1
|
Ferrari VB, Dos Santos Lima LM, de Matos Marques K, Gutierres FC, Guerini GG, Silveira MAV, de Figueiredo GM, Vital VG, Roswell MR, de Melo IS, Okamoto DN, de Vasconcellos SP. Caatinga, Amazon and Atlantic Forest as natural sources for microbial lignocellulolytic enzymes. Arch Microbiol 2024; 206:161. [PMID: 38483627 DOI: 10.1007/s00203-024-03883-y] [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: 11/24/2023] [Revised: 01/19/2024] [Accepted: 02/02/2024] [Indexed: 03/19/2024]
Abstract
Brazilian biomes are important sources for environmental microorganisms, including efficient metabolic machineries, like actinomycetes. These bacteria are known for their abilities to produce many bioactive compounds, including enzymes with multiple industrial applications. The present work aimed to evaluate lignocellulolytic abilities of actinomycetes isolated from soil and rhizosphere samples collected at Caatinga, Atlantic and Amazon Forest. Laccase (Lac), lignin peroxidase (LiP), manganese peroxidase (MnP) and cellulase were evaluated for their efficiency. These enzymes have an essential role in lignin decomposition, through oxidation of phenolic and non-phenolic compounds, as well as enzymatic hydrolysis of vegetal biomass. In this sense, a total of 173 actinomycetes were investigated. Eleven (11) of them were selected by their enzymatic performance. The actinomycete AC166 displayed some activity in all analysed scenarios in terms of Lac, MnP and LiP activity, while AC171 was selected as the most promising strain, showing the following activities: 29.7 U.L-1 for Lac; 2.5 U.L-1 for LiP and 23 U.L-1 for MnP. Cellulolytic activities were evaluated at two pH conditions, 4.8 and 7.4, obtaining the following results: 25 U.L-1 and 71 U.L-1, respectively. Thermostability (4, 30 and 60 o C) and salinity concentrations (0 to 4 M) and pH variation (2.0 to 9.0) stabilities of the obtained LiP and Lac enzymatic extracts were also verified. The actinomycete strain AC171 displayed an adaptable response in distinct pH and salt profiles, indicating that bacterial LiP was some halophilic type. Additionally, the strain AC149 produced an alkali and extreme halophilic lignin peroxidase, which are promising profiles for their future application under lignocellulosic biomass at bioethanol biorefineries.
Collapse
Affiliation(s)
- Vitor Baptista Ferrari
- Department of Pharmaceutical Sciences, Universidade Federal de São Paulo (UNIFESP), Diadema, SP, Brazil
| | | | - Kelly de Matos Marques
- Department of Pharmaceutical Sciences, Universidade Federal de São Paulo (UNIFESP), Diadema, SP, Brazil
| | - Fernanda Camila Gutierres
- Department of Pharmaceutical Sciences, Universidade Federal de São Paulo (UNIFESP), Diadema, SP, Brazil
| | | | - Marghuel Aparecida Vieira Silveira
- Laboratory of Biochemistry and Enzymology, Institute of Pharmacology and Molecular Biology, Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Vitor Gonçalves Vital
- Department of Pharmaceutical Sciences, Universidade Federal de São Paulo (UNIFESP), Diadema, SP, Brazil
| | - Mariana Rocha Roswell
- Department of Pharmaceutical Sciences, Universidade Federal de São Paulo (UNIFESP), Diadema, SP, Brazil
| | - Itamar Soares de Melo
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, Jaguariúna, SP, Brazil
| | - Debora Noma Okamoto
- Department of Pharmaceutical Sciences, Universidade Federal de São Paulo (UNIFESP), Diadema, SP, Brazil
| | | |
Collapse
|
2
|
ElKraly OA, Awad M, El-Saadany HM, Hassanein SE, Elrahman TA, Elnagdy SM. Impact of gut microbiota composition on black cutworm, Agrotis ipsilon (hufnagel) metabolic indices and pesticide degradation. Anim Microbiome 2023; 5:44. [PMID: 37715236 PMCID: PMC10504801 DOI: 10.1186/s42523-023-00264-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/03/2023] [Indexed: 09/17/2023] Open
Abstract
Endosymbionts are known to have significant effects on their insect hosts, including nutrition, reproduction, and immunity. Insects gut microbiota is a critical component that affects their physiological and behavioral characteristics. The black cutworm (BCW), Agrotis ipsilon, is an economically important lepidopteran pest that has a diverse gut microbiome composed of nine species belonging to three phyla: Proteobacteria, Actinobacteria, and Firmicutes. This study was conducted to investigate the diversity of gut bacteria isolated from BCW larvae and moths and their effects on metabolism and pesticide degradation. The bacterial isolates were identified using the 16 S rRNA gene. The study showed that the gut microbiome composition significantly affected the metabolism of BCW larvae. Based on the screening results of synthesis of digestive enzymes and pesticide degradation, Brachybacterium conglomeratum and Glutamicibacter sp were selected to perform the remaining experiments as single isolates and consortium. The consortium-fed larvae showed high metabolic indices compared to antibiotic-fed larvae and the control. The gut bacteria were also shown to degrade three pesticide groups. Concerns regarding the health risk of chlorpyrifos have been raised due to its extensive use in agriculture. The isolated B. conglomeratum was more effective in chlorpyrifos degradation than the consortium. Furthermore, the study also examined the presence of sex related endosymbionts (Wolbachia, Spiroplasma, and Rickettsia) in the reproductive tissues of adults. The outcomes demonstrated that none of the examined endosymbionts existed. In conclusion, the study highlights the importance of the gut microbiome in insect physiology and behavior and its potential applications in biotechnology. It provides insights into developing eco-friendly pest control and bioremediation strategies using gut bacteria.
Collapse
Affiliation(s)
- Omnia Abdullah ElKraly
- Botany and Microbiology Department, Faculty of Science, Cairo University, Gamma St, Giza, 12613, Giza, Egypt
- Bio-insecticides Production Unit, Plant Protection Research Institute (PPRI), Agricultural Research Center (ARC), Ministry of Agriculture, Dokki, Giza, Egypt
| | - Mona Awad
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, Cairo, Egypt.
| | - Hassan Mohamed El-Saadany
- Bio-insecticides Production Unit, Plant Protection Research Institute (PPRI), Agricultural Research Center (ARC), Ministry of Agriculture, Dokki, Giza, Egypt
| | - Sameh E Hassanein
- College of Biotechnology, Misr University for Science and Technology (MUST), Giza, Egypt
| | - Tahany Abd Elrahman
- Botany and Microbiology Department, Faculty of Science, Cairo University, Gamma St, Giza, 12613, Giza, Egypt
| | - Sherif M Elnagdy
- Botany and Microbiology Department, Faculty of Science, Cairo University, Gamma St, Giza, 12613, Giza, Egypt.
| |
Collapse
|
3
|
Han H, Zhong R, Zhang S, Wang M, Wen X, Yi B, Zhao Y, Chen L, Zhang H. Hydroxytyrosol attenuates diquat-induced oxidative stress by activating Nrf2 pathway and modulating colonic microbiota in mice. J Nutr Biochem 2023; 113:109256. [PMID: 36572071 DOI: 10.1016/j.jnutbio.2022.109256] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/16/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022]
Abstract
This study was conducted to investigate the antioxidant effects of hydroxytyrosol (HT) administration in diquat (DQ)-challenged mice. The results showed that HT treatment markedly alleviated DQ-induced oxidative stress, which was indicated by the enhanced total antioxidant capacity (T-AOC), increased activities of superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and catalase and decreased malondialdehyde (MDA) concentration in serum. Additionally, HT increased the mRNA expression levels of NF-E2-related factor 2 (Nrf2) and its downstream genes, including NADPH quinone oxidoreductase 1 (NQO1) and catalase (CAT) in the small intestine of DQ-challenged mice. 16S rRNA gene sequencing results showed that HT treatment increased the relative abundance of Firmicutes and Lactobacillus and decreased the relative abundance of Bacteroidetes. Interestingly, Pearson correlation analysis showed that there were strong association between colonic Firmicutes, Lactobacillus, and Bacteroidetes and the activities of serum antioxidant enzymes. Meanwhile, HT significantly enhanced the colonic butyrate concentration in DQ-challenged mice. Additionally, HT treatment decreased the serum metabolites involving in glycerophospholipid metabolism, pentose, and glucuronate interconversions, which were associated with alleviated oxidative stress. These results indicate that oral administration of 100 mg/kg body weight HT alleviates oxidative stress in DQ-challenged mice, which may involve Nrf2 signaling pathways via modulation of colonic microbiota.
Collapse
Affiliation(s)
- Hui Han
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China; Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Ruqing Zhong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shunfen Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengyu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaobin Wen
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bao Yi
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liang Chen
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
| |
Collapse
|
4
|
Arumugam R, Ravichandran P, Yeap SK, Sharma RSK, Zulkifly SB, Yawah D, Annavi G. Application of High-Throughput Sequencing (HTS) to Enhance the Well-Being of an Endangered Species (Malayan Tapir): Characterization of Gut Microbiome Using MG-RAST. Methods Mol Biol 2023; 2649:175-194. [PMID: 37258862 DOI: 10.1007/978-1-0716-3072-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The Tapirus indicus, also known as Malayan tapir, has been listed as a rapidly declining animal species in the past decades, along with being declared and categorized as an endangered species by the International Union for Conservation of Nature (IUCN) 2016. This tapir species is geographically distributed across several countries in Southeast Asia such as Peninsular Malaysia, Indonesia (Sumatra), South Thailand, and Myanmar. Amongst these countries, the Peninsula Malaysia forest is recorded to contain the highest number of Malayan tapir population. Unfortunately, in the past decades, the population of Malayan tapirs has declined swiftly due to serious deforestation, habitat fragmentation, and heavy vehicle accidents during road crossings at forest routes. Concerned by this predicament, the Department of Wildlife and National Parks (DWNP) Peninsular Malaysia collaborated with a few local universities to conduct various studies aimed at increasing the population number of tapirs in Malaysia. Several studies were conducted with the aim of enhancing the well-being of tapirs in captivity. Veterinarians face problems when it comes to selecting healthy and suitable tapirs for breeding programs at conservation centers. Conventional molecular methods using high-throughput sequencing provides a solution in determining the health condition of Malayan tapirs using the Next-Generation Sequencing (NGS) technology. Unaware by most, gut microbiome plays an important role in determining the health condition of an organism by various aspects: (1) digestion control; (2) benefiting the immune system; and (3) playing a role as a "second brain." Commensal gut bacterial communities (microbiomes) are predicted to influence organism health and disease. Imbalance of unhealthy and healthy microbes in the gut may contribute to weight gain, high blood sugar, high cholesterol, and other disorders. In infancy, neonatal gut microbiomes are colonized with maternal and environmental flora, and mature toward a stable composition in two to three years. Interactions between the microorganism communities and the host allow for the establishment of microbiological roles. Identifying the core microbiome(s) are essential in the prediction of diseases and changes in environmental behavior of microorganisms. The dataset of 16S rRNA amplicon sequencing of Malayan tapir was deposited in the MG-RAST portal. Parameters such as quality control, taxonomic prediction (unknown and predicted), diversity (rarefaction), and diversity (alpha) were analyzed using sequencing approaches (Amplicon sequencing). Comparisons of parameters, according to the type of sequencing, showed significant differences, except for the prediction variable. In the Amplicon sequencing datasets, the parameters Rarefaction and Unknown had the highest correlation, while Alpha and Predicted had the lowest. Firmicutes, Bacteroidetes, Proteobacteria, Bacilli, and Bacteroidia were the most representative genera in Malayan tapir amplicon sequences, which indicated that most of the tapirs were healthy. However, continuous assessment to maintain the well-being of tapir for long term is still required. This chapter focuses on the introduction of 16S rRNA amplicon metagenomics in analyzing Malayan tapir gut microbiome dataset.
Collapse
Affiliation(s)
- Ramitha Arumugam
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor Darul Ehsan, Malaysia
- Dataplx Consultancy, Puchong, Selangor, Malaysia
| | - Prithivan Ravichandran
- Perdana University Graduate School (PUGSOM), Perdana University, Serdang, Selangor, Malaysia
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | | | - Shahrizim Bin Zulkifly
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor Darul Ehsan, Malaysia
| | - Donny Yawah
- Department of Wildlife and National Parks (DWNP), Wildlife Genetic Resource Banking Laboratory, Ex-Situ Conservation Division, Peninsular Malaysia, Ministry of Natural Resources and Environment Malaysia (NRE), Kuala Lumpur, Malaysia
| | - Geetha Annavi
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor Darul Ehsan, Malaysia.
| |
Collapse
|
5
|
Dar MA, Xie R, Pandit RS, Danso B, Dong C, Sun J. Exploring the region-wise diversity and functions of symbiotic bacteria in the gut system of wood-feeding termite, Coptotermes formosanus, toward the degradation of cellulose, hemicellulose, and organic dyes. INSECT SCIENCE 2022; 29:1414-1432. [PMID: 35134272 DOI: 10.1111/1744-7917.13012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/28/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
The wood-feeding termite Coptotermes formosanus represents a unique and impressive system for lignocellulose degradation. The highly efficient digestion of lignocellulose is achieved through symbiosis with gut symbionts like bacteria. Despite extensive research during the last three decades, diversity of bacterial symbionts residing in individual gut regions of the termite and their associated functions is still lacking. To this end, cellulose, xylan, and dye-decolorization bacteria residing in foregut, midgut, and hindgut regions of C. formosanus were enlisted by using enrichment and culture-dependent molecular methods. A total of 87 bacterial strains were successfully isolated from different gut regions of C. formosanus which belonged to 27 different species of 10 genera, majorly affiliated with Proteobacteria (80%) and Firmicutes (18.3%). Among the gut regions, 37.9% of the total bacterial isolates were observed in the hindgut that demonstrated predominance of cellulolytic bacteria (47.6%). The majority of the xylanolytic and dye-decolorization bacteria (50%) were obtained from the foregut and midgut, respectively. Actinobacteria represented by Dietza sp. was observed in the hindgut only. Based on species richness, the highest diversity was observed in midgut and hindgut regions each of which harbored seven unique bacterial species. The members of Enterobacter, Klebsiella, and Pseudomonas were common among the gut regions. The lignocellulolytic activities of the selected potential bacteria signpost their assistance to the host for lignocellulose digestion. The overall results indicate that C. formosanus harbors diverse communities of lignocellulolytic bacteria in different regions of the gut system. These observations will significantly advance our understanding of the termite-bacteria symbiosis and their microbial ecology uniquely existed in different gut regions of C. formosanus, which may further shed a light on its potential values at termite-modeled biotechnology.
Collapse
Affiliation(s)
- Mudasir A Dar
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Department of Zoology, Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Rongrong Xie
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | | | - Blessing Danso
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Chenchen Dong
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu Province, China
| |
Collapse
|
6
|
Maibeche R, Boucherba N, Bendjeddou K, Prins A, Bouiche C, Hamma S, Benhoula M, Azzouz Z, Bettache A, Benallaoua S, Le Roes-Hill M. Peroxidase-producing actinobacteria from Algerian environments and insights from the genome sequence of peroxidase-producing Streptomyces sp. S19. Int Microbiol 2022; 25:379-396. [DOI: 10.1007/s10123-022-00236-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/08/2021] [Accepted: 01/17/2022] [Indexed: 11/28/2022]
|
7
|
Banerjee S, Maiti TK, Roy RN. Enzyme producing insect gut microbes: an unexplored biotechnological aspect. Crit Rev Biotechnol 2021; 42:384-402. [PMID: 34612103 DOI: 10.1080/07388551.2021.1942777] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
To explore the unmapped biotechnologically important microbial platforms for human welfare, the insect gut system is such a promising arena. Insects, the inhabitant of all ecological niches, harbor a healthy diversified microbial population in their versatile gut environment. This deep-rooted symbiotic relationship between insects and gut microbes is the result of several indispensable microbial performances that include: enzyme production, detoxification of plant defense compounds and insecticides, maintenance of life cycle, host fertility, bioremediation, pest biocontrol, production of antimicrobial compounds, and in addition provide vitamins, amino acids, and lactic acids to their hosts. Insects have developed such symbiotic interactions with different microorganisms for nutritional benefits like the digestion of dietary compounds by the production of several key hydrolytic enzymes viz: amylase, cellulase, lignocellulase, protease, lipase, xylanase, pectinase, chitinase, laccase, etc. The nutritional enrichment offered by these microbes to insects may be the key factor in the evolutionary attainment of this group. Around one million insect species are grouped under 31 orders, however, only ten of such groups' have been studied in relation to enzyme-producing gut microbes. Moreover, insect gut symbionts are a potential source of biotechnologically active biomolecules as these microbes go through a course of selection pressures in their host gut environment. As symbiosis has pronounced potential regarding the production of novel compounds, especially enzymes with multidimensional industrial capabilities, so there are ample scopes to explore this treasure box for human welfare. Biological significance as well as industrially compatible capabilities can categorize these insect gut symbionts as an unexplored biotechnological aspect.
Collapse
Affiliation(s)
- Sandipan Banerjee
- Microbiology Research Laboratory, Department of Botany, Dr. B. N. Dutta Smriti Mahavidyalaya, Hatgobindapur, Burdwan, India.,Mycology and Plant Pathology Laboratory, Department of Botany, Visva-Bharati University, Santiniketan, India
| | | | - Raj Narayan Roy
- Microbiology Research Laboratory, Department of Botany, Dr. B. N. Dutta Smriti Mahavidyalaya, Hatgobindapur, Burdwan, India
| |
Collapse
|
8
|
Yang Z, Jin Y, Hou F, Bowatte S. Soil microbial and chemical responses to foliar Epichloë fungal infection in Lolium perenne, Hordeum brevisubulatum and Achnatherum inebrians. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
9
|
Collaborative Response of the Host and Symbiotic Lignocellulytic System to Non-Lethal Toxic Stress in Coptotermes formosanus Skiraki. INSECTS 2021; 12:insects12060510. [PMID: 34073040 PMCID: PMC8227567 DOI: 10.3390/insects12060510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Coptotermes formosanus Shiraki is a wood feeding lower termite and is widely distributed in many areas. The dynamic adjustment of the C. formosanus digestive system to unfavorable survival environments was investigated via non-lethal toxic feeding. The toxic stress did not change the dominant role of microbial lignocellulases in cellulose degradation of C. formosanus. The core symbiotic community was stable in abundance during the tolerance to the toxic treatment. However, a large number of low abundance taxa were significantly enriched by the low toxic feeding. These rare bacterial lineages likely contribute to toxic stress tolerance of termite. Above all, these findings add important new knowledge to our understanding of environmental adaptation of the lignocellulose hydrolysis system in termites. Abstract Disturbing the lignocellulose digestive system of termites is considered to be a promising approach for termite control. The research on the tolerance mechanism of the termite lignocellulose digestive system to harmful environment conditions is limited. In this study, we keep Coptotermes formosanus Skiraki under a non-lethal toxic condition by feeding the termites with filter paper containing the kojic acid (a low toxic insecticide). The effects of low toxic stress on the activities and gene expressions of host/symbiotic originated lignocellulases, and on the symbiotic microbial community structure of C. formosanus were explored. Our result showed that the low toxic stress would lead to the synchronous decrease of cellulase and hemicellulase activities, and supplementary increase of corresponding gene expressions. The symbiotic community maintained its role as the main force in the lignocellulolytic system of C. formosanus. Meanwhile, a large number of rare taxa were significantly enriched by kojic acid treatment. These numerically inconspicuous bacterial populations might be responsible for the functions similar to phenoloxidase or insecticide detoxification and enable C. formosanus to tolerate the harmful environment. Overall, our data suggested that the digestive adaptation of C. formosanus to physiotoxic feeding is closely related to the triple collaboration of termites–flagellates–bacteria.
Collapse
|
10
|
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
|
11
|
Li J, Li C, Wang M, Wang L, Liu X, Gao C, Ren L, Luo Y. Gut Structure and Microbial Communities in Sirex noctilio (Hymenoptera: Siricidae) and Their Predicted Contribution to Larval Nutrition. Front Microbiol 2021; 12:641141. [PMID: 33897646 PMCID: PMC8060704 DOI: 10.3389/fmicb.2021.641141] [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: 12/13/2020] [Accepted: 03/15/2021] [Indexed: 12/25/2022] Open
Abstract
The European woodwasp, Sirex noctilio Fabricius, is a major invasive quarantine pest that attacks and kills pine trees outside of its native range. Insect gut structure and gut microbiota play crucial roles in various life activities. Despite a few reports in nutrition and survival, an extensive study on the S. noctilio larval gut microbiome is lacking. We studied the gut structure using a stereo microscope and used high throughput sequencing of the bacterial 16S rRNA genes and fungal internal transcribed spacer 2 (ITS2) regions to investigate gut microbiota in different developmental stages of S. noctilio, including larvae, adults, and larval frass. We used PICRUSt2 to predict the functional profiles. The larval gut was thin and thread-like from the oral cavity to the anus, carrying few xylem particles in the crop. Pseudomonas, Ralstonia, and Burkholderia s.l were the dominant bacteria in the guts of larvae, adults, and frass, respectively. Even though Pseudomonas was the most abundant among all bacteria, Zoogloea, Ruminobacter, and Nitrosospira, which might be involved in degrading organic matter and fixing nitrogen occurred exclusively in the larval gut indicating their possible role in the growth and development of larvae in pine tree xylem. Fungal communities did not change significantly across different developmental stages or the frass. Amylostereum was dominant in the woodwasp’s larval gut. Functional prediction of bacterial and fungal communities revealed that they may encod enzymes involved in degrading lignocellulose and fixing nitrogen. Ours is the first study that compares gut microbial communities present in S. noctilio larvae, adults, and frass. This study could provide an understanding of larval nutrient acquisition in nutrient-deficient host xylem to some extent. Our study may unlock novel strategies for the development of pest management approaches based on interfering with the gut microbiota and restricting their role in larval survival and development.
Collapse
Affiliation(s)
- Jiale Li
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Chengcheng Li
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Ming Wang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Lixiang Wang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Xiaobo Liu
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Chenglong Gao
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Lili Ren
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China.,Sino-France Joint Laboratory for Invasive Forest Pests in Eurasia, Beijing Forestry University, Beijing, China
| | - Youqing Luo
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China.,Sino-France Joint Laboratory for Invasive Forest Pests in Eurasia, Beijing Forestry University, Beijing, China
| |
Collapse
|
12
|
Silva JP, Ticona ARP, Hamann PRV, Quirino BF, Noronha EF. Deconstruction of Lignin: From Enzymes to Microorganisms. Molecules 2021; 26:2299. [PMID: 33921125 PMCID: PMC8071518 DOI: 10.3390/molecules26082299] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 11/20/2022] Open
Abstract
Lignocellulosic residues are low-cost abundant feedstocks that can be used for industrial applications. However, their recalcitrance currently makes lignocellulose use limited. In natural environments, microbial communities can completely deconstruct lignocellulose by synergistic action of a set of enzymes and proteins. Microbial degradation of lignin by fungi, important lignin degraders in nature, has been intensively studied. More recently, bacteria have also been described as able to break down lignin, and to have a central role in recycling this plant polymer. Nevertheless, bacterial deconstruction of lignin has not been fully elucidated yet. Direct analysis of environmental samples using metagenomics, metatranscriptomics, and metaproteomics approaches is a powerful strategy to describe/discover enzymes, metabolic pathways, and microorganisms involved in lignin breakdown. Indeed, the use of these complementary techniques leads to a better understanding of the composition, function, and dynamics of microbial communities involved in lignin deconstruction. We focus on omics approaches and their contribution to the discovery of new enzymes and reactions that impact the development of lignin-based bioprocesses.
Collapse
Affiliation(s)
- Jéssica P. Silva
- Enzymology Laboratory, Cell Biology Department, University of Brasilia, 70910-900 Brasília, Brazil; (J.P.S.); (A.R.P.T.); (P.R.V.H.)
| | - Alonso R. P. Ticona
- Enzymology Laboratory, Cell Biology Department, University of Brasilia, 70910-900 Brasília, Brazil; (J.P.S.); (A.R.P.T.); (P.R.V.H.)
| | - Pedro R. V. Hamann
- Enzymology Laboratory, Cell Biology Department, University of Brasilia, 70910-900 Brasília, Brazil; (J.P.S.); (A.R.P.T.); (P.R.V.H.)
| | - Betania F. Quirino
- Genetics and Biotechnology Laboratory, Embrapa-Agroenergy, 70770-901 Brasília, Brazil;
| | - Eliane F. Noronha
- Enzymology Laboratory, Cell Biology Department, University of Brasilia, 70910-900 Brasília, Brazil; (J.P.S.); (A.R.P.T.); (P.R.V.H.)
| |
Collapse
|
13
|
Jing TZ, Qi FH, Wang ZY. Most dominant roles of insect gut bacteria: digestion, detoxification, or essential nutrient provision? MICROBIOME 2020; 8:38. [PMID: 32178739 PMCID: PMC7077154 DOI: 10.1186/s40168-020-00823-y] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/05/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND The insect gut microbiota has been shown to contribute to the host's digestion, detoxification, development, pathogen resistance, and physiology. However, there is poor information about the ranking of these roles. Most of these results were obtained with cultivable bacteria, whereas the bacterial physiology may be different between free-living and midgut-colonizing bacteria. In this study, we provided both proteomic and genomic evidence on the ranking of the roles of gut bacteria by investigating the anal droplets from a weevil, Cryptorhynchus lapathi. RESULTS The gut lumen and the anal droplets showed qualitatively and quantitatively different subsets of bacterial communities. The results of 16S rRNA sequencing showed that the gut lumen is dominated by Proteobacteria and Bacteroidetes, whereas the anal droplets are dominated by Proteobacteria. From the anal droplets, enzymes involved in 31 basic roles that belong to 7 super roles were identified by Q-TOF MS. The cooperation between the weevil and its gut bacteria was determined by reconstructing community pathway maps, which are defined in this study. A score was used to rank the gut bacterial roles. The results from the proteomic data indicate that the most dominant role of gut bacteria is amino acid biosynthesis, followed by protein digestion, energy metabolism, vitamin biosynthesis, lipid digestion, plant secondary metabolite (PSM) degradation, and carbohydrate digestion, while the order from the genomic data is amino acid biosynthesis, vitamin biosynthesis, lipid digestion, energy metabolism, protein digestion, PSM degradation, and carbohydrate digestion. The PCA results showed that the gut bacteria form functional groups from the point of view of either the basic role or super role, and the MFA results showed that there are functional variations among gut bacteria. In addition, the variations between the proteomic and genomic data, analyzed with the HMFA method from the point of view of either the bacterial community or individual bacterial species, are presented. CONCLUSION The most dominant role of gut bacteria is essential nutrient provisioning, followed by digestion and detoxification. The weevil plays a pioneering role in diet digestion and mainly digests macromolecules into smaller molecules which are then mainly digested by gut bacteria.
Collapse
Affiliation(s)
- Tian-Zhong Jing
- School of Forestry, Northeast Forestry University, Harbin, 150040 China
| | - Feng-Hui Qi
- School of Life Sciences, Northeast Forestry University, Harbin, 150040 China
| | - Zhi-Ying Wang
- School of Forestry, Northeast Forestry University, Harbin, 150040 China
| |
Collapse
|
14
|
Hervé V, Liu P, Dietrich C, Sillam-Dussès D, Stiblik P, Šobotník J, Brune A. Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites. PeerJ 2020; 8:e8614. [PMID: 32095380 PMCID: PMC7024585 DOI: 10.7717/peerj.8614] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/21/2020] [Indexed: 02/06/2023] Open
Abstract
"Higher" termites have been able to colonize all tropical and subtropical regions because of their ability to digest lignocellulose with the aid of their prokaryotic gut microbiota. Over the last decade, numerous studies based on 16S rRNA gene amplicon libraries have largely described both the taxonomy and structure of the prokaryotic communities associated with termite guts. Host diet and microenvironmental conditions have emerged as the main factors structuring the microbial assemblages in the different gut compartments. Additionally, these molecular inventories have revealed the existence of termite-specific clusters that indicate coevolutionary processes in numerous prokaryotic lineages. However, for lack of representative isolates, the functional role of most lineages remains unclear. We reconstructed 589 metagenome-assembled genomes (MAGs) from the different gut compartments of eight higher termite species that encompass 17 prokaryotic phyla. By iteratively building genome trees for each clade, we significantly improved the initial automated assignment, frequently up to the genus level. We recovered MAGs from most of the termite-specific clusters in the radiation of, for example, Planctomycetes, Fibrobacteres, Bacteroidetes, Euryarchaeota, Bathyarchaeota, Spirochaetes, Saccharibacteria, and Firmicutes, which to date contained only few or no representative genomes. Moreover, the MAGs included abundant members of the termite gut microbiota. This dataset represents the largest genomic resource for arthropod-associated microorganisms available to date and contributes substantially to populating the tree of life. More importantly, it provides a backbone for studying the metabolic potential of the termite gut microbiota, including the key members involved in carbon and nitrogen biogeochemical cycles, and important clues that may help cultivating representatives of these understudied clades.
Collapse
Affiliation(s)
- Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Pengfei Liu
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Carsten Dietrich
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - David Sillam-Dussès
- Laboratory of Experimental and Comparative Ethology EA 4443, Université Paris 13, Villetaneuse, France
| | - Petr Stiblik
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Jan Šobotník
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| |
Collapse
|
15
|
Menke S, Heurich M, Henrich M, Wilhelm K, Sommer S. Impact of winter enclosures on the gut bacterial microbiota of red deer in the Bavarian Forest National Park. WILDLIFE BIOLOGY 2019. [DOI: 10.2981/wlb.00503] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sebastian Menke
- S. Menke, K. Wilhelm and S. Sommer , Inst. of Ecology and Conservation Genomics, Univ. of Ulm, Albert-Einstein Allee 11, DE-89081 Ulm, Germany
| | - Marco Heurich
- M. Heurich and M. Henrich, Dept of Conservation and Research, Bavarian Forest National Park, Zoology, Grafenau, Germany
| | - Maik Henrich
- M. Heurich and M. Henrich, Dept of Conservation and Research, Bavarian Forest National Park, Zoology, Grafenau, Germany
| | - Kerstin Wilhelm
- S. Menke, K. Wilhelm and S. Sommer , Inst. of Ecology and Conservation Genomics, Univ. of Ulm, Albert-Einstein Allee 11, DE-89081 Ulm, Germany
| | - Simone Sommer
- S. Menke, K. Wilhelm and S. Sommer , Inst. of Ecology and Conservation Genomics, Univ. of Ulm, Albert-Einstein Allee 11, DE-89081 Ulm, Germany
| |
Collapse
|
16
|
Pawlik A, Mazur A, Wielbo J, Koper P, Żebracki K, Kubik-Komar A, Janusz G. RNA Sequencing Reveals Differential Gene Expression of Cerrena Unicolor in Response to Variable Lighting Conditions. Int J Mol Sci 2019; 20:ijms20020290. [PMID: 30642073 PMCID: PMC6358801 DOI: 10.3390/ijms20020290] [Citation(s) in RCA: 10] [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: 11/30/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 11/16/2022] Open
Abstract
To elucidate the light-dependent gene expression in Cerrena unicolor FCL139, the transcriptomes of the fungus growing in white, blue, green, and red lighting conditions and darkness were analysed. Among 10,413 all-unigenes detected in C. unicolor, 7762 were found to be expressed in all tested conditions. Transcripts encoding putative fungal photoreceptors in the C. unicolor transcriptome were identified. The number of transcripts uniquely produced by fungus ranged from 20 during its growth in darkness to 112 in the green lighting conditions. We identified numerous genes whose expression differed substantially between the darkness (control) and each of the light variants tested, with the greatest number of differentially expressed genes (DEGs) (454 up- and 457 down-regulated) observed for the white lighting conditions. The DEGs comprised those involved in primary carbohydrate metabolism, amino acid metabolism, autophagy, nucleotide repair systems, signalling pathways, and carotenoid metabolism as defined using Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The analysis of the expression profile of genes coding for lignocellulose-degrading enzymes suggests that the wood-degradation properties of C. unicolor may be independent of the lighting conditions and may result from the overall stimulation of fungal metabolism by daylight.
Collapse
Affiliation(s)
- Anna Pawlik
- Department of Biochemistry, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland.
| | - Andrzej Mazur
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland.
| | - Jerzy Wielbo
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland.
| | - Piotr Koper
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland.
| | - Kamil Żebracki
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland.
| | - Agnieszka Kubik-Komar
- Chair of Applied Mathematics and Informatics, Lublin University of Life Sciences, Akademicka 13 St., 20-950 Lublin, Poland.
| | - Grzegorz Janusz
- Department of Biochemistry, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland.
| |
Collapse
|
17
|
Bie J, Liu X, Zhang X, Wang H. Detection and comparative analysis of cutaneous bacterial communities of farmed and wild Rana dybowskii (Amphibia: Anura). THE EUROPEAN ZOOLOGICAL JOURNAL 2019. [DOI: 10.1080/24750263.2019.1683627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- J. Bie
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - X. Liu
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - X. Zhang
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - H. Wang
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| |
Collapse
|
18
|
Dearing MD, Kohl KD. Beyond Fermentation: Other Important Services Provided to Endothermic Herbivores by their Gut Microbiota. Integr Comp Biol 2018; 57:723-731. [PMID: 28662572 DOI: 10.1093/icb/icx020] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
For decades, comparative biologists have recognized the importance of microbial partners in facilitating herbivory as a successful feeding strategy. Most of this success is attributed to the ability of gut microbes to digest recalcitrant dietary fiber and provides usable nutrients to their hosts. Gut microbes can also provide numerous other functions, such as vitamin synthesis, nitrogen recycling, and the detoxification of plant secondary compounds. Here, we review these microbial functions in herbivorous mammals and birds, highlighting studies that utilize recently developed metagenomic techniques. Several of these studies emphasize that microbial services are the product of interactions and exchanges within a complex microbial community, rather than the product of an individual member. Additionally, a number of these microbial functions are interdependent. For example, levels of dietary nitrogen or plant toxins can influence fiber digestibility. Further studies into the variety of microbial services provided to herbivorous hosts, and how these services might interact will broaden our understanding of host-microbe interactions.
Collapse
Affiliation(s)
- M Denise Dearing
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| |
Collapse
|
19
|
Janusz G, Pawlik A, Sulej J, Swiderska-Burek U, Jarosz-Wilkolazka A, Paszczynski A. Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution. FEMS Microbiol Rev 2017; 41:941-962. [PMID: 29088355 PMCID: PMC5812493 DOI: 10.1093/femsre/fux049] [Citation(s) in RCA: 351] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/12/2017] [Indexed: 12/11/2022] Open
Abstract
Extensive research efforts have been dedicated to describing degradation of wood, which is a complex process; hence, microorganisms have evolved different enzymatic and non-enzymatic strategies to utilize this plentiful plant material. This review describes a number of fungal and bacterial organisms which have developed both competitive and mutualistic strategies for the decomposition of wood and to thrive in different ecological niches. Through the analysis of the enzymatic machinery engaged in wood degradation, it was possible to elucidate different strategies of wood decomposition which often depend on ecological niches inhabited by given organism. Moreover, a detailed description of low molecular weight compounds is presented, which gives these organisms not only an advantage in wood degradation processes, but seems rather to be a new evolutionatory alternative to enzymatic combustion. Through analysis of genomics and secretomic data, it was possible to underline the probable importance of certain wood-degrading enzymes produced by different fungal organisms, potentially giving them advantage in their ecological niches. The paper highlights different fungal strategies of wood degradation, which possibly correlates to the number of genes coding for secretory enzymes. Furthermore, investigation of the evolution of wood-degrading organisms has been described.
Collapse
Affiliation(s)
- Grzegorz Janusz
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Anna Pawlik
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Justyna Sulej
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Urszula Swiderska-Burek
- Department of Botany and Mycology, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Anna Jarosz-Wilkolazka
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Andrzej Paszczynski
- School of Food Science, Food Research Center, Room 103, University of Idaho, Moscow, ID 83844, USA
| |
Collapse
|
20
|
Zhang J, Hu Q, Xu C, Liu S, Li C. Key Microbiota Identification Using Functional Gene Analysis during Pepper (Piper nigrum L.) Peeling. PLoS One 2016; 11:e0165206. [PMID: 27768750 PMCID: PMC5074590 DOI: 10.1371/journal.pone.0165206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 10/07/2016] [Indexed: 11/20/2022] Open
Abstract
Pepper pericarp microbiota plays an important role in the pepper peeling process for the production of white pepper. We collected pepper samples at different peeling time points from Hainan Province, China, and used a metagenomic approach to identify changes in the pericarp microbiota based on functional gene analysis. UniFrac distance-based principal coordinates analysis revealed significant changes in the pericarp microbiota structure during peeling, which were attributed to increases in bacteria from the genera Selenomonas and Prevotella. We identified 28 core operational taxonomic units at each time point, mainly belonging to Selenomonas, Prevotella, Megasphaera, Anaerovibrio, and Clostridium genera. The results were confirmed by quantitative polymerase chain reaction. At the functional level, we observed significant increases in microbial features related to acetyl xylan esterase and pectinesterase for pericarp degradation during peeling. These findings offer a new insight into biodegradation for pepper peeling and will promote the development of the white pepper industry.
Collapse
Affiliation(s)
- Jiachao Zhang
- College of Food Science and Technology, Hainan University, Haikou, 570228, P. R. China
| | - Qisong Hu
- College of Food Science and Technology, Hainan University, Haikou, 570228, P. R. China
| | - Chuanbiao Xu
- College of Food Science and Technology, Hainan University, Haikou, 570228, P. R. China
| | - Sixin Liu
- College of Materials and Chemical Engineering, Hainan University, Haikou, 570228, P. R. China
- * E-mail: (CL); (SL)
| | - Congfa Li
- College of Food Science and Technology, Hainan University, Haikou, 570228, P. R. China
- * E-mail: (CL); (SL)
| |
Collapse
|
21
|
Kohl KD, Dearing MD. The Woodrat Gut Microbiota as an Experimental System for Understanding Microbial Metabolism of Dietary Toxins. Front Microbiol 2016; 7:1165. [PMID: 27516760 PMCID: PMC4963388 DOI: 10.3389/fmicb.2016.01165] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/13/2016] [Indexed: 01/22/2023] Open
Abstract
The microbial communities inhabiting the alimentary tracts of mammals, particularly those of herbivores, are estimated to be one of the densest microbial reservoirs on Earth. The significance of these gut microbes in influencing the physiology, ecology and evolution of their hosts is only beginning to be realized. To understand the microbiome of herbivores with a focus on nutritional ecology, while evaluating the roles of host evolution and environment in sculpting microbial diversity, we have developed an experimental system consisting of the microbial communities of several species of herbivorous woodrats (genus Neotoma) that naturally feed on a variety of dietary toxins. We designed this system to investigate the long-standing, but experimentally neglected hypothesis that ingestion of toxic diets by herbivores is facilitated by the gut microbiota. Like several other rodent species, the woodrat stomach has a sacculated, non-gastric foregut portion. We have documented a dense and diverse community of microbes in the woodrat foregut, with several genera potentially capable of degrading dietary toxins and/or playing a role in stimulating hepatic detoxification enzymes of the host. The biodiversity of these gut microbes appears to be a function of host evolution, ecological experience and diet, such that dietary toxins increase microbial diversity in hosts with experience with these toxins while novel toxins depress microbial diversity. These microbial communities are critical to the ingestion of a toxic diet as reducing the microbial community with antibiotics impairs the host's ability to feed on dietary toxins. Furthermore, the detoxification capacity of gut microbes can be transferred from Neotoma both intra and interspecifically to naïve animals that lack ecological and evolutionary history with these toxins. In addition to advancing our knowledge of complex host-microbes interactions, this system holds promise for identifying microbes that could be useful in the treatment of diseases in humans and domestic animals.
Collapse
Affiliation(s)
- Kevin D. Kohl
- Department of Biological Sciences, Vanderbilt University, NashvilleTN, USA
| | | |
Collapse
|
22
|
Bouskill NJ, Wood TE, Baran R, Hao Z, Ye Z, Bowen BP, Lim HC, Nico PS, Holman HY, Gilbert B, Silver WL, Northen TR, Brodie EL. Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition. Front Microbiol 2016; 7:323. [PMID: 27014243 PMCID: PMC4791749 DOI: 10.3389/fmicb.2016.00323] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/29/2016] [Indexed: 01/29/2023] Open
Abstract
Climate model projections for tropical regions show clear perturbation of precipitation patterns leading to increased frequency and severity of drought in some regions. Previous work has shown declining soil moisture to be a strong driver of changes in microbial trait distribution, however, the feedback of any shift in functional potential on ecosystem properties related to carbon cycling are poorly understood. Here we show that drought-induced changes in microbial functional diversity and activity shape, and are in turn shaped by, the composition of dissolved and soil-associated carbon. We also demonstrate that a shift in microbial functional traits that favor the production of hygroscopic compounds alter the efflux of carbon dioxide following soil rewetting. Under drought the composition of the dissolved organic carbon pool changed in a manner consistent with a microbial metabolic response. We hypothesize that this microbial ecophysiological response to changing soil moisture elevates the intracellular carbon demand stimulating extracellular enzyme production, that prompts the observed decline in more complex carbon compounds (e.g., cellulose and lignin). Furthermore, a metabolic response to drought appeared to condition (biologically and physically) the soil, notably through the production of polysaccharides, particularly in experimental plots that had been pre-exposed to a short-term drought. This hysteretic response, in addition to an observed drought-related decline in phosphorus concentration, may have been responsible for a comparatively modest CO2 efflux following wet-up in drought plots relative to control plots.
Collapse
Affiliation(s)
- Nicholas J Bouskill
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Tana E Wood
- International Institute of Tropical Forestry, United States Department of Agriculture Forest ServiceRio Piedras, PR, USA; Fundación Puertorriqueña de ConservaciónSan Juan, PR, USA
| | - Richard Baran
- Environmental Genomics and Systems Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Zhao Hao
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Zaw Ye
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Ben P Bowen
- Environmental Genomics and Systems Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Hsiao Chien Lim
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Peter S Nico
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Hoi-Ying Holman
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Benjamin Gilbert
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Whendee L Silver
- Department of Environmental Science, Policy, and Management, University of California, Berkeley Berkeley, CA, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Eoin L Brodie
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National LaboratoryBerkeley, CA, USA; Department of Environmental Science, Policy, and Management, University of California, BerkeleyBerkeley, CA, USA
| |
Collapse
|
23
|
Berasategui A, Shukla S, Salem H, Kaltenpoth M. Potential applications of insect symbionts in biotechnology. Appl Microbiol Biotechnol 2016; 100:1567-1577. [PMID: 26659224 PMCID: PMC4737797 DOI: 10.1007/s00253-015-7186-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/15/2015] [Accepted: 11/17/2015] [Indexed: 12/21/2022]
Abstract
Symbiotic interactions between insects and microorganisms are widespread in nature and are often the source of ecological innovations. In addition to supplementing their host with essential nutrients, microbial symbionts can produce enzymes that help degrade their food source as well as small molecules that defend against pathogens, parasites, and predators. As such, the study of insect ecology and symbiosis represents an important source of chemical compounds and enzymes with potential biotechnological value. In addition, the knowledge on insect symbiosis can provide novel avenues for the control of agricultural pest insects and vectors of human diseases, through targeted manipulation of the symbionts or the host-symbiont associations. Here, we discuss different insect-microbe interactions that can be exploited for insect pest and human disease control, as well as in human medicine and industrial processes. Our aim is to raise awareness that insect symbionts can be interesting sources of biotechnological applications and that knowledge on insect ecology can guide targeted efforts to discover microorganisms of applied value.
Collapse
Affiliation(s)
- Aileen Berasategui
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany.
- Biochemistry Department, Max Planck Institute for Chemical Ecology, Jena, Germany.
| | - Shantanu Shukla
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Hassan Salem
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Martin Kaltenpoth
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany.
- Department for Evolutionary Ecology, Institute of Zoology, Johannes Gutenberg University, Mainz, Germany.
| |
Collapse
|
24
|
Saini A, Aggarwal NK, Sharma A, Yadav A. Actinomycetes: A Source of Lignocellulolytic Enzymes. Enzyme Res 2015; 2015:279381. [PMID: 26793393 PMCID: PMC4697097 DOI: 10.1155/2015/279381] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/01/2015] [Indexed: 01/17/2023] Open
Abstract
Lignocellulose is the most abundant biomass on earth. Agricultural, forest, and agroindustrial activities generate tons of lignocellulosic wastes annually, which present readily procurable, economically affordable, and renewable feedstock for various lignocelluloses based applications. Lignocelluloses are the focus of present decade researchers globally, in an attempt to develop technologies based on natural biomass for reducing dependence on expensive and exhaustible substrates. Lignocellulolytic enzymes, that is, cellulases, hemicellulases, and lignolytic enzymes, play very important role in the processing of lignocelluloses which is prerequisite for their utilization in various processes. These enzymes are obtained from microorganisms distributed in both prokaryotic and eukaryotic domains including bacteria, fungi, and actinomycetes. Actinomycetes are an attractive microbial group for production of lignocellulose degrading enzymes. Various studies have evaluated the lignocellulose degrading ability of actinomycetes, which can be potentially implemented in the production of different value added products. This paper is an overview of the diversity of cellulolytic, hemicellulolytic, and lignolytic actinomycetes along with brief discussion of their hydrolytic enzyme systems involved in biomass modification.
Collapse
Affiliation(s)
- Anita Saini
- Department of Microbiology, Kurukshetra University, Kurukshetra, Haryana 136119, India
| | - Neeraj K. Aggarwal
- Department of Microbiology, Kurukshetra University, Kurukshetra, Haryana 136119, India
| | - Anuja Sharma
- Department of Microbiology, Kurukshetra University, Kurukshetra, Haryana 136119, India
| | - Anita Yadav
- Department of Biotechnology, Kurukshetra University, Kurukshetra, Haryana 136119, India
| |
Collapse
|
25
|
Streptomyces fractus sp. nov., a novel streptomycete isolated from the gut of a South African termite. Antonie van Leeuwenhoek 2015; 107:1127-34. [PMID: 25663029 DOI: 10.1007/s10482-015-0404-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 02/03/2015] [Indexed: 10/24/2022]
Abstract
An actinobacterial strain, MV32(T), was isolated from the paunch region of the hindgut of a South African termite, Amitermes hastatus, as part of an investigation of the actinobacterial population residing within this higher order termite species. Strain MV32(T) was chosen for further study from amongst the many potentially novel actinomycete isolates because of its strong antibacterial activity against Mycobacterium aurum A+. 16S rRNA gene phylogenetic analyses clearly placed strain MV32(T) within the genus Streptomyces, with 99.3% sequence similarity to its closest relative, Streptomyces endophyticus YIM 65594(T). Despite this high sequence similarity, DNA-DNA hybridisation analysis showed a DNA relatedness value of 62 ± 2%, to S. endophyticus DSM 41984(T) (indicating that strain MV32(T) belongs to a different genomic species), as well as values of 14.4 ± 0.8 and 10.4 ± 2.9%, respectively, to its next closest relatives, Streptomyces kunmingensis NRRL B-16240(T) and Streptomyces cinnabarinus NRRL B-12382(T). Based on these results and supported by both chemotaxonomic data and a number of phenotypic differences, strain MV32(T) is proposed to represent a new species within the genus Streptomyces, with the name Streptomyces fractus (= DSM 42163(T) = NRRL B-59159(T)).
Collapse
|
26
|
Muangham S, Pathom-aree W, Duangmal K. Melanogenic actinomycetes from rhizosphere soil — antagonistic activity against Xanthomonas oryzae and plant-growth-promoting traits. Can J Microbiol 2015; 61:164-70. [DOI: 10.1139/cjm-2014-0645] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A total of 210 melanogenic actinomycetes were isolated from 75 rhizospheric soils using ISP6 and ISP7 agar supplemented with antifungal and antibacterial agents. Their morphological characteristics and the presence of ll-diaminopimelic acid in whole-cell hydrolyzates revealed that all isolates belonged to the genus Streptomyces. Their ability to inhibit the growth of 2 pathogenic rice bacteria, Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola, was observed using the agar overlay method. The results indicated that 61.9% of the isolates could inhibit at least one of the tested rice pathogens. Among these, isolate TY68-3 showed the highest antibacterial activity and siderophore production. The 16S rRNA gene sequence analysis of 46 representative isolates revealed that isolates with high similarity to Streptomyces bungoensis were frequently found. The present study indicated the potential of melanogenic actinomycetes for use as biocontrol agents against X. oryzae as well as their diversity in rhizospheric soils.
Collapse
Affiliation(s)
- Supattra Muangham
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Wasu Pathom-aree
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| |
Collapse
|
27
|
Nechitaylo TY, Westermann M, Kaltenpoth M. Cultivation reveals physiological diversity among defensive 'Streptomyces philanthi' symbionts of beewolf digger wasps (Hymenoptera, Crabronidae). BMC Microbiol 2014; 14:202. [PMID: 25266732 PMCID: PMC4236554 DOI: 10.1186/s12866-014-0202-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 07/18/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 'Candidatus Streptomyces philanthi' is a monophyletic clade of formerly uncultured bacterial symbionts in solitary digger wasps of the genera Philanthus, Philanthinus and Trachypus (Hymenoptera, Crabronidae). These bacteria grow in female-specific antennal reservoirs and - after transmission to the cocoon - produce antibiotics protecting the host larvae from fungal infection. However, the symbionts' refractoriness to cultivation has thus far hampered detailed in vitro studies on their physiology and on the evolutionary changes in metabolic versatility in response to the host environment. RESULTS Here we isolated in axenic culture 22 'Streptomyces philanthi' biovars from different host species. Sequencing of gyrB revealed no heterogeneity among isolates within host individuals, suggesting low levels of (micro)diversity or even clonality of the symbionts in individual beewolf antennae. Surprisingly, however, isolates from different host species differed strongly in their physiology. All biovars from the Eurasian/African Philanthus and the South American Trachypus host species had high nutritional demands and were susceptible to most antibiotics tested, suggesting a tight association with the hosts. By contrast, biovars isolated from the genus Philanthinus and the monophyletic North American Philanthus clade were metabolically versatile and showed broad antibiotic resistance. Concordantly, recent horizontal symbiont transfer events - reflected in different symbiont strains infecting the same host species - have been described only among North American Philanthus species, altogether indicative of facultative symbionts potentially capable of a free-living lifestyle. Phylogenetic analyses reveal a strong correlation between symbiont metabolic versatility and host phylogeny, suggesting that the host environment differentially affects the symbionts' evolutionary fate. Although opportunistic bacteria were occasionally isolated from the antennae of different host species, only filamentous Actinobacteria (genera Streptomyces, Amycolatopsis and Nocardia) could replace 'S. philanthi' in the antennal gland reservoirs. CONCLUSION Our results indicate that closely related bacteria from a monophyletic clade of symbionts can experience very different evolutionary trajectories in response to the symbiotic lifestyle, which is reflected in different degrees of metabolic versatility and host-dependency. We propose that the host-provided environment could be an important factor in shaping the degenerative metabolic evolution in the symbionts and deciding whether they evolve into obligate symbionts or remain facultative and capable of a host-independent lifestyle.
Collapse
|
28
|
Ni J, Tokuda G. Lignocellulose-degrading enzymes from termites and their symbiotic microbiota. Biotechnol Adv 2013; 31:838-50. [DOI: 10.1016/j.biotechadv.2013.04.005] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 04/10/2013] [Accepted: 04/15/2013] [Indexed: 01/17/2023]
|
29
|
Engel P, Moran NA. The gut microbiota of insects – diversity in structure and function. FEMS Microbiol Rev 2013; 37:699-735. [DOI: 10.1111/1574-6976.12025] [Citation(s) in RCA: 1300] [Impact Index Per Article: 118.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 05/06/2013] [Accepted: 05/13/2013] [Indexed: 02/07/2023] Open
|
30
|
Makonde HM, Boga HI, Osiemo Z, Mwirichia R, Mackenzie LM, Göker M, Klenk HP. 16S-rRNA-based analysis of bacterial diversity in the gut of fungus-cultivating termites (Microtermes and Odontotermes species). Antonie van Leeuwenhoek 2013; 104:869-83. [PMID: 23942613 DOI: 10.1007/s10482-013-0001-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 08/08/2013] [Indexed: 01/10/2023]
Abstract
The interaction between termites and their gut symbionts has continued to attract the curiosity of researchers over time. The aim of this study was to characterize and compare the bacterial diversity and community structure in the guts of three termites (Odontotermes somaliensis, Odontotermes sp. and Microtermes sp.) using 16S rRNA gene sequencing of clone libraries. Clone libraries were screened by restriction fragment length polymorphism and representative clones from O. somaliensis (100 out of 330 clones), Odontotermes sp. (100 out of 359 clones) and Microtermes sp. (96 out 336 clones) were sequenced. Phylogenetic analysis indicated seven bacterial phyla were represented: Bacteroidetes, Spirochaetes, Firmicutes, Proteobacteria, Synergistetes, Planctomycetes and Actinobacteria. Sequences representing the phylum Bacteroidetes (>60 %) were the most abundant group in Odontotermes while those of Spirochaetes (29 %) and Firmicutes (23 %) were the abundant groups in Microtermes. The gut bacterial community structure within the two Odontotermes species investigated here was almost identical at the phylum level, but the Microtermes sp. had a unique bacterial community structure. Bacterial diversity was higher in Odontotermes than in Microtermes. The affiliation and clustering of the sequences, often with those from other termites' guts, indicate a majority of the gut bacteria are autochthonous having mutualistic relationships with their hosts. The findings underscore the presence of termite-specific bacterial lineages, the majority of which are still uncultured.
Collapse
Affiliation(s)
- Huxley M Makonde
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7b, 38124, Brunswick, Germany,
| | | | | | | | | | | | | |
Collapse
|
31
|
Lacombe A, Li RW, Klimis-Zacas D, Kristo AS, Tadepalli S, Krauss E, Young R, Wu VCH. Lowbush wild blueberries have the potential to modify gut microbiota and xenobiotic metabolism in the rat colon. PLoS One 2013; 8:e67497. [PMID: 23840722 PMCID: PMC3696070 DOI: 10.1371/journal.pone.0067497] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/19/2013] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal tract is populated by an array of microbial species that play an important role in metabolic and immune functions. The composition of microorganisms is influenced by the components of the host's diet and can impact health. In the present study, dietary enrichment of lowbush wild blueberries (LWB) was examined to determine their effect on colon microbial composition and their potential in promoting gut health. The microbial composition and functional potential of the colon microbiota from Sprague Dawley rats fed control diets (AIN93) and LWB-enriched diets (AIN93+8% LWB powder substituting for dextrose) for 6 weeks were assessed using Illumina shotgun sequencing and bioinformatics tools. Our analysis revealed an alteration in the relative abundance of 3 phyla and 22 genera as representing approximately 14 and 8% of all phyla and genera identified, respectively. The LWB-enriched diet resulted in a significant reduction in the relative abundance of the genera Lactobacillus and Enterococcus. In addition, hierarchal analysis revealed a significant increase in the relative abundance of the phylum Actinobacteria, the order Actinomycetales, and several novel genera under the family Bifidobacteriaceae and Coriobacteriaceae, in the LWB group. Functional annotation of the shotgun sequences suggested that approximately 9% of the 4709 Kyoto Encyclopaedia of Gene and Genome (KEGG) hits identified were impacted by the LWB-diet. Open Reading Frames (ORFs) assigned to KEGG category xenobiotics biodegradation and metabolism were significantly greater in the LWB-enriched diet compared to the control and included the pathway for benzoate degradation [PATH:ko00362] and glycosaminoglycan degradation [PATH:ko00531]. Moreover, the number of ORFs assigned to the bacterial invasion of epithelial cells [PATH:ko05100] pathway was approximately 8 fold lower in the LWB group compared to controls. This study demonstrated that LWBs have the potential to promote gut health and can aid in the development of optimal diets.
Collapse
Affiliation(s)
- Alison Lacombe
- Department of Food Science and Human Nutrition, The University of Maine, Orono, Maine, United States of America
| | - Robert W. Li
- United States Department of Agriculture ARS, BARC, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Dorothy Klimis-Zacas
- Department of Food Science and Human Nutrition, The University of Maine, Orono, Maine, United States of America
| | - Aleksandra S. Kristo
- Department of Food Science and Human Nutrition, The University of Maine, Orono, Maine, United States of America
| | - Shravani Tadepalli
- Department of Food Science and Human Nutrition, The University of Maine, Orono, Maine, United States of America
| | - Emily Krauss
- Department of Food Science and Human Nutrition, The University of Maine, Orono, Maine, United States of America
| | - Ryan Young
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, Maine, United States of America
| | - Vivian C. H. Wu
- Department of Food Science and Human Nutrition, The University of Maine, Orono, Maine, United States of America
| |
Collapse
|
32
|
Kohl KD, Dearing MD. Experience matters: prior exposure to plant toxins enhances diversity of gut microbes in herbivores. Ecol Lett 2012; 15:1008-15. [PMID: 22715970 DOI: 10.1111/j.1461-0248.2012.01822.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/14/2012] [Accepted: 05/24/2012] [Indexed: 11/27/2022]
Abstract
For decades, ecologists have hypothesised that exposure to plant secondary compounds (PSCs) modifies herbivore-associated microbial community composition. This notion has not been critically evaluated in wild mammalian herbivores on evolutionary timescales. We investigated responses of the microbial communities of two woodrat species (Neotoma bryanti and N. lepida). For each species, we compared experienced populations that independently converged to feed on the same toxic plant (creosote bush, Larrea tridentata) to naïve populations with no exposure to creosote toxins. The addition of dietary PSCs significantly altered gut microbial community structure, and the response was dependent on previous experience. Microbial diversity and relative abundances of several dominant phyla increased in experienced woodrats in response to PSCs; however, opposite effects were observed in naïve woodrats. These differential responses were convergent in experienced populations of both species. We hypothesise that adaptation of the foregut microbiota to creosote PSCs in experienced woodrats drives this differential response.
Collapse
Affiliation(s)
- Kevin D Kohl
- Department of Biology, University of Utah, 257 S. 1400 East, Salt Lake City, UT 84112, USA.
| | | |
Collapse
|