (EEL), University of São Paulo, Lorena, 12.602.810, Brazil
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK.
| |
Collapse
|
36
|
Du G, Feng W, Cai H, Ma Z, Liu X, Yuan C, Shi J, Zhang B. Exogenous enzyme amendment accelerates maturity and changes microflora succession in horse and wildlife animal manure co-composting. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:21610-21620. [PMID: 33415619 DOI: 10.1007/s11356-020-11568-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
Composting has been a rational method to dispose of horse or wildlife animal manures, especially in the developed cities with horse clubs and wildlife parks. However, few studies have focused on the mechanism and improvement methods for composting the horse or wildlife animal manures. In this study, we investigated the effect of exogenous compound enzymes on thermophilic composting, which could potentially support the management of horse and wildlife animal manures. With the presence of exogenous enzymes, the duration of high temperature (> 60 °C) was significantly prolonged (p < 0.05), and the germination index was significantly improved (p < 0.05). More-efficient improvement of composting maturity was associated with the addition of that exogenous enzyme that might influence microflora succession and the interaction among microorganic communities, especially fungal, during the composting process. Furthermore, redundancy and canonical correspondence analyses indicated that the C/N ratio, temperature, and germination index were significant variations to influence bacterial communities (p < 0.05). The dominant Flavobacterium, Thermopolyspora, Thermomonospora, and Chaetomium and Saccobolus could play an essential role in carbohydrate and phytotoxin degradation, while Thermobispora and norank_f_Limnochordaceae could lead to temperature rising.
Collapse
Affiliation(s)
- Guilin Du
- Laboratory of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wenwen Feng
- Laboratory of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hanbin Cai
- Laboratory of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiguo Ma
- Laboratory of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangcen Liu
- Laboratory of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chenyang Yuan
- Laboratory of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jiping Shi
- Laboratory of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Baoguo Zhang
- Laboratory of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
37
|
Moon CD, Carvalho L, Kirk MR, McCulloch AF, Kittelmann S, Young W, Janssen PH, Leathwick DM. Effects of long-acting, broad spectra anthelmintic treatments on the rumen microbial community compositions of grazing sheep. Sci Rep 2021; 11:3836. [PMID: 33589656 PMCID: PMC7884727 DOI: 10.1038/s41598-021-82815-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022] Open
Abstract
Anthelmintic treatment of adult ewes is widely practiced to remove parasite burdens in the expectation of increased ruminant productivity. However, the broad activity spectra of many anthelmintic compounds raises the possibility of impacts on the rumen microbiota. To investigate this, 300 grazing ewes were allocated to treatment groups that included a 100-day controlled release capsule (CRC) containing albendazole and abamectin, a long-acting moxidectin injection (LAI), and a non-treated control group (CON). Rumen bacterial, archaeal and protozoal communities at day 0 were analysed to identify 36 sheep per treatment with similar starting compositions. Microbiota profiles, including those for the rumen fungi, were then generated for the selected sheep at days 0, 35 and 77. The CRC treatment significantly impacted the archaeal community, and was associated with increased relative abundances of Methanobrevibacter ruminantium, Methanosphaera sp. ISO3-F5, and Methanomassiliicoccaceae Group 12 sp. ISO4-H5 compared to the control group. In contrast, the LAI treatment increased the relative abundances of members of the Veillonellaceae and resulted in minor changes to the bacterial and fungal communities by day 77. Overall, the anthelmintic treatments resulted in few, but highly significant, changes to the rumen microbiota composition.
Collapse
Affiliation(s)
- Christina D Moon
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand.
| | - Luis Carvalho
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand
| | - Michelle R Kirk
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand
| | - Alan F McCulloch
- Invermay Research Centre, AgResearch Limited, Mosgiel, New Zealand
| | - Sandra Kittelmann
- Wilmar International Limited, WIL@NUS Corporate Laboratory, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Wayne Young
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand
| | - Peter H Janssen
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand
| | - Dave M Leathwick
- Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand
| |
Collapse
|
38
|
Li Y, Meng Z, Xu Y, Shi Q, Ma Y, Aung M, Cheng Y, Zhu W. Interactions between Anaerobic Fungi and Methanogens in the Rumen and Their Biotechnological Potential in Biogas Production from Lignocellulosic Materials. Microorganisms 2021; 9:190. [PMID: 33477342 PMCID: PMC7830786 DOI: 10.3390/microorganisms9010190] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/29/2022] Open
Abstract
Anaerobic fungi in the digestive tract of herbivores are one of the critical types of fiber-degrading microorganisms present in the rumen. They degrade lignocellulosic materials using unique rhizoid structures and a diverse range of fiber-degrading enzymes, producing metabolic products such as H2/CO2, formate, lactate, acetate, and ethanol. Methanogens in the rumen utilize some of these products (e.g., H2 and formate) to produce methane. An investigation of the interactions between anaerobic fungi and methanogens is helpful as it provides valuable insight into the microbial interactions within the rumen. During the last few decades, research has demonstrated that anaerobic fungi stimulate the growth of methanogens and maintain methanogenic diversity. Meanwhile, methanogens increase the fiber-degrading capability of anaerobic fungi and stimulate metabolic pathways in the fungal hydrogenosome. The ability of co-cultures of anaerobic fungi and methanogens to degrade fiber and produce methane could potentially be a valuable method for the degradation of lignocellulosic materials and methane production.
Collapse
Affiliation(s)
- Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Zhenxiang Meng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Yao Xu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Qicheng Shi
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Yuping Ma
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Min Aung
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
- Department of Animal Nutrition, University of Veterinary Science, Nay Pyi Taw 15013, Myanmar
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| |
Collapse
|
39
|
The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic Fungi. Microorganisms 2021; 9:microorganisms9010157. [PMID: 33445538 PMCID: PMC7827659 DOI: 10.3390/microorganisms9010157] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 12/17/2022] Open
Abstract
This work investigated the changes of the rumen microbiome of goats switched from a forage to a concentrate diet with special attention to anaerobic fungi (AF). Female goats were fed an alfalfa hay (AH) diet (0% grain; n = 4) for 20 days and were then abruptly shifted to a high-grain (HG) diet (40% corn grain, 60% AH; n = 4) and treated for another 10 days. Rumen content samples were collected from the cannulated animals at the end of each diet period (day 20 and 30). The microbiome structure was studied using high-throughput sequencing for bacteria, archaea (16S rRNA gene) and fungi (ITS2), accompanied by qPCR for each group. To further elucidate unclassified AF, clone library analyses were performed on the ITS1 spacer region. Rumen pH was significantly lower in HG diet fed goats, but did not induce subacute ruminal acidosis. HG diet altered prokaryotic communities, with a significant increase of Bacteroidetes and a decrease of Firmicutes. On the genus level Prevotella 1 was significantly boosted. Methanobrevibacter and Methanosphaera were the most abundant archaea regardless of the diet and HG induced a significant augmentation of unclassified Thermoplasmatales. For anaerobic fungi, HG triggered a considerable rise in Feramyces observed with both ITS markers, while a decline of Tahromyces was detected by ITS2 and decrease of Joblinomyces by ITS1 only. The uncultured BlackRhino group revealed by ITS1 and further elucidated in one sample by LSU analysis, formed a considerable part of the AF community of goats fed both diets. Results strongly indicate that the rumen ecosystem still acts as a source for novel microorganisms and unexplored microbial interactions and that initial rumen microbiota of the host animal considerably influences the reaction pattern upon diet change.
Collapse
|
40
|
Cotozzolo E, Cremonesi P, Curone G, Menchetti L, Riva F, Biscarini F, Marongiu ML, Castrica M, Castiglioni B, Miraglia D, Luridiana S, Brecchia G. Characterization of Bacterial Microbiota Composition along the Gastrointestinal Tract in Rabbits. Animals (Basel) 2020; 11:ani11010031. [PMID: 33375259 PMCID: PMC7824689 DOI: 10.3390/ani11010031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 12/26/2022] Open
Abstract
The microbiota is extremely important for the animal's health, but, to date, knowledge on the intestinal microbiota of the rabbit is very limited. This study aimed to describe bacterial populations that inhabit the different gastrointestinal compartments of the rabbit: stomach, duodenum, jejunum, ileum, caecum, and colon. Samples of the luminal content from all compartments of 14 healthy New White Zealand rabbits were collected at slaughter and analyzed using next generation 16S rRNA Gene Sequencing. The findings uncovered considerable differences in the taxonomic levels among the regions of the digestive tract. Firmicutes were the most abundant phylum in all of the sections (45.9%), followed by Bacteroidetes in the large intestine (38.9%) and Euryarchaeota in the foregut (25.9%). Four clusters of bacterial populations were observed along the digestive system: (i) stomach, (ii) duodenum and jejunum, (iii) ileum, and (iv) large intestine. Caecum and colon showed the highest richness and diversity in bacterial species, while the highest variability was found in the upper digestive tract. Knowledge of the physiological microbiota of healthy rabbits could be important for preserving the health and welfare of the host as well as for finding strategies to manipulate the gut microbiota in order to also promote productive performance.
Collapse
Affiliation(s)
- Elisa Cotozzolo
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy;
| | - Paola Cremonesi
- Institute of Agricultural Biology and Biotechnology (IBBA)—National Research Council (CNR), U.O.S. di Lodi, Via Einstein, 26900 Lodi, Italy; (P.C.); (F.B.); (B.C.)
| | - Giulio Curone
- Department of Veterinary Medicine, University of Milano, Via dell’Università 6, 26900 Lodi, Italy; (G.C.); (M.C.)
| | - Laura Menchetti
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40137 Bologna, Italy;
| | - Federica Riva
- Department of Veterinary Medicine, University of Milano, Via dell’Università 6, 26900 Lodi, Italy; (G.C.); (M.C.)
- Correspondence: (F.R.); (G.B.); Tel.: +39-02503-34519 (F.R.); Tel.: +39-02-50334583 (G.B.)
| | - Filippo Biscarini
- Institute of Agricultural Biology and Biotechnology (IBBA)—National Research Council (CNR), U.O.S. di Lodi, Via Einstein, 26900 Lodi, Italy; (P.C.); (F.B.); (B.C.)
| | - Maria Laura Marongiu
- Department of Veterinary Medicine, University of Sassari, Via Vienna, 2, 07100 Sassari, Italy; (M.L.M.); (S.L.)
| | - Marta Castrica
- Department of Veterinary Medicine, University of Milano, Via dell’Università 6, 26900 Lodi, Italy; (G.C.); (M.C.)
| | - Bianca Castiglioni
- Institute of Agricultural Biology and Biotechnology (IBBA)—National Research Council (CNR), U.O.S. di Lodi, Via Einstein, 26900 Lodi, Italy; (P.C.); (F.B.); (B.C.)
| | - Dino Miraglia
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy;
| | - Sebastiano Luridiana
- Department of Veterinary Medicine, University of Sassari, Via Vienna, 2, 07100 Sassari, Italy; (M.L.M.); (S.L.)
| | - Gabriele Brecchia
- Department of Veterinary Medicine, University of Milano, Via dell’Università 6, 26900 Lodi, Italy; (G.C.); (M.C.)
- Correspondence: (F.R.); (G.B.); Tel.: +39-02503-34519 (F.R.); Tel.: +39-02-50334583 (G.B.)
| |
Collapse
|
41
|
Makin DF, Kotler BP, Brown JS, Garrido M, Menezes JFS. The Enemy Within: How Does a Bacterium Inhibit the Foraging Aptitude and Risk Management Behavior of Allenby's Gerbils? Am Nat 2020; 196:717-729. [PMID: 33211558 DOI: 10.1086/711397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractMicrobes inhabiting multicellular organisms have complex, often subtle effects on their hosts. Gerbillus andersoni allenbyi are commonly infected with Mycoplasma haemomuris-like bacteria, which may cause mild nutrient (choline, arginine) deficiencies. However, are there more serious ecological consequences of infection, such as effects on foraging aptitudes and risk management? We tested two alternatives: the nutrient compensation hypothesis (does nutrient deficiency induce infected gerbils to make up for the shortfall by foraging more and taking greater risks?) and (2) the lethargy hypothesis (do sick gerbils forage less, and are they compromised in their ability to detect predators or risky microhabitats?). We compared the foraging and risk management behavior of infected and noninfected gerbils. We experimentally infected gerbils with the bacteria, which allowed us to compare between noninfected, acutely infected (peak infection loads), and chronically infected (low infection loads) individuals. Our findings supported the lethargy hypothesis over the nutrient compensation hypothesis. Infected individuals incurred dramatically elevated foraging costs, including less efficient foraging, diminished "quality" of time spent vigilant, and increased owl predation. Interestingly, gerbils that were chronically infected (lower bacteria load) experienced larger ecological costs than acutely infected individuals (i.e., peak infection loads). This suggests that the debilitating effects of infection occur gradually, with a progressive decline in the quality of time gerbils allocated to foraging and managing risk. These increased long-term costs of infection demonstrate how small direct physiological costs of infection can lead to large indirect ecological costs. The indirect ecological costs of this parasite appear to be much greater than the direct physiological costs.
Collapse
|
42
|
Stabel M, Hanafy RA, Schweitzer T, Greif M, Aliyu H, Flad V, Young D, Lebuhn M, Elshahed MS, Ochsenreither K, Youssef NH. Aestipascuomyces dupliciliberans gen. nov, sp. nov., the First Cultured Representative of the Uncultured SK4 Clade from Aoudad Sheep and Alpaca. Microorganisms 2020; 8:E1734. [PMID: 33167420 PMCID: PMC7694369 DOI: 10.3390/microorganisms8111734] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/18/2022] Open
Abstract
We report on the isolation of the previously-uncultured Neocallimastigomycota SK4 lineage, by two independent research groups, from a wild aoudad sheep rumen sample (Texas, USA) and an alpaca fecal sample (Baden-Württemberg, Germany). Isolates from both locations showed near-identical morphological and microscopic features, forming medium-sized (2-5 mm) white filamentous colonies with a white center of sporangia, on agar roll tubes and a heavy biofilm in liquid media. Microscopic analysis revealed monocentric thalli, and spherical polyflagellated zoospores with 7-20 flagella. Zoospore release occurred through an apical pore as well as by sporangial wall rupturing, a duality that is unique amongst described anaerobic gut fungal strains. Isolates were capable of growing on a wide range of mono-, oligo-, and polysaccharide substrates as the sole carbon source. Phylogenetic assessment based on the D1-D2 28S large rRNA gene subunit (D1-D2 LSU) and internal transcribed spacer-1 (ITS-1) regions demonstrated high sequence identity (minimum identity of 99.07% and 96.96%, respectively) between all isolates; but low sequence identity (92.4% and 86.7%, respectively) to their closest cultured relatives. D1-D2 LSU phylogenetic trees grouped the isolates as a new monophyletic clade within the Orpinomyces-Neocallimastix-Pecoramyces-Feramyces-Ghazallamyces supragenus group. D1-D2 LSU and ITS-1 sequences recovered from the obtained isolates were either identical or displayed extremely high sequence similarity to sequences recovered from the same aoudad sheep sample on which isolation was conducted, as well as several sequences recovered from domestic sheep and few other herbivores. Interestingly, members of the SK4 clade seem to be encountered preferably in animals grazing on summer pasture. We hence propose accommodating these novel isolates in a new genus, Aestipascuomyces (derived from the Latin word for "summer pasture"), and a new species, A. dupliciliberans. The type strain is Aestipascuomycesdupliciliberans strain R4.
Collapse
Affiliation(s)
- Marcus Stabel
- Process Engineering in Life Sciences 2: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (M.S.); (T.S.); (M.G.); (H.A.)
| | - Radwa A. Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA; (R.A.H.); (M.S.E.)
| | - Tabea Schweitzer
- Process Engineering in Life Sciences 2: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (M.S.); (T.S.); (M.G.); (H.A.)
| | - Meike Greif
- Process Engineering in Life Sciences 2: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (M.S.); (T.S.); (M.G.); (H.A.)
| | - Habibu Aliyu
- Process Engineering in Life Sciences 2: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (M.S.); (T.S.); (M.G.); (H.A.)
| | - Veronika Flad
- Bavarian State Research Center for Agriculture, Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Lange Point 6, 85354 Freising, Germany; (V.F.); (D.Y.); (M.L.)
| | - Diana Young
- Bavarian State Research Center for Agriculture, Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Lange Point 6, 85354 Freising, Germany; (V.F.); (D.Y.); (M.L.)
| | - Michael Lebuhn
- Bavarian State Research Center for Agriculture, Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Lange Point 6, 85354 Freising, Germany; (V.F.); (D.Y.); (M.L.)
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA; (R.A.H.); (M.S.E.)
| | - Katrin Ochsenreither
- Process Engineering in Life Sciences 2: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (M.S.); (T.S.); (M.G.); (H.A.)
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074, USA; (R.A.H.); (M.S.E.)
| |
Collapse
|
43
|
State of the Art in the Culture of the Human Microbiota: New Interests and Strategies. Clin Microbiol Rev 2020; 34:34/1/e00129-19. [PMID: 33115723 DOI: 10.1128/cmr.00129-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. Other culture conditions target phenotypic and metabolic features of bacterial species to facilitate their isolation. Preexisting technologies such as next-generation sequencing and flow cytometry have also been utilized to develop innovative methods to isolate previously uncultured bacteria or explore viability in samples of interest. These techniques have been applied to isolate CPR (Candidate Phyla Radiation) among other, more classic approaches. Methanogenic archaeal and fungal cultures present different challenges than bacterial cultures. Efforts to improve the available systems to grow archaea have been successful through coculture systems. For fungi that are more easily isolated from the human microbiota, the challenge resides in the identification of the isolates, which has been approached by applying matrix-assisted laser desorption ionization-time of flight mass spectrometry technology to fungi. Bacteriotherapy represents a nonnegligible avenue in the future of medicine to correct dysbiosis and improve health or response to therapy. Although great strides have been achieved in the last 5 years, efforts in bacterial culture need to be sustained to continue deciphering the dark matter of metagenomics, particularly CPR, and extend these methods to archaea and fungi.
Collapse
|
44
|
Hess M, Paul SS, Puniya AK, van der Giezen M, Shaw C, Edwards JE, Fliegerová K. Anaerobic Fungi: Past, Present, and Future. Front Microbiol 2020; 11:584893. [PMID: 33193229 PMCID: PMC7609409 DOI: 10.3389/fmicb.2020.584893] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/29/2020] [Indexed: 11/13/2022] Open
Abstract
Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent marker-gene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed -omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.
Collapse
Affiliation(s)
- Matthias Hess
- Systems Microbiology & Natural Product Discovery Laboratory, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Shyam S. Paul
- Gut Microbiome Lab, ICAR-Directorate of Poultry Research, Indian Council of Agricultural Research, Hyderabad, India
| | - Anil K. Puniya
- Anaerobic Microbiology Lab, ICAR-National Dairy Research Institute, Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Mark van der Giezen
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
| | - Claire Shaw
- Systems Microbiology & Natural Product Discovery Laboratory, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Joan E. Edwards
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Kateřina Fliegerová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Prague, Czechia
| |
Collapse
|
45
|
Azad E, Fehr KB, Derakhshani H, Forster R, Acharya S, Khafipour E, McGeough E, McAllister TA. Interrelationships of Fiber-Associated Anaerobic Fungi and Bacterial Communities in the Rumen of Bloated Cattle Grazing Alfalfa. Microorganisms 2020; 8:microorganisms8101543. [PMID: 33036363 PMCID: PMC7601590 DOI: 10.3390/microorganisms8101543] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 12/21/2022] Open
Abstract
Frothy bloat is major digestive disorder of cattle grazing alfalfa pastures. Among the many factors identified to contribute to the development of frothy bloat, the disruption of rumen microbiota appears to be of central importance. Anaerobic rumen fungi (ARF) play an important role in sequential breakdown and fermentation of plant polysaccharides and promote the physical disruption of plant cell walls. In the present study, we investigated the dynamics of ARF during the development of alfalfa-induced frothy bloat and in response to bloat preventive treatments. By sequencing the internal transcribed spacer (ITS1) region of metagenomic DNA from the solid fraction of rumen contents, we were able to identify eight distinct genera of ARF, including Neocallimastix, Caecomyces, Orpinomyces, Piromyces, Cyllamyces, Anaeromyces, Buwchfawromyces, and unclassified Neocallimastigaceae. Overall, transition of steers from a baseline hay diet to alfalfa pastures was associated with drastic changes in the composition of the fungal community, but the overall composition of ARF did not differ (p > 0.05) among bloated and non-bloated steers. A correlation network analysis of the proportion of ARF and ruminal bacterial communities identified hub fungal species that were negatively correlated with several bacterial species, suggesting the presence of inter-kingdom competition among these rumen microorganisms. Interestingly, the number of negative correlations among ARF and bacteria decreased with frothy bloat, indicating a potential disruption of normal microbial profiles within a bloated rumen ecosystem. A better understanding of fungal-bacterial interactions that differ among bloated and non-bloated rumen ecosystem could advance our understanding of the etiology of frothy bloat.
Collapse
Affiliation(s)
- Elnaz Azad
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.A.); (K.B.F.); (E.K.); (E.M.)
| | - Kelsey B. Fehr
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.A.); (K.B.F.); (E.K.); (E.M.)
| | - Hooman Derakhshani
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada;
| | - Robert Forster
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (R.F.); (S.A.)
| | - Surya Acharya
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (R.F.); (S.A.)
| | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.A.); (K.B.F.); (E.K.); (E.M.)
- Diamond V, Cedar Rapids, IA 52404, USA
| | - Emma McGeough
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.A.); (K.B.F.); (E.K.); (E.M.)
| | - Tim A. McAllister
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.A.); (K.B.F.); (E.K.); (E.M.)
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (R.F.); (S.A.)
- Correspondence: ; Tel.: +1-403-315-9916
| |
Collapse
|
46
|
Squalene-Tetrahymanol Cyclase Expression Enables Sterol-Independent Growth of Saccharomyces cerevisiae. Appl Environ Microbiol 2020; 86:AEM.00672-20. [PMID: 32561581 PMCID: PMC7440791 DOI: 10.1128/aem.00672-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/14/2020] [Indexed: 02/08/2023] Open
Abstract
The laboratory experiments described in this report simulate a proposed horizontal gene transfer event during the evolution of strictly anaerobic fungi. The demonstration that expression of a single heterologous gene sufficed to eliminate anaerobic sterol requirements in the model eukaryote Saccharomyces cerevisiae therefore contributes to our understanding of how sterol-independent eukaryotes evolved in anoxic environments. This report provides a proof of principle for a metabolic engineering strategy to eliminate sterol requirements in yeast strains that are applied in large-scale anaerobic industrial processes. The sterol-independent yeast strains described in this report provide a valuable platform for further studies on the physiological roles and impacts of sterols and sterol surrogates in eukaryotic cells. Biosynthesis of sterols, which are considered essential components of virtually all eukaryotic membranes, requires molecular oxygen. Anaerobic growth of the yeast Saccharomyces cerevisiae therefore strictly depends on sterol supplementation of synthetic growth media. Neocallimastigomycota are a group of strictly anaerobic fungi which, instead of containing sterols, contain the pentacyclic triterpenoid “sterol surrogate” tetrahymanol, which is formed by cyclization of squalene. Here, we demonstrate that expression of the squalene-tetrahymanol cyclase gene TtTHC1 from the ciliate Tetrahymena thermophila enables synthesis of tetrahymanol by S. cerevisiae. Moreover, expression of TtTHC1 enabled exponential growth of anaerobic S. cerevisiae cultures in sterol-free synthetic media. After deletion of the ERG1 gene from a TtTHC1-expressing S. cerevisiae strain, native sterol synthesis was abolished and sustained sterol-free growth was demonstrated under anaerobic as well as aerobic conditions. Anaerobic cultures of TtTHC1-expressing S. cerevisiae on sterol-free medium showed lower specific growth rates and biomass yields than ergosterol-supplemented cultures, while their ethanol yield was higher. This study demonstrated that acquisition of a functional squalene-tetrahymanol cyclase gene offers an immediate growth advantage to S. cerevisiae under anaerobic, sterol-limited conditions and provides the basis for a metabolic engineering strategy to eliminate the oxygen requirements associated with sterol synthesis in yeasts. IMPORTANCE The laboratory experiments described in this report simulate a proposed horizontal gene transfer event during the evolution of strictly anaerobic fungi. The demonstration that expression of a single heterologous gene sufficed to eliminate anaerobic sterol requirements in the model eukaryote Saccharomyces cerevisiae therefore contributes to our understanding of how sterol-independent eukaryotes evolved in anoxic environments. This report provides a proof of principle for a metabolic engineering strategy to eliminate sterol requirements in yeast strains that are applied in large-scale anaerobic industrial processes. The sterol-independent yeast strains described in this report provide a valuable platform for further studies on the physiological roles and impacts of sterols and sterol surrogates in eukaryotic cells.
Collapse
|
47
|
Hanafy RA, Johnson B, Youssef NH, Elshahed MS. Assessing anaerobic gut fungal diversity in herbivores using D1/D2 large ribosomal subunit sequencing and multi-year isolation. Environ Microbiol 2020; 22:3883-3908. [PMID: 32656919 DOI: 10.1111/1462-2920.15164] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/22/2020] [Accepted: 07/10/2020] [Indexed: 11/30/2022]
Abstract
The anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tracts of herbivores where they play a central role in the breakdown of plant material. Here, we report on the development of the hypervariable domains D1/D2 of the large ribosomal subunit (D1/D2 LSU) as a barcoding marker for the AGF. We generated a reference D1/D2 LSU database for all cultured AGF genera, as well as the majority of candidate genera encountered in prior internal transcribed spacer 1 (ITS1)-based surveys. Subsequently, a D1/D2 LSU-based diversity survey using long read PacBio SMRT sequencing was conducted on faecal samples from 21 wild and domesticated herbivores. Twenty-eight genera and candidate genera were identified, including multiple novel lineages that were predominantly, but not exclusively, identified in wild herbivores. Association between certain AGF genera and animal lifestyles, or animal host family was observed. Finally, to address the current paucity of AGF isolates, concurrent isolation efforts utilizing multiple approaches to maximize recovery yielded 216 isolates belonging to 12 different genera, several of which have no prior cultured-representatives. Our results establish the utility of D1/D2 LSU and PacBio sequencing for AGF diversity surveys, the culturability of multiple AGF taxa, and demonstrate that wild herbivores represent a yet-untapped reservoir of AGF diversity.
Collapse
Affiliation(s)
- Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Britny Johnson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| |
Collapse
|
48
|
Abstract
In this review, we discuss the current status and future challenges for fully elucidating the fungal tree of life. In the last 15 years, advances in genomic technologies have revolutionized fungal systematics, ushering the field into the phylogenomic era. This has made the unthinkable possible, namely access to the entire genetic record of all known extant taxa. We first review the current status of the fungal tree and highlight areas where additional effort will be required. We then review the analytical challenges imposed by the volume of data and discuss methods to recover the most accurate species tree given the sea of gene trees. Highly resolved and deeply sampled trees are being leveraged in novel ways to study fungal radiations, species delimitation, and metabolic evolution. Finally, we discuss the critical issue of incorporating the unnamed and uncultured dark matter taxa that represent the vast majority of fungal diversity.
Collapse
Affiliation(s)
- Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA;
| | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science and Innovation, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA;
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA;
| |
Collapse
|
49
|
Chicken Intestinal Mycobiome: Initial Characterization and Its Response to Bacitracin Methylene Disalicylate. Appl Environ Microbiol 2020; 86:AEM.00304-20. [PMID: 32358003 DOI: 10.1128/aem.00304-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
The gastrointestinal (GI) tract harbors a diverse population of microorganisms. While much work has been focused on the characterization of the bacterial community, very little is known about the fungal community, or mycobiota, in different animal species and chickens in particular. Here, we characterized the biogeography of the mycobiota along the GI tract of day 28 broiler chicks and further examined its possible shift in response to bacitracin methylene disalicylate (BMD), a commonly used in-feed antibiotic, through Illumina sequencing of the internal transcribed spacer 2 (ITS2) region of fungal rRNA genes. Out of 124 samples sequenced, we identified a total of 468 unique fungal features that belong to four phyla and 125 genera in the GI tract. Ascomycota and Basidiomycota represented 90% to 99% of the intestinal mycobiota, with three genera, i.e., Microascus, Trichosporon, and Aspergillus, accounting for over 80% of the total fungal population in most GI segments. Furthermore, these fungal genera were dominated by Scopulariopsis brevicaulis (Scopulariopsis is the anamorph form of Microascus), Trichosporon asahii, and two Aspergillus species. We also revealed that the mycobiota are more diverse in the upper than lower GI tract. The cecal mycobiota transitioned from being S. brevicaulis dominant on day 14 to T. asahii dominant on day 28. Furthermore, 2-week feeding of 55 mg/kg BMD tended to reduce the cecal mycobiota α-diversity. Taken together, we provided a comprehensive biogeographic view and succession pattern of the chicken intestinal mycobiota and its influence by BMD. A better understanding of intestinal mycobiota may lead to the development of novel strategies to improve animal health and productivity.IMPORTANCE The intestinal microbiota is critical to host physiology, metabolism, and health. However, the fungal community has been often overlooked. Recent studies in humans have highlighted the importance of the mycobiota in obesity and disease, making it imperative that we increase our understanding of the fungal community. The significance of this study is that we revealed the spatial and temporal changes of the mycobiota in the GI tract of the chicken, a nonmammalian species. To our surprise, the chicken intestinal mycobiota is dominated by a limited number of fungal species, in contrast to the presence of hundreds of bacterial taxa in the bacteriome. Additionally, the chicken intestinal fungal community is more diverse in the upper than the lower GI tract, while the bacterial community shows an opposite pattern. Collectively, this study lays an important foundation for future work on the chicken intestinal mycobiome and its possible manipulation to enhance animal performance and disease resistance.
Collapse
|
50
|
The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance. mSystems 2020; 5:5/3/e00061-20. [PMID: 32457237 PMCID: PMC7253362 DOI: 10.1128/msystems.00061-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Gut microbiota diversity has become the subject of extensive research in human and nonhuman animals, linking diversity and composition to gut function and host health. Because wild primates are good indicators of tropical ecosystem health, we developed the idea that they are a suitable model to observe the consequences of advancing global change (e.g., habitat degradation) on gut microbiota. So far, most of the studies focus mainly on gut bacteria; however, they are not the only component of the gut: fungi also serve essential functions in gut homeostasis. Here, for the first time, we explore and measure diversity and composition of both bacterial and fungal microbiota components of two tropical primate species living in highly different habitat types (intact versus degraded forests). Results on their microbiota diversity and composition are discussed in light of conservation issues and potential applications. Human exploitation and destruction of tropical resources are currently threatening innumerable wild animal species, altering natural ecosystems and thus, food resources, with profound effects on gut microbiota. Given their conservation status and the importance to tropical ecosystems, wild nonhuman primates make excellent models to investigate the effect of human disturbance on the diversity of host-associated microbiota. Previous investigations have revealed a loss of fecal bacterial diversity in primates living in degraded compared to intact forests. However, these data are available for a limited number of species, and very limited information is available on the fungal taxa hosted by the gut. Here, we estimated the diversity and composition of gut bacterial and fungal communities in two primates living sympatrically in both human-modified and pristine forests in the Udzungwa Mountains of Tanzania. Noninvasively collected fecal samples of 12 groups of the Udzungwa red colobus (Procolobus gordonorum) (n = 89), a native and endangered primate (arboreal and predominantly leaf-eating), and five groups of the yellow baboon (Papio cynocephalus) (n = 69), a common species of least concern (ground-feeding and omnivorous), were analyzed by the V1-V3 region of the 16S rRNA gene (bacterial) and ITS1-ITS2 (fungal) sequencing. Gut bacterial diversities were associated with habitat in both species, most likely depending on their ecological niches and associated digestive physiology, dietary strategies, and locomotor behavior. In addition, fungal communities also show distinctive traits across hosts and habitat type, highlighting the importance of investigating this relatively unexplored gut component. IMPORTANCE Gut microbiota diversity has become the subject of extensive research in human and nonhuman animals, linking diversity and composition to gut function and host health. Because wild primates are good indicators of tropical ecosystem health, we developed the idea that they are a suitable model to observe the consequences of advancing global change (e.g., habitat degradation) on gut microbiota. So far, most of the studies focus mainly on gut bacteria; however, they are not the only component of the gut: fungi also serve essential functions in gut homeostasis. Here, for the first time, we explore and measure diversity and composition of both bacterial and fungal microbiota components of two tropical primate species living in highly different habitat types (intact versus degraded forests). Results on their microbiota diversity and composition are discussed in light of conservation issues and potential applications.
Collapse
|