1
|
Bustamante-Brito R, Vera-Ponce de León A, Rosenblueth M, Martínez-Romero E. Comparative genomics of the carmine cochineal symbiont Candidatus Dactylopiibacterium carminicum reveals possible protection to the host against viruses via CRISPR/Cas. Syst Appl Microbiol 2024; 47:126540. [PMID: 39068732 DOI: 10.1016/j.syapm.2024.126540] [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: 03/14/2024] [Revised: 06/25/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
We present new genomes from the bacterial symbiont Candidatus Dactylopiibacterium carminicum obtained from non-domesticated carmine cochineals belonging to the scale insect Dactylopius (Hemiptera: Coccoidea: Dactylopiidae). As Dactylopiibacterium has not yet been cultured in the laboratory, metagenomes and metatranscriptomics have been key in revealing putative symbiont functions. Dactylopiibacterium is a nitrogen-fixing beta-proteobacterium that may be vertically transmitted and shows differential gene expression inside the cochineal depending on the tissue colonized. Here we found that all cochineal species tested had Dactylopiibacterium carminicum which has a highly conserved genome. All Dactylopiibacterium genomes analyzed had genes involved in nitrogen fixation and plant polymer degradation. Dactylopiibacterium genomes resemble those from free-living plant bacteria, some found as endophytes. Notably, we found here a new putative novel function where the bacteria may protect the insect from viruses, since all Dactylopiibacterium genomes contain CRISPRs with a spacer matching nucleopolyhedrovirus that affects insects.
Collapse
Affiliation(s)
- Rafael Bustamante-Brito
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico
| | - Arturo Vera-Ponce de León
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico; Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Mónica Rosenblueth
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico
| | - Esperanza Martínez-Romero
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico.
| |
Collapse
|
2
|
Sun X, Sitters J, Ruytinx J, Wassen MJ, Olde Venterink H. Microbial community composition in the dung of five sympatric European herbivore species. Ecol Evol 2024; 14:e11071. [PMID: 38481755 PMCID: PMC10933625 DOI: 10.1002/ece3.11071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 01/29/2024] [Accepted: 02/09/2024] [Indexed: 06/21/2024] Open
Abstract
The dung microbiome is a complex system that is highly influenced by species and diet. This study characterized the dung bacterial and fungal communities of five herbivore species inhabiting the National Park Zuid-Kennemerland, the Netherlands. The five selected herbivore species were rabbit (Oryctolagus cuniculus L.), cow (Bos taurus L.), horse (Equus ferus caballus L.), fallow deer (Dama dama L.), and European bison (Bison bonasus L.). We explored the effects of distinct digestive physiology (ruminants vs. non-ruminants) and diverse dietary preferences on the microbial community composition of herbivore dung. Firmicutes and Bacteroidetes were dominant bacterial phyla in the dung of all five herbivore species, and Ascomycota was the predominant fungal phylum. Verrucomicrobiota and Mucoromycota were more present in horse dung and Proteobacteria were more abundant in rabbit dung than the three ruminant dung types. There were few significant differences in the microbial community structure among the three ruminant dung types. The alpha and beta diversity of dung microbial communities significantly differed between ruminants and non-ruminants, especially in bacterial communities. Based on MetaCyc pathways, we found that the primary functions of bacteria in herbivore dung were focused on biosynthesis, various super pathways, and degradation, with a few differences between ruminant and non-ruminant dung. FUNGuild analysis showed that horse dung had more saprotrophic fungi, while the fungi in fallow deer dung had more symbiotrophic properties, with the fungal functions of bison, cow, and rabbit dung somewhere in between. There was also a correlation between microbial community and nutrient composition of the substrate in herbivore dung. Understanding the dung microbial community composition of these herbivore species can enrich the database of mammalian gut microbiomes for studying the mechanisms of microbial community variation while preparing for exploring a new perspective to study the impact of herbivores on ecosystems through dung deposition.
Collapse
Affiliation(s)
- Xingzhao Sun
- Research Group WILDVrije Universiteit BrusselBrusselsBelgium
| | - Judith Sitters
- Research Group WILDVrije Universiteit BrusselBrusselsBelgium
- B‐WARE Research CentreNijmegenThe Netherlands
| | - Joske Ruytinx
- Research Groups Microbiology and Plant GeneticsVrije Universiteit BrusselBrusselsBelgium
| | - Martin J. Wassen
- Environmental Sciences, Copernicus Institute of Sustainable DevelopmentUtrecht UniversityUtrechtThe Netherlands
| | | |
Collapse
|
3
|
Zhang NN, Chen XX, Liang J, Zhao C, Xiang J, Luo L, Wang ET, Shi F. Rhizocompartmental microbiomes of arrow bamboo ( Fargesia nitida) and their relation to soil properties in Subalpine Coniferous Forests. PeerJ 2023; 11:e16488. [PMID: 38047031 PMCID: PMC10693234 DOI: 10.7717/peerj.16488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/27/2023] [Indexed: 12/05/2023] Open
Abstract
Arrow bamboo (Fargesia nitida) is a pioneer plant in secondary forest succession in the Sichuan Province mountains. To comprehensively investigate the microbial communities and their functional variations in different rhizocompartments (root endosphere, rhizosphere, and root zone) of arrow bamboo (Fargesia nitida), a high-throughput metagenomic study was conducted in the present study. The results showed that the abundances of the dominant bacterial phyla Proteobacteria and Actinobacteria in the bamboo root endosphere were significantly lower than those in the rhizosphere and root zones. In contrast, the dominant fungal phyla, Ascomycota and Basidiomycota, showed the opposite tendency. Lower microbial diversity, different taxonomic composition and functional profiles, and a greater abundance of genes involved in nitrogen fixation (nifB), cellulose degradation (beta-glucosidase), and cellobiose transport (cellulose 1, 4-beta-cellobiosidase) were found in the bamboo root endosphere than in the other rhizocompartments. Greater soil total carbon, total nitrogen, NH4+-N, microbial biomass carbon, and greater activities of invertase and urease were found in the bamboo root zone than in the adjacent soil (spruce root zone). In contrast, the soil microbial community and functional profiles were similar. At the phylum level, invertase was significantly related to 31 microbial taxa, and the effect of NH4+-N on the microbial community composition was greater than that of NO3--N. The soil physicochemical properties and enzyme activities were significantly correlated with microbial function. These results indicate that the root endosphere microbiomes of arrow bamboo were strongly selected by the host plant, which caused changes in the soil nutrient properties in the subalpine coniferous forest.
Collapse
Affiliation(s)
- Nan Nan Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiao Xia Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jin Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | | | - Jun Xiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Lin Luo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - En Tao Wang
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Fusun Shi
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| |
Collapse
|
4
|
Liu D, Hao Y, Gao H, Yu H, Li Q. Applying synchronous fluorescence spectra with Gaussian band fitting and two-dimensional correlation to characterize structural composition of DOM from soils in an aquatic-terrestrial ecotone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160081. [PMID: 36372163 DOI: 10.1016/j.scitotenv.2022.160081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/21/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
Dissolved organic matter (DOM), the primary participant of carbon and nitrogen cycle, has a great impact on the behavior and fate of organic pollutants and heavy metals in eutrophic lakes. The dynamic spectral properties of DOM fractions were revealed in an aquatic-terrestrial ecotone under the different types of land use. Composite soil samples of different depths (0-20, 20-40 and 40-60 cm) were collected from four different land uses along a disturbed-impact gradient in Taihu Lake, China, i.e., grassland (GRL), forest land (FOL), paddy field (PAF), and vegetable field (VEF). DOM mainly consisted of tyrosine-like material (TYLF), tryptophan-like material (TRLF), microbial humic-like material (MHLF), fulvic-like material (FLF) and humic-like material (HLF) within all soil profiles, where TRLF was the dominant component (61.30 %) using synchronous fluorescence spectroscopy (SFS) combined with principal component analysis and Gaussian band fitting. Based on two-dimensional correlation spectroscopy with SFS and Fourier transform infrared, the variation order of DOM fractions was FLF → MHLF → HLF → TRLF → TYLF within the GRL soil profile, and MHLF exhibited an oppositive change with aliphatic OH and amide I in protein. The order of DOM fractions was MHLF → FLF → HLF → TYLF → TRLF within the FOL soil profile, and the change trend of MHLF remained oppositive with aliphatic OH and CO in ester. The order of DOM within the PAF soil profile fractions was TRLF → MHLF → HLF → TYLF → FLF, and changing trends of TYLF were oppositive to aliphatic OH, CH bending vibration, CH bending vibration and CO in ester. The order of DOM fractions was HLF → TYLF → TRLF → FLF → MHLF within the VEF soil profile, where the changing trend TYLF remained oppositive to aliphatic OH, CH deformations in lignin and aliphatic group and amide I in protein. This study may provide important support for alleviating lake water eutrophication or pollution.
Collapse
Affiliation(s)
- Dongping Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Yan Hao
- Ningxia Environmental Science Research Institute Co., Ltd, Yinchuan 750002, China
| | - Hongjie Gao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Huibin Yu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Qingqian Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| |
Collapse
|
5
|
Chen W, Yu L, Zhu B, Qin L. Dendrobium officinale Endophytes May Colonize the Intestinal Tract and Regulate Gut Microbiota in Mice. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:2607506. [PMID: 35990847 PMCID: PMC9388241 DOI: 10.1155/2022/2607506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/11/2022] [Accepted: 07/19/2022] [Indexed: 11/18/2022]
Abstract
Dendrobium officinale is a traditional Chinese medicine for treating gastrointestinal diseases by nourishing "Yin" and thickening the stomach lining. To study whether D. officinale endophytes can colonize the intestinal tract and regulate gut microbiota in mice, we used autoclave steam sterilizing and 60Co-γ radiation to eliminate D. officinale endophytes from its juice. Then, high-throughput ITS1-ITS2 rDNA and 16S rRNA gene amplicons were sequenced to analyze the microbial community of D. officinale endophytes and fecal samples of mice after administration of fresh D. officinale juice. Sterilization of D. officinale juice by autoclaving for 40 min (ASDO40) could more effectively eliminate the D. officinale endophytes and decrease their interference on the gut microbiota. D. officinale juice could increase beneficial gut microbiota and metabolites including short-chain fatty acids. D. officinale endophytes Pseudomonas mosselii, Trichocladium asperum, Titata maxilliformis, Clonostachys epichloe, and Rhodotorula babjevae could colonize the intestinal tract of mice and modulate gut microbiota after oral administration of the juice for 28 days. Thus, the regulatory effect of D. officinale juice on gut microbiota was observed, which provides a basis for inferring that D. officinale endophytes might colonize the intestinal tract and participate in regulating gut microbiota to treat diseases. Thus, this study further provides a new approach for the treatment of diseases by colonizing plant endophytes in the intestinal tract and regulating gut microbiota.
Collapse
Affiliation(s)
- Wenhua Chen
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Lilong Yu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Bo Zhu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Luping Qin
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| |
Collapse
|
6
|
Pandey SS, Jain R, Bhardwaj P, Thakur A, Kumari M, Bhushan S, Kumar S. Plant Probiotics – Endophytes pivotal to plant health. Microbiol Res 2022; 263:127148. [DOI: 10.1016/j.micres.2022.127148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/22/2022] [Accepted: 07/26/2022] [Indexed: 12/11/2022]
|
7
|
Hu H, Chen Q, He J. The end of hunger: fertilizers, microbes and plant productivity. Microb Biotechnol 2022; 15:1050-1054. [PMID: 34767687 PMCID: PMC8966006 DOI: 10.1111/1751-7915.13973] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 11/05/2022] Open
Abstract
It is a grand challenge to ensure the food security for a predicted world population of exceeding 9.7 billion by 2050, especially in an era of global climate change, land degradation and biodiversity loss. Current agricultural productions are mainly relying on synthetic chemical fertilisers to boost plant productivity but have undesirable effects on the environment and soil biodiversity. A promising direction in sustainable agriculture is to harness naturally occurring processes of beneficial plant-associated microbiomes to ensure sustained crop production and global food security. Despite the significant progress made in the development of beneficial microbes as inoculants to enhance plant performance, challenges remain with the translation of knowledge of plant and soil microbiomes to successful microbial products in the agricultural sector. Here, we highlight how fertilizer technology should be renovated by harnessing microbiome-based innovations to promote plant productivity and contribute to the end of hunger.
Collapse
Affiliation(s)
- Hang‐Wei Hu
- School of Agriculture and FoodFaculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVic.3010Australia
- ARC Hub for Smart FertilisersThe University of MelbourneParkvilleVic.3010Australia
| | - Qing‐Lin Chen
- School of Agriculture and FoodFaculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVic.3010Australia
| | - Ji‐Zheng He
- School of Agriculture and FoodFaculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVic.3010Australia
- ARC Hub for Smart FertilisersThe University of MelbourneParkvilleVic.3010Australia
| |
Collapse
|
8
|
Montes-Carreto LM, Aguirre-Noyola JL, Solís-García IA, Ortega J, Martinez-Romero E, Guerrero JA. Diverse methanogens, bacteria and tannase genes in the feces of the endangered volcano rabbit ( Romerolagus diazi). PeerJ 2021; 9:e11942. [PMID: 34458021 PMCID: PMC8378336 DOI: 10.7717/peerj.11942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/19/2021] [Indexed: 12/27/2022] Open
Abstract
Background The volcano rabbit is the smallest lagomorph in Mexico, it is monotypic and endemic to the Trans-Mexican Volcanic Belt. It is classified as endangered by Mexican legislation and as critically endangered by the IUCN, in the Red List. Romerolagus diazi consumes large amounts of grasses, seedlings, shrubs, and trees. Pines and oaks contain tannins that can be toxic to the organisms which consume them. The volcano rabbit microbiota may be rich in bacteria capable of degrading fiber and phenolic compounds. Methods We obtained the fecal microbiome of three adults and one young rabbit collected in Coajomulco, Morelos, Mexico. Taxonomic assignments and gene annotation revealed the possible roles of different bacteria in the rabbit gut. We searched for sequences encoding tannase enzymes and enzymes associated with digestion of plant fibers such as cellulose and hemicellulose. Results The most representative phyla within the Bacteria domain were: Proteobacteria, Firmicutes and Actinobacteria for the young rabbit sample (S1) and adult rabbit sample (S2), which was the only sample not confirmed by sequencing to correspond to the volcano rabbit. Firmicutes, Actinobacteria and Cyanobacteria were found in adult rabbit samples S3 and S4. The most abundant phylum within the Archaea domain was Euryarchaeota. The most abundant genera of the Bacteria domain were Lachnoclostridium (Firmicutes) and Acinetobacter (Proteobacteria), while Methanosarcina predominated from the Archaea. In addition, the potential functions of metagenomic sequences were identified, which include carbohydrate and amino acid metabolism. We obtained genes encoding enzymes for plant fiber degradation such as endo 1,4 β-xylanases, arabinofuranosidases, endoglucanases and β-glucosidases. We also found 18 bacterial tannase sequences.
Collapse
Affiliation(s)
- Leslie M Montes-Carreto
- Facultad de Ciencias Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - José Luis Aguirre-Noyola
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Itzel A Solís-García
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Xalapa, Veracruz, Mexico
| | - Jorge Ortega
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de Mexico, Mexico
| | | | - José Antonio Guerrero
- Facultad de Ciencias Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| |
Collapse
|
9
|
Mills S, Ross RP. Colliding and interacting microbiomes and microbial communities - consequences for human health. Environ Microbiol 2021; 23:7341-7354. [PMID: 34390616 DOI: 10.1111/1462-2920.15722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/26/2022]
Abstract
Living 'things' coexist with microorganisms, known as the microbiota/microbiome that provides essential physiological functions to its host. Despite this reliance, the microbiome is malleable and can be altered by several factors including birth-mode, age, antibiotics, nutrition, and disease. In this minireview, we consider how other microbiomes and microbial communities impact the host microbiome and the host through the concept of microbiome collisions (initial exposures) and interactions. Interactions include changes in host microbiome composition and functionality and/or host responses. Understanding the impact of other microbiomes and microbial communities on the microbiome and host are important considering the decline in human microbiota diversity in the developed world - paralleled by the surge of non-communicable, inflammatory-based diseases. Thus, surrounding ourselves with rich and diverse beneficial microbiomes and microbial communities to collide and interact with should help to diminish the loss in microbial diversity and protect from certain diseases. In the same vein, our microbiomes not only influence our health but potentially the health of those close to us. We also consider strategies for enhanced host microbiome collisions and interactions through the surrounding environment that ensure increased microbiome diversity and functionality contributing to enhanced symbiotic return to the host in terms of health benefit.
Collapse
Affiliation(s)
- Susan Mills
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | |
Collapse
|
10
|
Succession of Intestinal Microbial Structure of Giant Pandas ( Ailuropoda melanoleuca) during Different Developmental Stages and Its Correlation with Cellulase Activity. Animals (Basel) 2021; 11:ani11082358. [PMID: 34438815 PMCID: PMC8388744 DOI: 10.3390/ani11082358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Giant pandas (Ailuropoda melanoleuca) are endangered animals and are uniquely inhabitant in China. These rare animals have gradually developed bamboo-eating adaptability through persistent evolution. Intestinal microbes play an important role in the digestion, absorption, metabolism, and development of giant pandas especially by facilizing the degradation of bamboo polysaccharides such as cellulose. Currently, genes directly related to cellulose degradation have not been identified in the genome of giant panda, and cellulose digestion is therefore likely dependent on intestinal microbes. This study analyzed the changes in intestinal microbial structure of giant pandas (cubs, sub-adults, and adults) in different developmental stages. The impact was also assessed with the changes in food composition probed into the succession regularity of intestinal microbes and the activities of intestinal flora on the digestion and utilization of cellulose in bamboo. Abstract The interaction between intestinal microbial flora and giant pandas (Ailuropoda melanoleuca) is indispensable for the healthy development of giant pandas. In this study, we analysed the diversity of bacteria and fungi in the intestines of six giant pandas (two pandas in each development stage) with a high-throughput sequencing technique to expand the relative variation in abundance of dominant microbes and potential cellulose-degradation genera in the intestines of the giant pandas and to explore the correlation between dominant microbial genera in the intestines and cellulose digestion activities of giant pandas. The results showed that the intestinal bacterial diversity of young giant pandas was higher than that of sub-adult and adult giant pandas, and Shannon’s diversity index was about 2.0. The intestinal bacterial diversity of giant pandas from sub-adult to adult (mature stage) stage showed an increasing trend, but the intestinal fungal diversity showed no considerable regular relations with their ages. The microbial composition and abundance of giant pandas changed in different developmental stages. Pearson correlation analysis and path analysis showed that there was a close relationship between the dominant microbes in the intestines of giant pandas, and the interaction between microbial genera might affect the cellulose digestion ability of giant pandas. Generally, the digestibility of cellulose degraders in pandas was still insufficient, with low enzymic activity and immature microbial structure. Therefore, the utilization and digestion of bamboo cellulose still might not be a main source of energy for pandas.
Collapse
|
11
|
Yanez-Montalvo A, Gaona O, Águila B, Arias-Domínguez N, Falcón LI, Pérez-Flores J. Tapirus bairdii-Associated Fecal Microbiome from a Critical Conservation Area: Calakmul, México. Curr Microbiol 2021; 78:2648-2659. [PMID: 33990869 DOI: 10.1007/s00284-021-02531-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 05/03/2021] [Indexed: 11/28/2022]
Abstract
Baird's tapir (Tapirus bairdii) is the largest native terrestrial mammal in the Neotropics, which is endangered primarily as a consequence of habitat loss and overhunting. Baird's tapir is predominantly nocturnal and exists at low densities which complicates field studies. Baird's tapir is a large-bodied herbivore that plays a key role in maintaining healthy tropical forests through seed dispersal in its feces. Studies of gut microbiome are essential and valuable to assess the health status of the host and the interaction with the environment. In this study, we collected fresh fecal samples of T. bairdii to analyze its gut microbiome during the rainy and dry seasons in the Calakmul region, which is a critical rainforest conservation area in Mexico. The results of a high-throughput 16S rDNA gene sequencing approach suggest that the fecal microbiome of Baird's tapir has no significant differences in composition among seasons. The most common phyla were Firmicutes, Bacteroidetes, Proteobacteria, Kiritimatiellaeota, and Spirochaetes. This study suggests that the stability of the fecal microbiome is related to similar feeding strategies throughout the year, and emphasizes the value of tapir in seed dispersal (and associated microbes) to the well-conserved forests of the Greater Calakmul region as biodiversity hotspots for conservation.
Collapse
Affiliation(s)
- Alfredo Yanez-Montalvo
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, 97302, Mérida, México.,El Colegio de La Frontera Sur, Unidad de Chetumal, Avenida Centenario Km 5.5, 77014, Chetumal, Quintana Roo, México
| | - Osiris Gaona
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, 97302, Mérida, México
| | - Bernardo Águila
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, 97302, Mérida, México
| | | | - Luisa I Falcón
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, 97302, Mérida, México
| | - Jonathan Pérez-Flores
- El Colegio de La Frontera Sur, Unidad de Chetumal, Avenida Centenario Km 5.5, 77014, Chetumal, Quintana Roo, México. .,Universidad Tecnológica de Calakmul, Carretera Estatal Xpujil-Dzibalchen Km 2, 24640, Calakmul, Campeche, México.
| |
Collapse
|