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研究生：	翁正軒 Weng, Cheng Hsuan
論文名稱：	探索斑腿樹蛙腸道菌以及其網絡關係 Exploring gut microbiota of Polypedates megacephalus and the inference of its microbial interactions
指導教授：	王達益 Wang, Dar-Yi
學位類別：	博士 Doctor
系所名稱：	生命科學系 Department of Life Science
論文出版年：	2019
畢業學年度：	107
語文別：	英文
論文頁數：	132
中文關鍵詞：	network 、gut microbiota 、artificial hibernation 、probiotics 、Polypedates megacephalus
英文關鍵詞：	network, gut microbiota, artificial hibernation, probiotics, Polypedates megacephalus
DOI URL：	http://doi.org/10.6345/DIS.NTNU.SLS.006.2019.D01
論文種類：	學術論文
相關次數：	點閱：106 下載：4
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無中文摘要

The concerted activity of intestinal microbes is crucial to the health and development of their host organisms. Studies have suggested that microbial assemblages in the intestine of animals are engines of globally important host physiological processes between hibernating and non-hibernating states. The advances in Next Generation Sequencing (NGS) technologies facilitate our understanding of gut microbiota with high resolutions in diversity and metabolic functioning between hibernating and non-hibernating seasons. Polypedates megacephalus is an invasive species in Taiwan since 2006. The approach of habitat usage and population dispersal of this invasive treefrogs across seasons have suggested a rapid expansion across counties in Taiwan. However, it still lacks an effective solution to control the expansion of invasive P. megacephalus. Due to the reciprocal interactions between gut microbiota and host physiology, I attempt to explore gut microbiota of P. megacephalus, decipher microbial interactions to understand the potential mechanisms of microbial ecosystem, and further manipulate host response by modulating gut microbiota according to the guidance by computational network analysis. This study not only delineated seasonal changes of gut microbiota in composition and metabolic functioning but demonstrated the potentials of computational network inference toward practical applications on animal systems.
The compositional and predicted functional changes of gut microbiota across non-hibernating and artificial hibernating seasons were identified based on 16S rRNA amplicon analysis. The abundance profile and predicted functions of microbial community significantly change between artificial hibernating (AH) and non-hibernating (NH) treefrogs. Artificial hibernation significantly reduces microbial diversity and the level of Firmicutes and increases the level of Proteobacteria in the treefrog gut microbiota. In addition, AH treefrogs harbor core taxonomic units that are rarely abundant in NH treefrogs. Moreover, artificial hibernation significantly increased relative abundance of red-leg syndrome-related genera such as Citrobacter and Aeromonas. Functional predictions via PICRUSt and Tax4Fun suggested that artificial hibernation has effects on most pathways including metabolism and signal transduction. These results suggest that artificial hibernation restructure gut microbiota in treefrogs and significantly reduce microbial complexity of gut microbiome.
The use of computational methods to decipher microbial interactions have been applied on microbiome data in a time-series fashion. A time-series microbiome data could monitor the population changes of each bacterium in the community over time. Due to the adjustable gut microbiome complexity of hibernating animals, the growth microbiome time-series (GMT) dataset is proposed to apply on the computational network inference methods. Among varieties of network inference tools, regression-based network model is selected and utilized due to its better performance tested by using in silico dataset. Lotka-Volterra models, also known as predator–prey equations, are the most currently used regression-based method, and predict both dynamics of microbial communities and how communities are structured and sustained. The interaction network of gut microbiota at the genus level in the treefrog was constructed using Metagenomic Microbial Interaction Simulator (MetaMIS) package. The interaction network contained 1,568 commensal, 1,737 amensal, 3,777 mutual, and 3,232 competitive relationships, e.g., Lactococcus garvieae has a commensal relationship with Corynebacterium variabile. To validate the interacting relationships, I took advantage of probiotic system to evaluate the responses of gut microbiota to the probiotic trials. The trials involved different groups including single strain (L. garvieae, C. variabile, and Bacillus coagulans, respectively) and a combination of L. garvieae, C. variabile, and B. coagulans, because of the cooperative relationship among their respective genera identified in the interaction network. After a two-week trial, the combination of cooperative microbes yielded significantly higher probiotic concentrations than single strains, and the immune response (interleukin-10 expression) also significantly changed in a manner consistent with improved probiotic effects.

  Introduction    13
1    Strong links between animal gut microbiome and its physiology and behaviour    13
1.1    The amount and importance of microorganisms in the gastrointestinal tract (gut microbiota)    13
1.2    Phylogenetic diversity and structural assembly of gut microbiota correlates to host physiology and behaviour    13
2    Seasonal behavioural observations of Polypedates megacephalus    15
2.1    Population distribution of P. megacephalus in Taiwan    15
2.2    Seasonal dispersal and habitat usage of P. megacephalus in Taiwan    15
2.3    Invasive P. megacephalus, potential threat, and current solutions for invasion    16
3    Seasonal alterations on gut microbiota in hibernators    17
3.1    Compositional changes of gut microbiota during hibernation    17
3.2    Seasonal shifts of dominant bacterial populations in hibernators identified by conventional methods    18
3.3    Seasonal restructure of gut bacterial assembly in hibernators characterized by advanced sequencing technology    19
4    Network inference provides insight into the mechanisms of gut bacterial assembly    21
4.1    The potentials of top-down approach on microbial community    21
4.2    Deciphering microbial interaction provides insights into causal relationships    22
4.3    Network inference theory    24
4.4    From static network to dynamic network: time-series data    26
4.5    Current pitfalls of network inference    28
5    Well-developed intestinal probiotic system    29
5.1    Lactic acid bacteria (LAB) – the wild used probiotics    29
5.2    The interactions between probiotic strains and other bacteria    30
5.3    Host immune responses by probiotics    31
6    Probiotics used in real applications    32
6.1    Probiotic strains used in raniculture    32
6.2    The growing process of probiotics development    33
7    From network theory to practical probiotic system    33
7.1    Network inference by the growth microbiome time-series (GMT) datasets    33
7.2    Network validation by probiotic system    34
7.3    Research objectives    34
  Materials and Methods    37
1    Animal individuals    37
1.1    Treefrogs from season fall, winter, and spring    37
1.2    AH treefrogs in the laboratory    38
2    Microbiome dataset of seasonal changes    39
2.1    Feces collection and DNA extraction    39
2.2    16S rRNA sequencing    40
2.3    16S rRNA amplicon analysis    41
2.4    Functional predictions    41
3    The growth microbiome time-series dataset    42
3.1    Animal individuals    42
3.2    16S rRNA sequencing    43
3.3    16S rRNA amplicon analysis    44
4    Network inference tools    44
4.1    Correlation-based network inference tool    44
4.2    Regression-based network inference tool    46
4.3    Training dataset and validation    47
5    Network analysis    49
5.1    The probiotic sub-network for validation and application    49
5.2    Network visualization    49
6    Microbiome dataset of probiotic trials    50
6.1    Probiotic selection and culturing    50
6.2    Animal individuals    51
6.3    16S rRNA sequencing and 16S rRNA amplicon analysis    51
6.4    Validation of network inference    51
6.5    Level of IL-10    52
7    Statistical analysis    53
7.1    Alpha and beta diversity    53
  Results – compositional and metabolic functional changes of gut microbiota over AH treefrogs    55
1    Sampling information in fall, winter, spring, and artificial hibernation    55
1.1    Environmental parameters    55
2    Microbiome in fall, winter, spring, and artificial hibernation    56
2.1    Sequencing quality and throughput    56
2.2    Microbial diversity    56
2.3    Microbial compositions    57
3    Functional prediction    59
  Results – inference, validation, and potential application of microbial interactions    63
1    Model selection    64
1.1    Performance of correlation-based and regression-based model    64
2    The growth microbiota time-series (GMT) dataset    64
2.1    Preliminary test for the GMT dataset    64
2.2    Sequencing throughput    65
2.3    Diversity changes in the GMT dataset    65
2.4    Compositional changes in the GMT dataset    66
3    The inferred interaction relations    66
4    Probiotic selection    67
5    The inferred positive relation facilitates the growth of probiotics, L. garvieae    68
6    The up-regulated IL-10 caused by the increased L. garvieae    69
7    Validation on probiotic system    71
  Discussion    73
1    Seasonal impacts on gut microbiome of hibernators    74
1.1    Hibernation decreases microbial diversity among all hibernating animals    74
1.2    Hibernating animals shared similar phyla of gut microbiota    76
1.3    Seasonal changes in composition of gut microbiota among hibernators    77
1.4    Seasonal changes in functions of gut microbiota among hibernators    77
2    Habitat impacts on gut microbiome of amphibian    78
2.1    Gut microbiota of adult amphibian harbor similar composition in aquatic animals than terrestrial animals    79
3    Artificial hibernation increases the risk of pathogenic infection in treefrogs    81
3.1    The increase of pathogenic bacteria in artificial hibernation    81
3.2    High risk of pathogenic infection in artificial hibernation    81
4    The potential control agent for invasive treefrog: a perspective from gut microbiota    83
5    Regression-based models provide better performance than correlation-based methods    84
5.1    Performance comparison between regression-based and correlation-based methods    85
6    The breakthrough of gut microbiota in amphibians – microbial interactions    86
6.1    The potentials of network inference in amphibian studies    87
6.2    Inference of microbial interactions based on the GMT datasets    88
7    The interactions between probiotics and other gut microbes in amphibians    90
7.1    Consistency of microbial interactions between bottom-up and top-down research and more insights from network inference    90
8    The probiotic consortia    91
8.1    Potential probiotic consortia determined by network inference    91
9    Validation of network inference using probiotics    92
9.1    Network validation according to real abundance of bacterial changes in the community    92
10    The bridge between network theory and applications    94
  Conclusions and future directions    95
1    Future directions    96
1.1    Incorporate species network with metabolic network    96
1.2    Pathogen resist gut microbiota    97
Figures and Tables    99
Figures    99
Figure 1 – The diagram of correlation-based method.    99
Figure 2 – The flowchart of a null model.    100
Figure 3 – Simulated time series dataset of 50 operational taxonomic units spending 10 time points    101
Figure 4 – Weekly records of temperature and humidity in October, November, December, January, February, and March.    101
Figure 5 – Alpha-diversity rarefaction plot of fecal microbioas between AH and NH treefrogs.    102
Figure 6 – Heatmap.    103
Figure 7 – Compositional variation in microbial communities between AH and NH treefrogs.    104
Figure 8 – Core genera of AH and NH treefrogs.    104
Figure 9 – Rarefaction analyses for the observed number of genera from 12 time points.    105
Figure 10 – Time dependent taxonomic composition spanning 15 days over AH.    106
Figure 11 – Inferred interaction partners of Bacillus, Corynebacterium, and Lactococcus.    107
Figure 12 – Relative abundance of IIPs of Bacillus, Corynebacterium, and Lactococcus after two-week oral trials.    108
Tables    109
Table 1 – Summary of sample information for AH and NH treefrogs.    109
Table 2 – Sample information of preliminary time-series.    109
Table 3 – Summary of sample information of the GMT dataset.    110
Table 4 – The intrinsic growth rate and initial abundance of 50 OTUs from simulation dataset    111
Table 5 – Summary of sample information of oral administration for bacterial composition.    112
Table 6 – Summary of sample information of oral administration for quantitative PCR.    112
Table 7 – Phylogenetic diversity indices of AH and NH treefrogs.    113
Table 8 – Relative abundance of dominant phyla in AH and NH treefrogs.    113
Table 9 – PICRUSt showing predicted relative abundance of KEGG ortholog groups (Level 2 KOs).    114
Table 10 – The performance of correlation-based and regression-based methods    115
Table 11 – Time-dependent diversity spanning 15 days over AH    115
Table 12 – Expression analysis of IL-10 and level of Lactococcus.    116
Table 13 – Validation of IIPs that correlate with Lactococcus, Corynebacterium, or Bacillus.    116
Supplementary Tables    117
Supplementary Table 1 – Interacting matrix between 50 OTUs.    117
Supplementary Table 2 – Tax4Fun showing predicted relative abundance of KEGG ortholog groups.    117
Supplementary Table 3 – Microbial interactions inferred by Pearson’s correlation coefficient based on simulated datasets.    117
Supplementary Table 4 – Ten thousand and three hundred fourteen significant inferred interacting pairs (IIPs) identified by MetaMIS.    117
Supplementary Table 5 – The raw data for the interaction network at the species level.    117
Supplementary Table 6 – Fold change of the inferred relationships with Lactococcus, Corynebacterium, and Bacillus.    117
Supplementary Table 7 – Relative abundance of IIPs of Bacillus, Corynebacterium, and Lactococcus after two-week oral trials.    118
References    119
                                

Ahlberg, P. E. and A. R. J. N. Milner (1994). "The origin and early diversification of tetrapods." Nature 368(6471): 507.
Ahn, J., R. Sinha, Z. Pei, C. Dominianni, J. Wu, J. Shi, J. J. Goedert, R. B. Hayes and L. J. J. o. t. N. C. I. Yang (2013). "Human gut microbiome and risk for colorectal cancer." Journal of the National Cancer Institute 105(24): 1907-1911.
Alshawaqfeh, M., E. Serpedin and A. B. J. B. g. Younes (2017). "Inferring microbial interaction networks from metagenomic data using sglv-ekf algorithm." 18(3): 228.
Aly, S. M., Y. A.-G. Ahmed, A. A.-A. Ghareeb, M. F. J. F. Mohamed and s. immunology (2008). "Studies on Bacillus subtilis and Lactobacillus acidophilus, as potential probiotics, on the immune response and resistance of Tilapia nilotica (Oreochromis niloticus) to challenge infections." Fish and Shellfish Immunology 25(1-2): 128-136.
Amin, M., M. Adams, C. J. Bolch and C. M. Burke (2017). "In vitro screening of lactic acid bacteria isolated from gastrointestinal tract of Atlantic Salmon (Salmo salar) as probiont candidates." Aquaculture International 25(1): 485-498.
Andersson, C., D. Hodge, K. A. Berglund and U. J. B. p. Rova (2007). "Effect of different carbon sources on the production of succinic acid using metabolically engineered Escherichia coli." Biotechnology Progress 23(2): 381-388.
Andre, S. E., J. Parker and C. J. J. J. o. W. D. Briggs (2008). "Effect of temperature on host response to Batrachochytrium dendrobatidis infection in the mountain yellow-legged frog (Rana muscosa)." Journa of Wildlife Diseases 44(3): 716-720.
Arumugam, M., J. Raes, E. Pelletier, D. Le Paslier, T. Yamada, D. R. Mende, G. R. Fernandes, J. Tap, T. Bruls and J.-M. J. n. Batto (2011). "Enterotypes of the human gut microbiome." Nature 473(7346): 174.
Asadullah, K., W. Sterry and H. J. P. r. Volk (2003). "Interleukin-10 therapy—review of a new approach." Pharmacological Reviews 55(2): 241-269.
Aßhauer, K. P., B. Wemheuer, R. Daniel and P. Meinicke (2015). "Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data." Bioinformatics 31(17): 2882-2884.
Bäckhed, F., R. E. Ley, J. L. Sonnenburg, D. A. Peterson and J. I. Gordon (2005). "Host-bacterial mutualism in the human intestine." Science 307(5717): 1915-1920.
Balcázar, J. L., I. De Blas, I. Ruiz-Zarzuela, D. Vendrell, O. Gironés and J. L. Muzquiz (2007). "Enhancement of the immune response and protection induced by probiotic lactic acid bacteria against furunculosis in rainbow trout (Oncorhynchus mykiss)." FEMS Immunology & Medical Microbiology 51(1): 185-193.
Balslev-Clausen, A., J. M. McCarthy, H. V. J. C. B. Carey, P. P. A. Molecular and I. Physiology (2003). "Hibernation reduces pancreatic amylase levels in ground squirrels." Comparative Biochemistry and Physiology Part A: Molecular and Integrative Physiology 134(3): 573-578.
Banas, J., W. Loesche and G. Nace (1988). "Classification and distribution of large intestinal bacteria in nonhibernating and hibernating leopard frogs (Rana pipiens)." Applied and environmental microbiology 54(9): 2305-2310.
Banas, J., W. Loesche and G. Nace (1988). "Possible mechanisms responsible for the reduced intestinal flora in hibernating leopard frogs (Rana pipiens)." Applied and environmental microbiology 54(9): 2311-2317.
Barnes, E. M. and G. C. Burton (1970). "The Effect of Hibernation on the Caecal Flora of the Thirteen‐lined Ground Squirrel (Citellus tridecemlineatus)." Journal of Applied Microbiology 33(3): 505-514.
Becker, M. H., R. N. Harris, K. P. Minbiole, C. R. Schwantes, L. A. Rollins-Smith, L. K. Reinert, R. M. Brucker, R. J. Domangue and B. Gratwicke (2011). "Towards a better understanding of the use of probiotics for preventing chytridiomycosis in Panamanian golden frogs." Ecohealth 8(4): 501-506.
Berry, D. and S. Widder (2014). "Deciphering microbial interactions and detecting keystone species with co-occurrence networks." Frontiers in microbiology 5.
Bhargava, S. C. (1989). "Generalized Lotka-Volterra equations and the mechanism of technological substitution." Technological Forecasting and Social Change 35(4): 319-326.
Bletz, M. C., D. J. Goedbloed, E. Sanchez, T. Reinhardt, C. C. Tebbe, S. Bhuju, R. Geffers, M. Jarek, M. Vences and S. J. N. c. Steinfartz (2016). "Amphibian gut microbiota shifts differentially in community structure but converges on habitat-specific predicted functions." Nature 7: 13699.
Bletz, M. C., A. H. Loudon, M. H. Becker, S. C. Bell, D. C. Woodhams, K. P. Minbiole and R. N. Harris (2013). "Mitigating amphibian chytridiomycosis with bioaugmentation: characteristics of effective probiotics and strategies for their selection and use." Ecology letters 16(6): 807-820.
Bolnick, D. I., L. K. Snowberg, P. E. Hirsch, C. L. Lauber, R. Knight, J. G. Caporaso and R. J. E. l. Svanbäck (2014). "Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch)." Ecology Letters 17(8): 979-987.
Book, S. G. (1974). "Amphibians: Guidelines for the breeding, care and management of laboratory animals."
Borrelli, L., S. Aceto, C. Agnisola, S. De Paolo, L. Dipineto, R. M. Stilling, T. G. Dinan, J. F. Cryan, L. F. Menna and A. Fioretti (2016). "Probiotic modulation of the microbiota-gut-brain axis and behaviour in zebrafish." Scientific reports 6.
Bouma, H. R., H. V. Carey and F. G. J. J. o. l. b. Kroese (2010). "Hibernation: the immune system at rest?" Journal of Leukocyte Biology 88(4): 619-624.
Brodkin, M. A., M. P. Simon, A. M. DeSantis and K. J. Boyer (1992). "Response of Rana pipiens to graded doses of the bacterium Pseudomonas aeruginosa." Journal of Herpetology: 490-495.
Bucci, V., B. Tzen, N. Li, M. Simmons, T. Tanoue, E. Bogart, L. Deng, V. Yeliseyev, M. L. Delaney and Q. Liu (2016). "MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses." Genome biology 17(1): 121.
Buffie, C. G., V. Bucci, R. R. Stein, P. T. McKenney, L. Ling, A. Gobourne, D. No, H. Liu, M. Kinnebrew and A. Viale (2015). "Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile." Nature 517(7533): 205-208.
Cammarota, G., G. Ianiro, S. Bibbò, A. J. I. Gasbarrini and e. medicine (2014). "Gut microbiota modulation: probiotics, antibiotics or fecal microbiota transplantation?" Internal and Emergency Medicine 9(4): 365-373.
Cao, H. T., T. E. Gibson, A. Bashan and Y. Y. J. B. Liu (2017). "Inferring human microbial dynamics from temporal metagenomics data: Pitfalls and lessons." BioEssays 39(2): 1600188.
Caporaso, J. G., K. Bittinger, F. D. Bushman, T. Z. DeSantis, G. L. Andersen and R. Knight (2010). "PyNAST: a flexible tool for aligning sequences to a template alignment." Bioinformatics 26(2): 266-267.
Caporaso, J. G., J. Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman, E. K. Costello, N. Fierer, A. G. Pena, J. K. Goodrich and J. I. Gordon (2010). "QIIME allows analysis of high-throughput community sequencing data." Nature methods 7(5): 335-336.
Cardinale, B. J., K. Gross, K. Fritschie, P. Flombaum, J. W. Fox, C. Rixen, J. van Ruijven, P. B. Reich, M. Scherer-Lorenzen and B. J. Wilsey (2013). "Biodiversity simultaneously enhances the production and stability of community biomass, but the effects are independent." Ecology 94(8): 1697-1707.
Carey, H. V., W. A. Walters and R. Knight (2013). "Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 304(1): R33-R42.
Carey, H. V. J. A. J. o. P.-R., Integrative and C. Physiology (1990). "Seasonal changes in mucosal structure and function in ground squirrel intestine." APS Regulatory, Integrative and Comparative Physiology 259(2): R385-R392.
Carr, A. H., R. L. Amborski, D. D. Culley Jr and G. F. Amborski (1976). "Aerobic bacteria in the intestinal tracts of bullfrogs (Rana catesbeiana) maintained at low temperatures." Herpetologica 32: 239-244.
Carroll, I. M., T. Ringel‐Kulka, J. P. Siddle, Y. J. N. Ringel and Motility (2012). "Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea‐predominant irritable bowel syndrome." Wiley Online Library 24(6): 521-e248.
Chang, C.-W., B.-H. Huang, S.-M. Lin, C.-L. Huang and P.-C. Liao (2016). "Changes of diet and dominant intestinal microbes in farmland frogs." BMC microbiology 16(1): 33.
Chang, J. Y., D. A. Antonopoulos, A. Kalra, A. Tonelli, W. T. Khalife, T. M. Schmidt and V. B. J. T. J. o. i. d. Young (2008). "Decreased diversity of the fecal microbiome in recurrent Clostridium difficile—associated diarrhea." The Journal of Infectious Diseases 197(3): 435-438.
Chen, E. Z. and H. J. B. Li (2016). "A two-part mixed-effects model for analyzing longitudinal microbiome compositional data." Bioinformatics 32(17): 2611-2617.
Christy, M. T., C. S. Clark, D. E. Gee, D. Vice, D. S. Vice, M. P. Warner, C. L. Tyrrell, G. H. Rodda and J. A. J. P. S. Savidge (2007). "Recent records of alien anurans on the Pacific Island of Guam." Pacific Science 61(4): 469-483.
Christy, M. T., J. A. Savidge, G. H. J. D. Rodda and Distributions (2007). "Multiple pathways for invasion of anurans on a Pacific island." Diversity and Distributions 13(5): 598-607.
Clarke, K. and R. Warwick (2001). "ChangeinMarineCommunities: AnApproach toStatisticalAnalysisandInterpretation." 2ndEdition.(PRIMER-E Ltd: Plymouth, United Kingdom.).
Colombo, B. M., T. Scalvenzi, S. Benlamara and N. J. F. i. i. Pollet (2015). "Microbiota and mucosal immunity in amphibians." Frontiers in Immunology 6: 111.
Cooper, J., J. Needham and J. Griffin (1978). "A bacterial disease of the Darwin's frog (Rhinoderma darwini)." Laboratory animals 12(2): 91-93.
Coppola, S., G. Blaiotta and D. Ercolini (2008). Dairy products. Molecular Techniques in the Microbial Ecology of Fermented Foods, Springer: 31-90.
Costello, E. K., J. I. Gordon, S. M. Secor and R. Knight (2010). "Postprandial remodeling of the gut microbiota in Burmese pythons." The ISME journal 4(11): 1375-1385.
Cotter, P. D. and C. Hill (2003). "Surviving the acid test: responses of gram-positive bacteria to low pH." Microbiology and Molecular Biology Reviews 67(3): 429-453.
Cross, M. L. (2002). "Microbes versus microbes: immune signals generated by probiotic lactobacilli and their role in protection against microbial pathogens." FEMS Immunology & Medical Microbiology 34(4): 245-253.
Cryan, J. F., S. J. N. O’mahony and Motility (2011). "The microbiome‐gut‐brain axis: from bowel to behavior." Neurogastroenterology and Motility 23(3): 187-192.
Curtis, T. P., I. M. Head and D. W. Graham (2003). Peer reviewed: Theoretical ecology for engineering biology, ACS Publications.
D’Incà, R., M. Barollo, M. Scarpa, A. R. Grillo, P. Brun, M. G. Vettorato, I. Castagliuolo, G. C. J. D. d. Sturniolo and sciences (2011). "Rectal administration of Lactobacillus casei DG modifies flora composition and Toll-like receptor expression in colonic mucosa of patients with mild ulcerative colitis." Digestive Diseases and Sciences 56(4): 1178-1187.
de LeBlanc, A. d. M. and G. J. P. o. t. N. S. Perdigón (2010). "The application of probiotic fermented milks in cancer and intestinal inflammation." Proceedings of the Nutrition Society 69(3): 421-428.
de Moreno de LeBlanc, A., S. Del Carmen, M. Zurita-Turk, C. Santos Rocha, M. Van de Guchte, V. Azevedo, A. Miyoshi and J. G. LeBlanc (2011). "Importance of IL-10 modulation by probiotic microorganisms in gastrointestinal inflammatory diseases." ISRN gastroenterology 2011.
Densmore, C. L. and D. E. Green (2007). "Diseases of amphibians." Ilar Journal 48(3): 235-254.
Derrien, M., E. E. Vaughan, C. M. Plugge and W. M. de Vos (2004). "Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium." International journal of systematic and evolutionary microbiology 54(5): 1469-1476.
Dethlefsen, L., S. Huse, M. L. Sogin and D. A. Reiman (2008). "The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16Ss rRNA Sequencing." PLoS Biology 6(11): 2383-2401.
Dethlefsen, L. and D. A. Relman (2011). "Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation." Proceedings of the National Academy of Sciences 108(Supplement 1): 4554-4561.
Devaraj, S., P. Hemarajata and J. J. C. c. Versalovic (2013). "The human gut microbiome and body metabolism: implications for obesity and diabetes." Clinical Chemistry 59(4): 617-628.
Dias, D. d. C., M. V. De Stéfani, C. M. Ferreira, F. M. França, M. J. T. Ranzani‐Paiva and A. A. Santos (2010). "Haematologic and immunologic parameters of bullfrogs, Lithobates catesbeianus, fed probiotics." Aquaculture Research 41(7): 1064-1071.
Dill‐McFarland, K. A., K. L. Neil, A. Zeng, R. J. Sprenger, C. C. Kurtz, G. Suen and H. V. Carey (2014). "Hibernation alters the diversity and composition of mucosa‐associated bacteria while enhancing antimicrobial defence in the gut of 13‐lined ground squirrels." Molecular ecology 23(18): 4658-4669.
Durbán, A., J. J. Abellán, N. Jiménez‐Hernández, P. Salgado, M. Ponce, J. Ponce, V. Garrigues, A. Latorre and A. J. E. m. r. Moya (2012). "Structural alterations of faecal and mucosa‐associated bacterial communities in irritable bowel syndrome." Environmental Microbiology Reports 4(2): 242-247.
Edgar, R. C. (2010). "Search and clustering orders of magnitude faster than BLAST." Bioinformatics 26(19): 2460-2461.
Faust, K. and J. Raes (2012). "Microbial interactions: from networks to models." Nature Reviews Microbiology 10(8): 538-550.
Faust, K., J. F. Sathirapongsasuti, J. Izard, N. Segata, D. Gevers, J. Raes and C. J. P. c. b. Huttenhower (2012). "Microbial co-occurrence relationships in the human microbiome." 8(7): e1002606.
Finke, M. D. (2013). "Complete nutrient content of four species of feeder insects." Zoo biology 32(1): 27-36.
Fisher, C. K. and P. Mehta (2014). "Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression." PloS one 9(7): e102451.
Gao, X., B.-T. Huynh, D. Guillemot, P. Glaser and L. J. F. i. m. Opatowski (2018). "Inference of significant microbial interactions from longitudinal metagenomics data." 9.
Geraylou, Z., M. P. Vanhove, C. Souffreau, E. Rurangwa, J. Buyse and F. Ollevier (2014). "In vitro selection and characterization of putative probiotics isolated from the gut of Acipenser baerii (Brandt, 1869)." Aquaculture Research 45(2): 341-352.
Gibbs, E. L. (1973). "Rana Pipiens: Health and Disease: How Little We Know." American Zoologist: 93-96.
Gibbs, E. L., T. J. Gibbs and P. Van Dyck (1966). "Rana pipiens: health and disease." Laboratory animal care 16(2): 142-160.
Gilbert, J. A. and C. L. Dupont (2011). "Microbial metagenomics: beyond the genome." Annual Review of Marine Science 3: 347-371.
Gill, H. and F. Guarner (2004). "Probiotics and human health: a clinical perspective." Postgraduate Medical Journal 80(947): 516-526.
Giovannoni, S. J. and U. Stingl (2005). "Molecular diversity and ecology of microbial plankton." Nature 437(7057): 343-348.
Glorioso, J., R. Amborski, G. Amborski and D. Culley (1974). "Microbiological studies on septicemic bullfrogs (Rana catesbeiana)." American journal of veterinary research 35(9): 1241-1245.
Goldizen, A. W., J. Terborgh, F. Cornejo, D. Porras and R. J. T. j. o. a. E. Evans (1988). "Seasonal food shortage, weight loss, and the timing of births in saddle-back tamarins (Saguinus fuscicollis)." 893-901.
Gossling, J., W. Loesche and G. Nace (1982). "Large intestine bacterial flora of nonhibernating and hibernating leopard frogs (Rana pipiens)." Applied and environmental microbiology 44(1): 59-66.
Gossling, J., W. Loesche and G. Nace (1982). "Response of intestinal flora of laboratory-reared leopard frogs (Rana pipiens) to cold and fasting." Applied and environmental microbiology 44(1): 67-71.
Haas, B. J., D. Gevers, A. M. Earl, M. Feldgarden, D. V. Ward, G. Giannoukos, D. Ciulla, D. Tabbaa, S. K. Highlander and E. Sodergren (2011). "Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons." Genome research 21(3): 494-504.
Hai, N. V. (2015). "Research findings from the use of probiotics in tilapia aquaculture: A review." Fish Shellfish Immunol 45(2): 592-597.
Hallowell, E. (1861). [1860] Report upon the Reptilia of the North Pacific exploring expedition, under command of Capt. John Roger. Proc Acad Nat Sci Phil.
Hamdan, A. M., A. F. M. El‐Sayed and M. M. Mahmoud (2016). "Effects of a novel marine probiotic, Lactobacillus plantarum AH 78, on growth performance and immune response of Nile tilapia (Oreochromis niloticus)." Journal of applied microbiology.
Handelsman, J. (2004). "Metagenomics: application of genomics to uncultured microorganisms." Microbiology and molecular biology reviews 68(4): 669-685.
Harper, G., M. Monfort, I. Saoud, M. Emery, S. Mustafa, M. Rawling, B. Eynon, S. Davies and D. Merrifield (2011). "An ex vivo approach to studying the interactions of probiotic Pediococcus acidilactici and Vibrio (Listonella) anguillarum in the anterior intestine of rainbow trout Oncorhynchus mykiss." Journal of Aquaculture Research and Development.
Hawksworth, D. L. (1974). The changing flora and fauna of Britain. London, Academic Press.
Hecker, M., S. Lambeck, S. Toepfer, E. Van Someren and R. J. B. Guthke (2009). "Gene regulatory network inference: data integration in dynamic models—a review." 96(1): 86-103.
Hendricks, F. S. J. T. S. N. (1973). "Intestinal contents of Rana pipiens Schreber (Ranidae) larvae." 18(1): 99-101.
Hernandez, D., E. Cardell and V. Zarate (2005). "Antimicrobial activity of lactic acid bacteria isolated from Tenerife cheese: initial characterization of plantaricin TF711, a bacteriocin-like substance produced by Lactobacillus plantarum TF711." J Appl Microbiol 99(1): 77-84.
Holling, C. S. (1973). "Resilience and stability of ecological systems." 4(1): 1-23.
Holling, C. S. (1973). "Resilience and stability of ecological systems." Annual review of ecology and systematics: 1-23.
Hooper, D. U., F. Chapin Iii, J. Ewel, A. Hector, P. Inchausti, S. Lavorel, J. Lawton, D. Lodge, M. Loreau and S. Naeem (2005). "Effects of biodiversity on ecosystem functioning: a consensus of current knowledge." Ecological monographs 75(1): 3-35.
Hooper, L. V., D. R. Littman and A. J. Macpherson (2012). "Interactions between the microbiota and the immune system." Science 336(6086): 1268-1273.
Hourdry, J., A. L'Hermite and R. J. P. Z. Ferrand (1996). "Changes in the digestive tract and feeding behavior of anuran amphibians during metamorphosis." 69(2): 219-251.
Hsiao, E. Y., S. W. McBride, S. Hsien, G. Sharon, E. R. Hyde, T. McCue, J. A. Codelli, J. Chow, S. E. Reisman and J. F. Petrosino (2013). "Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders." Cell 155(7): 1451-1463.
Hsiao, E. Y., S. W. McBride, S. Hsien, G. Sharon, E. R. Hyde, T. McCue, J. A. Codelli, J. Chow, S. E. Reisman and J. F. J. C. Petrosino (2013). "The microbiota modulates gut physiology and behavioral abnormalities associated with autism." 155(7): 1451.
Huang, L., J. Li, H. Anboukaria, Z. Luo, M. Zhao and H. Wu (2016). "Comparative transcriptome analyses of seven anurans reveal functions and adaptations of amphibian skin." Scientific reports 6.
Huse, S. M., D. M. Welch, H. G. Morrison and M. L. Sogin (2010). "Ironing out the wrinkles in the rare biosphere through improved OTU clustering." Environmental microbiology 12(7): 1889-1898.
Hyronimus, B., C. Le Marrec and M. Urdaci (1998). "Coagulin, a bacteriocin-like-inhibitory substance produced by Bacillus coagulans I." Journal of Applied Microbiology 85(1): 42-50.
Ives, A. R. and S. R. Carpenter (2007). "Stability and diversity of ecosystems." science 317(5834): 58-62.
Ives, A. R. and S. R. J. s. Carpenter (2007). "Stability and diversity of ecosystems." 317(5834): 58-62.
Jenssen, T. A. J. C. (1967). "Food habits of the green frog, Rana clamitans, before and during metamorphosis." 214-218.
Kanehisa, M., S. Goto, Y. Sato, M. Furumichi and M. Tanabe (2011). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic acids research 40(D1): D109-D114.
Kesarcodi-Watson, A., H. Kaspar, M. J. Lategan and L. Gibson (2008). "Probiotics in aquaculture: the need, principles and mechanisms of action and screening processes." Aquaculture 274(1): 1-14.
Ko-Huan Lee, T.-H. C., Gaus Shang, Simon Clulow, Yi-Ju Yang, Si-Min Lin (2019). "A check list and population trends of invasive amphibians and reptiles in Taiwan." ZooKeys Submission #27535.
Kohl, K. D., J. Amaya, C. A. Passement, M. D. Dearing and M. D. McCue (2014). "Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts." FEMS microbiology ecology 90(3): 883-894.
Kohl, K. D., T. L. Cary, W. H. Karasov and M. D. Dearing (2013). "Restructuring of the amphibian gut microbiota through metamorphosis." Environmental microbiology reports 5(6): 899-903.
Kohl, K. D., T. L. Cary, W. H. Karasov and M. D. J. E. m. r. Dearing (2013). "Restructuring of the amphibian gut microbiota through metamorphosis." 5(6): 899-903.
Konopka, A. (2009). "What is microbial community ecology?" The ISME journal 3(11): 1223-1230.
Kunin, V., A. Engelbrektson, H. Ochman and P. Hugenholtz (2010). "Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates." Environmental microbiology 12(1): 118-123.
Lam, B. A., J. B. Walke, V. T. Vredenburg and R. N. Harris (2010). "Proportion of individuals with anti-Batrachochytrium dendrobatidis skin bacteria is associated with population persistence in the frog Rana muscosa." Biological Conservation 143(2): 529-531.
Langille, M. G., J. Zaneveld, J. G. Caporaso, D. McDonald, D. Knights, J. A. Reyes, J. C. Clemente, D. E. Burkepile, R. L. V. Thurber and R. Knight (2013). "Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences." Nature biotechnology 31(9): 814-821.
Lederberg, J. J. S. (2000). "Infectious history." 288(5464): 287-293.
Lee, Y. K. and S. K. Mazmanian (2010). "Has the microbiota played a critical role in the evolution of the adaptive immune system?" Science 330(6012): 1768-1773.
Liévin-Le Moal, V. and A. L. Servin (2006). "The front line of enteric host defense against unwelcome intrusion of harmful microorganisms: mucins, antimicrobial peptides, and microbiota." Clinical microbiology reviews 19(2): 315-337.
Lima-Mendez, G., K. Faust, N. Henry, J. Decelle, S. Colin, F. Carcillo, S. Chaffron, J. C. Ignacio-Espinosa, S. Roux and F. J. S. Vincent (2015). "Determinants of community structure in the global plankton interactome." 348(6237): 1262073.
Lin, Y. H., Y. S. Chen, H. C. Wu, S. F. Pan, B. Yu, C. M. Chiang, C. M. Chiu and F. Yanagida (2013). "Screening and characterization of LAB‐produced bacteriocin‐like substances from the intestine of grey mullet (Mugil cephalus L.) as potential biocontrol agents in aquaculture." Journal of applied microbiology 114(2): 299-307.
Linzey, D. W. J. H. (1967). "Food of the leopard frog, Rana p. pipiens, in central New York." 23(1): 11-17.
Lozupone, C. A., M. Hamady, S. T. Kelley and R. Knight (2007). "Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities." Applied and environmental microbiology 73(5): 1576-1585.
Maestre, F. T., A. P. Castillo‐Monroy, M. A. Bowker and R. Ochoa‐Hueso (2012). "Species richness effects on ecosystem multifunctionality depend on evenness, composition and spatial pattern." Journal of Ecology 100(2): 317-330.
Magoč, T. and S. L. Salzberg (2011). "FLASH: fast length adjustment of short reads to improve genome assemblies." Bioinformatics 27(21): 2957-2963.
Marino, S., N. T. Baxter, G. B. Huffnagle, J. F. Petrosino and P. D. Schloss (2014). "Mathematical modeling of primary succession of murine intestinal microbiota." Proceedings of the National Academy of Sciences 111(1): 439-444.
Marino, S., N. T. Baxter, G. B. Huffnagle, J. F. Petrosino and P. D. J. P. o. t. N. A. o. S. Schloss (2014). "Mathematical modeling of primary succession of murine intestinal microbiota." 111(1): 439-444.
Mashoof, S., A. Goodroe, C. C. Du, J. O. Eubanks, N. Jacobs, J. M. Steiner, I. Tizard, J. S. Suchodolski and M. F. Criscitiello (2013). "Ancient T-independence of mucosal IgX/A: gut microbiota unaffected by larval thymectomy in Xenopus laevis." Mucosal immunology 6(2): 358-368.
Mastrangeli, G., S. Corinti, C. Butteroni, C. Afferni, A. Bonura, M. Boirivant, P. Colombo, G. J. I. a. o. a. Di Felice and immunology (2009). "Effects of live and inactivated VSL# 3 probiotic preparations in the modulation of in vitro and in vivo allergen-induced Th2 responses." 150(2): 133-143.
Mathipa, M. G. and M. S. J. G. p. Thantsha (2017). "Probiotic engineering: towards development of robust probiotic strains with enhanced functional properties and for targeted control of enteric pathogens." 9(1): 28.
Matsui, M., T. Seto and T. J. J. o. H. Utsunomiya (1986). "Acoustic and karyotypic evidence for specific separation of Polypedates megacephalus from P. leucomystax." 483-489.
Matsuoka, K. and T. Kanai (2015). The gut microbiota and inflammatory bowel disease. Seminars in immunopathology, Springer.
Mauel, M. J., D. L. Miller, K. S. Frazier and M. E. Hines (2002). "Bacterial pathogens isolated from cultured bullfrogs (Rana castesbeiana)." Journal of Veterinary Diagnostic Investigation 14(5): 431-433.
May, R. M. (1973). Stability and complexity in model ecosystems, Princeton University Press.
May, R. M. (1974). "Biological populations with nonoverlapping generations: stable points, stable cycles, and chaos." 186(4164): 645-647.
May, R. M. (1974). "Biological populations with nonoverlapping generations: stable points, stable cycles, and chaos." Science 186(4164): 645-647.
May, R. M. J. P. U. P., Princeton. Montague, JR, and J. N. p. i. n. p. o. m. D. E. Jaenike (1973). "Complexity and stability in model ecosystems." 66: 624-626.
Mazmanian, S. K., J. L. Round and D. L. Kasper (2008). "A microbial symbiosis factor prevents intestinal inflammatory disease." Nature 453(7195): 620.
McCarthy, J., L. O’mahony, L. O’callaghan, B. Sheil, E. Vaughan, N. Fitzsimons, J. Fitzgibbon, G. O’sullivan, B. Kiely and J. J. G. Collins (2003). "Double blind, placebo controlled trial of two probiotic strains in interleukin 10 knockout mice and mechanistic link with cytokine balance." 52(7): 975-980.
McCutcheon, J. P. and C. D. von Dohlen (2011). "An interdependent metabolic patchwork in the nested symbiosis of mealybugs." Current Biology 21(16): 1366-1372.
McFall-Ngai, M., M. G. Hadfield, T. C. Bosch, H. V. Carey, T. Domazet-Lošo, A. E. Douglas, N. Dubilier, G. Eberl, T. Fukami and S. F. Gilbert (2013). "Animals in a bacterial world, a new imperative for the life sciences." Proceedings of the National Academy of Sciences 110(9): 3229-3236.
McGuckin, M. A., R. Eri, L. A. Simms, T. H. Florin and G. Radford‐Smith (2009). "Intestinal barrier dysfunction in inflammatory bowel diseases." Inflammatory bowel diseases 15(1): 100-113.
Mee, M. T. and H. H. Wang (2012). "Engineering ecosystems and synthetic ecologies." Molecular BioSystems 8(10): 2470-2483.
Mendoza, G. M., S. E. Pasteris, C. E. Ale, M. C. Otero, M. I. Bühler and M. E. F. Nader-Macías (2012). "Cultivable microbiota of Lithobates catesbeianus and advances in the selection of lactic acid bacteria as biological control agents in raniculture." Research in veterinary science 93(3): 1160-1167.
Milo, R., S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii and U. Alon (2002). "Network motifs: simple building blocks of complex networks." Science 298(5594): 824-827.
Mounier, J., C. Monnet, T. Vallaeys, R. Arditi, A.-S. Sarthou, A. Hélias and F. Irlinger (2008). "Microbial interactions within a cheese microbial community." Applied and environmental microbiology 74(1): 172-181.
Mounier, J., C. Monnet, T. Vallaeys, R. Arditi, A.-S. Sarthou, A. Hélias, F. J. A. Irlinger and e. microbiology (2008). "Microbial interactions within a cheese microbial community." 74(1): 172-181.
Nayak, S. (2010). "Probiotics and immunity: a fish perspective." Fish & shellfish immunology 29(1): 2-14.
Nicholson, J. K., E. Holmes, J. Kinross, R. Burcelin, G. Gibson, W. Jia and S. Pettersson (2012). "Host-gut microbiota metabolic interactions." Science 336(6086): 1262-1267.
Nikoskelainen, S., S. Salminen, G. Bylund and A. C. Ouwehand (2001). "Characterization of the properties of human-and dairy-derived probiotics for prevention of infectious diseases in fish." Applied and Environmental Microbiology 67(6): 2430-2435.
Olaoye, O. A. (2016). "Antimicrobial Activities of Five Strains Of Lactococcus Isolated from Beef Against Indicator Organisms of Public Health Significance." Turkish Journal of Agriculture-Food Science and Technology 4(10): 887-892.
Ooi, L.-G. and M.-T. J. I. j. o. m. s. Liong (2010). "Cholesterol-lowering effects of probiotics and prebiotics: a review of in vivo and in vitro findings." 11(6): 2499-2522.
Overdorff, D. J., S. G. Strait and A. J. A. J. o. P. Telo (1997). "Seasonal variation in activity and diet in a small‐bodied folivorous primate, Hapalemur griseus, in southeastern Madagascar." 43(3): 211-223.
Pace, N. R. (1997). "A molecular view of microbial diversity and the biosphere." Science 276(5313): 734-740.
Paker, R. (1974). "Probiotics, the other half of the antibiotics story." Anim Nutr Health 29: 4-8.
Panigrahi, A., V. Kiron, J. Puangkaew, T. Kobayashi, S. Satoh and H. Sugita (2005). "The viability of probiotic bacteria as a factor influencing the immune response in rainbow trout Oncorhynchus mykiss." Aquaculture 243(1): 241-254.
Panigrahi, A., V. Kiron, J. Puangkaew, T. Kobayashi, S. Satoh and H. J. A. Sugita (2005). "The viability of probiotic bacteria as a factor influencing the immune response in rainbow trout Oncorhynchus mykiss." 243(1-4): 241-254.
Pasteris, S., M. Bühler and M. Nader-Macías (2006). "Microbiological and histological studies of farmed-bullfrog (Rana catesbeiana) tissues displaying red-leg syndrome." Aquaculture 251(1): 11-18.
Pasteris, S. E., M. G. Guidoli, M. C. Otero, M. I. Bühler and M. E. Nader-Macías (2011). "In vitro inhibition of Citrobacter freundii, a red-leg syndrome associated pathogen in raniculture, by indigenous Lactococcus lactis CRL 1584." Veterinary microbiology 151(3): 336-344.
Pasteris, S. E., E. V. Pingitore, G. R. Babot, M. C. Otero, M. I. Bühler and M. E. Nader-Macías (2009). "Characterization of the beneficial properties of lactobacilli isolated from bullfrog (Rana catesbeiana) hatchery." Antonie Van Leeuwenhoek 95(4): 373.
Pasteris, S. E., E. V. Pingitore, G. R. Babot, M. C. Otero, M. I. Bühler and M. E. J. A. V. L. Nader-Macías (2009). "Characterization of the beneficial properties of lactobacilli isolated from bullfrog (Rana catesbeiana) hatchery." 95(4): 373.
Pasteris, S. E., G. Roig Babot, M. C. Otero, M. I. Bühler and M. E. Nader‐Macías (2009). "Beneficial properties of lactic acid bacteria isolated from a Rana catesbeiana hatchery." Aquaculture Research 40(14): 1605-1615.
Payot, T., Z. Chemaly and M. Fick (1999). "Lactic acid production by Bacillus coagulans—kinetic studies and optimization of culture medium for batch and continuous fermentations." Enzyme and Microbial Technology 24(3): 191-199.
Pedrós-Alió, C. (2012). "The rare bacterial biosphere." Annual review of marine science 4: 449-466.
Peterson, D. A., N. P. McNulty, J. L. Guruge and J. I. Gordon (2007). "IgA response to symbiotic bacteria as a mediator of gut homeostasis." Cell host & microbe 2(5): 328-339.
Qi, Z. and P. Nie (2008). "Comparative study and expression analysis of the interferon gamma gene locus cytokines in Xenopus tropicalis." Immunogenetics 60(11): 699-710.
Qi, Z., P. Nie, C. J. Secombes and J. Zou (2010). "Intron-containing type I and type III IFN coexist in amphibians: refuting the concept that a retroposition event gave rise to type I IFNs." The Journal of Immunology 184(9): 5038-5046.
Qi, Z., Q. Zhang, Z. Wang, W. Zhao and Q. Gao (2015). "Cloning of Interleukin-10 from African Clawed Frog (Xenopus tropicalis), with the Finding of IL-19/20 Homologue in the IL-10 Locus." Journal of immunology research 2015.
Ramos, M. A., J. F. Goncalves, S. Batista, B. Costas, M. A. Pires, P. Rema and R. O. Ozorio (2015). "Growth, immune responses and intestinal morphology of rainbow trout (Oncorhynchus mykiss) supplemented with commercial probiotics." Fish Shellfish Immunol 45(1): 19-26.
Ramsey, J. P., A. Mercurio, J. A. Holland, R. N. Harris and K. P. Minbiole (2015). "The cutaneous bacterium Janthinobacterium lividum inhibits the growth of Trichophyton rubrum in vitro." International journal of dermatology 54(2): 156-159.
Remien, C. H., M. J. Eckwright and B. J. J. b. Ridenhour (2018). "Parameter Identifiability of the Generalized Lotka-Volterra Model for Microbiome Studies." 463372.
Ridaura, V. K., J. J. Faith, F. E. Rey, J. Cheng, A. E. Duncan, A. L. Kau, N. W. Griffin, V. Lombard, B. Henrissat and J. R. Bain (2013). "Gut microbiota from twins discordant for obesity modulate metabolism in mice." Science 341(6150): 1241214.
Rivière, A., M. Gagnon, S. Weckx, D. Roy, L. J. A. De Vuyst and e. microbiology (2015). "Mutual cross-feeding interactions between Bifidobacterium longum NCC2705 and Eubacterium rectale ATCC 33656 explain the bifidogenic and butyrogenic effects of arabinoxylan-oligosaccharides." AEM. 02089-02015.
Roselli, M., A. Finamore, S. Nuccitelli, P. Carnevali, P. Brigidi, B. Vitali, F. Nobili, R. Rami, I. Garaguso and E. J. I. b. d. Mengheri (2009). "Prevention of TNBS-induced colitis by different Lactobacillus and Bifidobacterium strains is associated with an expansion of γδT and regulatory T cells of intestinal intraepithelial lymphocytes." 15(10): 1526-1536.
Round, J. L. and S. K. J. N. r. i. Mazmanian (2009). "The gut microbiota shapes intestinal immune responses during health and disease." 9(5): 313.
Russell, C. W., S. Bouvaine, P. D. Newell and A. E. Douglas (2013). "Shared metabolic pathways in a coevolved insect-bacterial symbiosis." Applied and environmental microbiology 79(19): 6117-6123.
Schadich, E. and A. Cole (2009). "Inhibition of frog antimicrobial peptides by extracellular products of the bacterial pathogen Aeromonas hydrophila." Letters in applied microbiology 49(3): 384-387.
Schippa, S., V. Iebba, M. Barbato, G. Di Nardo, V. Totino, M. P. Checchi, C. Longhi, G. Maiella, S. Cucchiara and M. P. J. B. m. Conte (2010). "A distinctive'microbial signature'in celiac pediatric patients." 10(1): 175.
Schloss, P. D., S. L. Westcott, T. Ryabin, J. R. Hall, M. Hartmann, E. B. Hollister, R. A. Lesniewski, B. B. Oakley, D. H. Parks and C. J. Robinson (2009). "Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities." Applied and environmental microbiology 75(23): 7537-7541.
Schmid, B., P. Balvanera, B. J. Cardinale, J. Godbold, A. B. Pfisterer, D. Raffaelli, M. Solan and D. S. Srivastava (2009). "Consequences of species loss for ecosystem functioning: meta-analyses of data from biodiversity experiments." Biodiversity, ecosystem functioning and human wellbeing: an ecological and economic perspective (eds S. Naeem, DE Bunker, A. Hector, M. Loreau & C. Perrings): 14-29.
Sender, R., S. Fuchs and R. Milo (2016). "Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans." Cell 164(3): 337-340.
Sha, S., B. Xu, X. Wang, Y. Zhang, H. Wang, X. Kong, H. Zhu, K. J. D. m. Wu and i. disease (2013). "The biodiversity and composition of the dominant fecal microbiota in patients with inflammatory bowel disease." 75(3): 245-251.
Shannon, P., A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski and T. Ideker (2003). "Cytoscape: a software environment for integrated models of biomolecular interaction networks." Genome research 13(11): 2498-2504.
Shaw, G. T.-W., A.-C. Liu, C.-Y. Weng, C.-Y. Chou and D. J. P. o. Wang (2017). "Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste." 12(7): e0181395.
Shaw, G. T.-W., Y.-Y. Pao and D. Wang (2016). "MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles." BMC bioinformatics 17(1): 488.
Shaw, G. T.-W., Y.-Y. Pao and D. J. B. b. Wang (2016). "MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles." 17(1): 488.
Shi, S., E. E. Nuccio, Z. J. Shi, Z. He, J. Zhou and M. K. J. E. l. Firestone (2016). "The interconnected rhizosphere: high network complexity dominates rhizosphere assemblages." 19(8): 926-936.
Sommer, F., M. Ståhlman, O. Ilkayeva, J. M. Arnemo, J. Kindberg, J. Josefsson, C. B. Newgard, O. Fröbert and F. Bäckhed (2016). "The gut microbiota modulates energy metabolism in the hibernating brown bear Ursus arctos." Cell reports 14(7): 1655-1661.
Sommer, F., M. Ståhlman, O. Ilkayeva, J. M. Arnemo, J. Kindberg, J. Josefsson, C. B. Newgard, O. Fröbert and F. J. C. r. Bäckhed (2016). "The gut microbiota modulates energy metabolism in the hibernating brown bear Ursus arctos." 14(7): 1655-1661.
Sonnenburg, J. L., J. Xu, D. D. Leip, C.-H. Chen, B. P. Westover, J. Weatherford, J. D. Buhler and J. I. Gordon (2005). "Glycan foraging in vivo by an intestine-adapted bacterial symbiont." Science 307(5717): 1955-1959.
Sonoyama, K., R. Fujiwara, N. Takemura, T. Ogasawara, J. Watanabe, H. Ito and T. Morita (2009). "Response of gut microbiota to fasting and hibernation in Syrian hamsters." Applied and environmental microbiology 75(20): 6451-6456.
Stein, R. R., V. Bucci, N. C. Toussaint, C. G. Buffie, G. Rätsch, E. G. Pamer, C. Sander and J. B. Xavier (2013). "Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota." PLoS Comput Biol 9(12): e1003388.
SUGITA, H., N. MATSUO, K. SHIBUYA and Y. J. J. o. M. B. DEGUCHI (1996). "Production of antibacterial substances by intestinal bacteria isolated from coastal crab and fish species." 4(4): 220-223.
Sutherland, D. B. and S. Fagarasan (2012). "IgA synthesis: a form of functional immune adaptation extending beyond gut." Current opinion in immunology 24(3): 261-268.
Teixeira, L. M., V. L. C. Merquior, M. d. C. E. Vianni, M. d. G. S. Carvalho, S. E. Fracalanzza, A. G. Steigerwalt, D. J. Brenner and R. R. Facklam (1996). "Phenotypic and genotypic characterization of atypical Lactococcus garvieae strains isolated from water buffalos with subclinical mastitis and confirmation of L. garvieae as a senior subjective synonym of Enterococcus seriolicida." International Journal of Systematic and Evolutionary Microbiology 46(3): 664-668.
Theodoropoulos, G., S. J. Hicks, A. P. Corfield, B. G. Miller and S. D. J. T. i. p. Carrington (2001). "The role of mucins in host–parasite interactions: part II–helminth parasites." 17(3): 130-135.
Trosvik, P., N. C. Stenseth and K. Rudi (2010). "Convergent temporal dynamics of the human infant gut microbiota." The ISME journal 4(2): 151-158.
Tsai (2013). "The Adhesion Ability in Habitat Research of Introduced Polypedates megacephalus and Native Polypedates braueri." 1-65.
Turnbaugh, P. J., M. Hamady, T. Yatsunenko, B. L. Cantarel, A. Duncan, R. E. Ley, M. L. Sogin, W. J. Jones, B. A. Roe and J. P. Affourtit (2009). "A core gut microbiome in obese and lean twins." nature 457(7228): 480.
Ulrich, W. and N. J. J. E. Gotelli (2010). "Null model analysis of species associations using abundance data." 91(11): 3384-3397.
Van den Abbeele, P., T. Van de Wiele, W. Verstraete and S. Possemiers (2011). "The host selects mucosal and luminal associations of coevolved gut microorganisms: a novel concept." FEMS microbiology reviews 35(4): 681-704.
Van der Waaij, D., B. Cohen and G. Nace (1974). "Colonization patterns of aerobic gram-negative bacteria in the cloaca of Rana pipiens." Laboratory animal science 24(2): 307-317.
van Passel, M. W., R. Kant, E. G. Zoetendal, C. M. Plugge, M. Derrien, S. A. Malfatti, P. S. Chain, T. Woyke, A. Palva and W. M. J. P. o. de Vos (2011). "The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes." 6(3): e16876.
Vázquez, J., M. P. González and M. Murado (2005). "Effects of lactic acid bacteria cultures on pathogenic microbiota from fish." Aquaculture 245(1): 149-161.
Verschuere, L., G. Rombaut, P. Sorgeloos and W. Verstraete (2000). "Probiotic bacteria as biological control agents in aquaculture." Microbiology and molecular biology reviews 64(4): 655-671.
Verschuere, L., G. Rombaut, P. Sorgeloos, W. J. M. Verstraete and m. b. reviews (2000). "Probiotic bacteria as biological control agents in aquaculture." 64(4): 655-671.
Vieira-Silva, S. and E. P. Rocha (2010). "The systemic imprint of growth and its uses in ecological (meta) genomics." PLoS genetics 6(1): e1000808.
Wagg, C., S. F. Bender, F. Widmer and M. G. van der Heijden (2014). "Soil biodiversity and soil community composition determine ecosystem multifunctionality." Proceedings of the National Academy of Sciences 111(14): 5266-5270.
Weiss, S., W. Van Treuren, C. Lozupone, K. Faust, J. Friedman, Y. Deng, L. C. Xia, Z. Z. Xu, L. Ursell and E. J. J. T. I. j. Alm (2016). "Correlation detection strategies in microbial data sets vary widely in sensitivity and precision." 10(7): 1669.
Wiggins, P. J., J. M. Smith, R. N. Harris and K. P. J. J. o. H. Minbiole (2011). "Gut of red-backed salamanders (Plethodon cinereus) may serve as a reservoir for an antifungal cutaneous bacterium." 45(3): 329-332.
Wu, D., S. C. Daugherty, S. E. Van Aken, G. H. Pai, K. L. Watkins, H. Khouri, L. J. Tallon, J. M. Zaborsky, H. E. Dunbar and P. L. Tran (2006). "Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters." PLoS biology 4(6): e188.
Wu, G. D., J. Chen, C. Hoffmann, K. Bittinger, Y.-Y. Chen, S. A. Keilbaugh, M. Bewtra, D. Knights, W. A. Walters and R. Knight (2011). "Linking long-term dietary patterns with gut microbial enterotypes." Science 334(6052): 105-108.
Xie, Z.-Y., Y.-C. Zhou, S.-F. Wang, B. Mei, X.-D. Xu, W.-Y. Wen and Y.-Q. Feng (2009). "First isolation and identification of Elizabethkingia meningoseptica from cultured tiger frog, Rana tigerina rugulosa." Veterinary microbiology 138(1): 140-144.
Yang, C., G. Cao, P. Ferket, T. Liu, L. Zhou, L. Zhang, Y. Xiao and A. Chen (2012). "Effects of probiotic, Clostridium butyricum, on growth performance, immune function, and cecal microflora in broiler chickens." Poultry Science 91(9): 2121-2129.
Yang, G., X. Tian, S. Dong, M. Peng and D. Wang (2015). "Effects of dietary Bacillus cereus G19, B. cereus BC-01, and Paracoccus marcusii DB11 supplementation on the growth, immune response, and expression of immune-related genes in coelomocytes and intestine of the sea cucumber (Apostichopus japonicus Selenka)." Fish Shellfish Immunol 45(2): 800-807.
Yang, Y.-J. and W.-B. Gong (2014). "Distribution of Polypedates megacephalus Hallowell, 1861 (Rhacophoridae, Anura, Amphibia) in Taiwan." 16(1): 21-32.
Yang, Y.-J., G. Norval, C. R. Bursey, S. R. Goldberg and J.-J. J. C. P. Mao (2014). "Gastrointestinal helminths of the Hong Kong whipping frog, Polypedates megacephalus (Anura: Rhacophoridae), from northern Taiwan, Republic of China." 81(1): 119-121.
Yang YJ, G. W. (2014). "Controlling and Monitoring the Alien Tree Frog –
Polypedates megacephalus." 102FD-07.1-C-17(2).
Ye, J., G. Coulouris, I. Zaretskaya, I. Cutcutache, S. Rozen and T. L. Madden (2012). "Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction." BMC bioinformatics 13(1): 1.
Ye, L., J. Amberg, D. Chapman, M. Gaikowski and W.-T. J. T. I. j. Liu (2014). "Fish gut microbiota analysis differentiates physiology and behavior of invasive Asian carp and indigenous American fish." 8(3): 541.
Zhang, J.-M. and J. An (2007). "Cytokines, inflammation and pain." International anesthesiology clinics 45(2): 27.
Zhu, H.-J., Y. Chen, Y.-H. Li, J.-M. Wang, J.-T. Ding, X.-P. Chen, Y.-F. J. J. o. a. Peng and f. chemistry (2015). "A 90 day safety assessment of genetically modified rice expressing Cry1Ab/1Ac protein using an aquatic animal model." 63(14): 3627-3633.

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