Source: PURDUE UNIVERSITY submitted to NRP
GENETIC CHANGES AND ADAPTATION OF MICROBIAL COMMUNITIES TO THEIR ENVIRONMENT
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
1010571
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Oct 1, 2016
Project End Date
Sep 30, 2021
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
PURDUE UNIVERSITY
(N/A)
WEST LAFAYETTE,IN 47907
Performing Department
Agronomy
Non Technical Summary
The microbial community is integral in the cycling of chemical compounds in the ecosystem. The cycling of chemicals are involved in various essential ecosystem processes ranging from cycling of essential nutrients to degradation of pollutants. Traditionally microorganisms from the environment have been cultivated in the laboratory to characterize them. Due to limitations in cultivated environmental microorganisms (Staley & Konopka, 1985) the functional potential of the majority of microbes have yet been realized. Even when microorganisms can be cultivated for further study in the laboratory it is difficult to differentiate the environmentally relevant microbes from those that just grow well in the lab. By using methods based on molecular genetic approaches the dynamics of the entire microbial communities can now be studied. After identification of the most relevant microbes then we can utilize them to our benefit. My research includes but is not limited to environments exposed to a variety of perturbations, such as, soils contaminated with metal and/or hydrocarbon (pesticides and haloaromatic compounds), soils and water exposed to human and animal waste, soils used for agricultural crop growth, human/animal gut exposed to different diets and human/animal microbiomes associated with health benefits. In recent years investigations have been attempting to directly couple fundamental or "basic" molecular research of microbial community dynamics to "mission-based" applied microbial research. Critical interactions between abiotic and biotic components of ecosystems are underlying factors that control productivity. In agricultural systems these interactions control factors such as the nutrient status of the biota and disease pressure of soil borne pathogens. In gut ecosystems change of diet components can change microbiome composition with benefits to health. Ultimately, this research and its approach have the potential to discovery novel approaches to manage and optimize productivity of ecosystems. For example, identification of beneficial and detrimental microorganisms in the soil may permit rapid screening for viable new or alternative cropping systems to diversify current agro-ecosystems. Also, ecosystems can be manipulated to reduce fitness of invasive plant species. We have already demonstrated that the gut microbiome can be changed by addition of a certain dietary fiber to the diet that leads to improved calcium absorption. Other health benefits of this fiber still need to be explored. Increasing inherent environmental quality not only increases biodiversity and health but can also improve economic viability. Otherwise these ecosystems would be sub-optimally used and degrade over time making them of limited value to humans.
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1010110107025%
1014099107025%
7024099107025%
3024099107025%
Knowledge Area
302 - Nutrient Utilization in Animals; 702 - Requirements and Function of Nutrients and Other Food Components; 101 - Appraisal of Soil Resources;

Subject Of Investigation
4099 - Microorganisms, general/other; 0110 - Soil;

Field Of Science
1070 - Ecology;
Goals / Objectives
The overarching hypothesis is that specific individuals or groups of microbiota that are part of the microbiome communities in ecosystems are indicators of the state of degradation (or restoration) of these habitats. Using metagenomic approaches (both targeted and non-targeted), bioformatics and statistical methods the specific research objectives are:To determine changes in microbial community diversity (richness and evenness) associated with perturbations to their ecosystem (e.g., rhizhosphere, guts, water).To determine differences in functional potential (using a metagenomic approach) of microbial communities associated with perturbations to their ecosystem.
Project Methods
Traditional microbiological and cutting edge molecular biology approaches will be used to compare changes and determine differences in microbial communities after exposure to perturbations. An approach that targets a common genetic biomarker, in this case the 16S rRNA gene, which is present in all prokaryotic biota will provide data to determine composition of microbial communities in a sample as well as make comparisons among samples.Dr. Weaver's group will supply fecal samples from human clinical studies on diet and calcium absorption, Dr. Ajuwon's group will provide pig fecal samples from nutrition studies, Dr. Jones-Hall will supply mouse fecal samples from Crohn's disease studies, Dr. Byappanahalli and Ms Nevers will provide water samples and Dr. Pavlovic will supply rhizospheres and soils samples associated with invasive plant species.General MethodDNA extraction. Total genomic DNA will be extracted from samples from the environment of interest (QBioGene soil kit) using the approaches that we previously optimized and used successfully in a number of studies (Nakatsu et al., 2005, Nebe et al., 2009, Ariefdjohan et al., 2010). Briefly, the cells in soils (50-100 mg), concentrated water samples (1L filtered water) or other substrate (e.g., feces, luminal content, etc.) are mechanically lysed using the FastPrepÔ system followed by purification using the Fast DNA Soil Spin kit (QBIOgene, Carlsbad, CA). Nucleic acid quality will be checked using a 0.7% agarose gel and Nanodrop 1000 spectrophotometer (Thermo Scientific, Wilmington, DE) and then quantified using a Nanodrop 3300 fluorospectrometer (Thermo Scientific).Methods specific for Obj1Targeted 16S rRNA gene sequencing. Primers will be used that amplify the 16S rRNA gene, for example using primers targeting the V3-V4 region (forward TAC GGR AGG CAG CAG and reverse CTA CCR GGG TAT CTA ATC C primers) to take advantage of primer accuracy and coverage of phylogenetic information that has been determined for short sequencing reads (Liu et al., 2008, Nossa et al., 2010). The sequencing instrument used at the Purdue Genomics facilities is an Illumina MiSeq. Primers have duel index tags to differentiate multiple samples in a single run following the manufacturer's (Illumina, San Diego, CA) suggested step out protocol (Gloor et al., 2010). PCR will be carried out using Q5® High Fidelity DNA Polymerase (New England Biolabs) to minimize error rates (100 times lower than Taq polymerase). PCR amplicons will be purified using Agencourt AMPure XP kit (Beckman Coulter) and quantified by fluorometry after staining using the QuantiFluor dsDNA System (Promega). Amplicons from each sample will be combined in equivalent quantities and sent to the Purdue Genomics core facilities for 2x300 paired end sequencing using the MiSeq Illumina system. The reads from MiSeq sequencing will be pre-processed by staff at the Genomics Core using software to remove primer tags and low quality sequences and then merge paired end reads.Targeted 16S rRNA gene sequence analysis. Sequences will be analyzed using the QIIME (Quantitative Insights Into Microbial Ecology, http://qiime.org/) pipeline that includes software programs from many sources that allows Operational Taxonomic Unit (OTU) and phylogenetic assignments, as well as a number of different alpha (within sample) and beta (among samples) diversity measures (Caporaso et al., 2010). Alpha biodiversity estimations (e.g., Shannon and Chao1 indices) and rarefaction analysis will be used to obtain estimations of microbial community diversity, richness and coverage within in each sample. Beta diversity analysis (e.g., Bray Curtis, weighted Unifrac and unweighted Unifrac) will be used to make comparisons among bacterial communities and then use this information to identify bacterial taxa correlated with habitat characteristics.Statistical analyses. Basic statistical analyses to compare differences in proportions of microbial populations and environmental characteristics between locations, sampling time, and sample type will be performed using software available in QIIME, Paleontological Statistics package version 2.16 (PAST) and PC-ORD 5.0 (McCune & Mefford, 2006) e.g., PERMANOVA, PERMDISP, ANOSIM, Mann Whitney and Spearman's ranked correlations. Relationship among microbial communities and their environment will be determined using Canonical Correspondence Analysis (CCA) (Ter Braak, 1986, Ter Braak, 1994). The microbial data will be in the main matrix, and location or environmental characteristics in the second matrix. The second matrix factors will be first assessed for significant correspondence to the data structure in the main matrix in individual runs based on p-values from post-ordination randomization testing. Treatments and factors explaining the most data variation in the first matrix will then be combined in composite CCA runs to visualize their relationships with the samples and scored bands within the resultant ordinations. We will use the CCA in PC-ORD 5.0 software (Oksanen & Minchin, 1997, McCune & Mefford, 2006). Significance for the genes in the ordinations will be assessed with the indicator species analysis method (Dufrene & Legendre, 1997) as implemented in PC-ORD when CCA finds overall significance for treatments and factors in the data sets.Methods specific for Obj2Microbial community metagenome sequencing. The metagenome sequences will be determined using the HiSeq 2500 system (Illumina). The extracted DNA will be sent to the Purdue Genomics facilities where experienced staff will prepare samples using the TruSeq DNA sample protocol. The high throughput mode will be used to maximize sequence yield using 2X100bp paired end reads. Metagenomic sequence depth will be determined to ensure sufficient coverage. For example, human microbiome samples have been determined by the NIH Human Microbiome Project (HMP) to be about 13 Gb (± 4.3) per sample (Wendl et al., 2012). To achieve this sequence depth 4-5 multiple tagged samples needs to be run per HiSeq Illumina lane. Due to the high diversity of microbes in most soil only one soil sample will be run per HiSeq lane.Metagenomic sequence processing. From each of the samples low quality bases in the Illumina reads will be trimmed and reads shorter than 50 bases will be filtered using the FASTXtool kit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads that map to non-microbial DNA will be filtered out and the remaining high quality reads will be used for metagenomic analysis. The reads will be assembled using Meta-IDBA (Peng et al., 2011) or MetaVelvet (Namiki et al., 2012). The resulting contigs will be used for gene prediction and annotation. The longer contigs will also be useful for identifying ORFs, operons, and promoters. Both taxonomic and functional gene annotations will be used to compare samples from different groups (treatments). The reads and contigs from the assemblies will be further analyzed using MG-RAST (Meyer et al., 2008) for functional annotation against several databases (non-redundant protein database, UniProt, Pfam etc). MG-RAST analysis allows for comparison of abundance variation among various samples. The genes identified will be used to identify pathways involved in the response to the perturbation being studied.Statistical analyses. Basic statistical analyses to compare differences in proportions of microbial populations and genes with respect to environmental characteristics (e.g., locations, sampling time, sample type) will be performed using software available in Paleontological Statistics package version 2.16 (PAST) and PC-ORD 5.0 (McCune & Mefford, 2006) e.g., PERMANOVA, PERMDISP, ANOSIM, Mann Whitney and Spearman's ranked correlations. Relationship among microbial communities and their environment will be determined using Canonical Correspondence Analysis (CCA) (Ter Braak, 1986, Ter Braak, 1994) as described above.

Progress 10/01/16 to 09/30/21

Outputs
Target Audience:Target audiences include all individuals and industries interested in the well-being of the environment and/or health of humans and animals. For example, researchers, industries or members of the public who are interested in using or understanding the role of microbial communities to maintain and contribute to a healthy environment. With respect to human or animal health, those interested in improving health or preventing disease through the consumption of healthy diets, especially diets that include microbially fermented polyphenols and fibers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The impact of foods that are rich in polyphenols (e.g., grapes, blueberries and plums) on gut microbiome structure and composition continue to be studied. Some of this work was presented in two posters by Abigayle Simpson an undergrad researcher in my laboratory. In addition, she was included as a second author on paper published on this topic. Informal teaching and mentoring, mainly in microbial community analysis, was provided to undergraduate and graduate students, and researchers from the programs of collaborators. These trainees from other research groups have also published papers that included their microbiome analyses. For example, Rajani Sapkota from the Department of Entomology, Yiying Zhao, Chao Yang, and Kilia Liu from the Department of Nutrition Sciences, and Hang Lu, Hui Yan and Paul Oladele from Department of Animal Sciences How have the results been disseminated to communities of interest?Dissemination of findings to the community includes publications in topic relevant journals, presentation at conferences and invited presentations given to academic, government and industrial research groups. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Microbial communities associated with degraded compared to healthy environments differed and using various statistical analyses taxa contributing to these differences were identified. Nutritional perturbations tested regardless of the ecosystem resulted in changes to community diversity. Correlated with these changes in microbial community were changes to measured functions in the ecosystem. The major role of microbial communities in contributing to ecosystem perturbations continue to be found in all the systems that we have studies. We have now shown the impact of a variety of polyphenol rich foods on microbiomes. Foods rich in polyphenols that are being studied are grapes, blueberries and plums. For example, most recently a study testing the dietary addition of polyphenol supplements to diets clearly showed that microbiomes differed with increasing doses of polyphenol supplements, but that extremely high doses appear to be detrimental to the host microbiome. More insight has also been gained into the role of microbiomes in river and lake water related to degradation of these ecosystem. Most recently, our publication in Frontiers Microbiology shows that methods for processing samples can yield different results that can lead to very different strategies for contamination mitigation efforts. Results from all our studies have collectively highlighted that understanding microbiome composition and structure is useful for identifying impact of perturbations on an ecosystem and then strategies can be developed to optimize changes to restore or maintain the health of the ecosystem. Some future application of this knowledge is highlighted review paper we wrote, led by Laramy Enders in Entomology, in Nature Plants.

Publications

  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Sapkota. R., C. H. Nakatsu, M.E. Scharf. Regulation of host phenotypic plasticity by gut symbiont communities in the Eastern Subterranean termite (Reticulitermes flavipes Kollar). Journal of Experimental Biology 224:jeb242553.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Bai, X., C.H. Nakatsu and A.K. Bhunia. 2021. Bacterial biofilms and their implications in pathogenesis and food safety. Foods 10:2117
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Byappanahalli, M., M.B. Nevers, D. Shively, C. Nakatsu, J. Kinzelman, and M.S. Phanikumar. 2021. Influence of filter pore size on composition and relative abundance of bacterial communities and select MST markers in coastal waters of southern Lake Michigan Frontiers Microbiol. 12:665664.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Cladis, D.P., A.M.R. Simpson, K.J. Cooper, C.H. Nakatsu, M.G. Ferruzzi, and C. M. Weaver. 2021. Blueberry polyphenols alter gut microbiota and phenolic metabolism in rats. Food and Function 12:2442-2456.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: French, E, I. Kaplan, A. Iyer-Pascuzzi, C. H. Nakatsu, and L. Enders. 2021. Progress and emerging strategies for precision microbiome management of crops in diverse agroecosystem. Nature Plants 7(3):256-267.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Lu, H., Yan, H., R. Potu, H. M. ONeill, C. Bradley, M. Bedford, P. Wilcock, C. H. Nakatsu, O. Adeola, and K. M. Ajuwon. 2021. Effect of xylanase and live yeast supplementation on growth performance, nutrient digestibility and gut microbiome diversity of pigs. Canadian Journal of Animal Science 101:459-472
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Sato, A.Y., G.G. Pellegrini, M. Cregor, K.McAndrews, R.B. Choi, M. Maiz, O. Johnson, L.D. McCabe, G.P. McCabe, M.G. Ferruzzi, M.A. Lila, M. Peacock, D.B. Burr, C.H. Nakatsu, C.M. Weaver and T.M. Bellido. 2021. Skeletal protection and promotion of microbiome diversity by dietary boosting of the endogenous antioxidant response. Journal of Bone and Mineral Research 36(4): 768-778
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Liu, K.Y., C. H. Nakatsu, A. Kozik Y. Jones-Hall, and Q. Jiang. 2021. Alpha and beta tocopherol Free Radical Biology and Medicine 163:180-189
  • Type: Book Chapters Status: Published Year Published: 2021 Citation: Nakatsu, C. H. 2021. Microbial Genetics. In T. J. Gentry, J. J. Fuhrmann, and D. A. Zuberer (ed.). Principles and applications of soil microbiology. 3rd edition. Elsevier ISBN 978032385404. pp.89-109
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Simpson, A.M.R., D.P. Cladis, M.G. Ferruzzi, C. M. Weaver. and C.H. Nakatsu. The rat microbiome is altered by blueberry polyphenols. World Microbe Forum Abstracts.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Simpson, A.M.R., D.P. Cladis, M.G. Ferruzzi, C. M. Weaver. and C.H. Nakatsu. The rat microbiome is altered by blueberry polyphenols. Beyond Borders: Indiana Academies Symposium and Indiana Branch of the American Society for Microbiology Annual Meeting Abstracts.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Zhao, Y., C.H. Nakatsu, Y. Jones-Hall and Q. Jiang. The synergistic effect of a vitamin E metabolite and a lactic acid bacterium against ulcerative colitis in mice.. Indiana Branch of the American Society for Microbiology Annual Meeting Abstracts
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Yang, C., Y. Zhao, S. Im, C. Nakatsu, Y. Jones-Hall, and Q. Jiang. 2021. Vitamin E delta-tocotrienol and metabolite 13-carboxychromanol inhibit colitis-associated colon tumorigenesis and modulate gut microbiota in mice. The Journal of Nutritional Biochemistry. 89:108567.


Progress 10/01/19 to 09/30/20

Outputs
Target Audience:All individuals and industries interested in the well-being of the environment and/or health of humans and animals. For example, researchers, industries or members of the public who are interested in using or understanding the role of microbial communities to maintain and contribute to a healthy environment. With respect to human or animal health, those interested in improving health or preventing disease through the consumption of healthy diets, especially diets that include microbially fermented polyphenols and fibers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?A third year honors student from the Department of Biological Sciences has been conducting research in my laboratory on microbiomes for academic credits. Informal teaching and mentoring, mainly in microbial community analysis, was provided to undergraduate and graduate students, and researchers from the programs of other collaborators. How have the results been disseminated to communities of interest?Numerous approaches are being used to gain a better understanding of the role microorganisms in the environment. My laboratory has worked extensively to apply molecular genetic tools for the interrogation of various environments. This has led to collaboration with researchers both within and outside of Purdue. Within the Agronomy Department I am collaborating with Drs. Jim Camberato and Cankui Zhang on projects related to factors impacting nutrient cycling in soil systems. My contribution to these projects is to determine differences in soil microbiome composition/structure in relation to different nutrient conditions. For example, with Dr. Camberato we are looking at changes in nitrogen cycling and the associated microbiota with the use of nitrification and urease inhibitors. This work is sponsored by industry and is ongoing. In addition to soil microbial community analysis my group has a number of different collaborations to determine the influence of diet/disease on intestinal microbiomes. I have continued a collaborative project with Kola Ajuwon in the Department of Animal Sciences showing the impact of diet modification on pig production of metabolites beneficial to health. Two papers on this topic have been accepted for publication in the Canadian Journal of Animal Science. Research also continues on examining the impact of polyphenol rich foods on microbiomes. Foods rich in polyphenols that being studies are grapes, blueberries and plums. Some of this work was present as a poster by Dr. Teresita Bellido's group American Society for Bone and Mineral Research meeting. In addition, a new collaboration has been started with Dr. Palacio at Florida International University on a project being called MetA-Bone trial, a project examining the impact of fiber on improving bone mass in children. The protocol for this trial has been published. My group will be continuing on our previous research on the role of gut microbiome in bone health. A major collaboration outside of Purdue is with scientists at the USGS. A collaborative project with the USGS Lake Michigan scientists Murulee What do you plan to do during the next reporting period to accomplish the goals?Continue on the same lines of research

Impacts
What was accomplished under these goals? Microbial communities associated with degraded compared to healthy environments differed and using various statistical analyses taxa contributing to these differences were identified. Nutritional perturbations tested regardless of the ecosystem resulted in changes to community diversity. Correlated with these changes in microbial community were changes to measured functions in the ecosystem. The major role of microbial communities in contributing to ecosystem perturbations continue to be found in all the systems that we have studies. We have now shown the impact of a variety of polyphenol rich foods on microbiomes. Foods rich in polyphenols that are being studied are grapes, blueberries and plums. For example, most recently a study testing the dietary addition of different blueberry varieties on minimizing bone loss with aging using a mouse model clearly showed that microbiomes differed. The differences were most evident with one of the blueberry varieties. Further, it was only this variety that significantly improved bone health in female mice but not males. These differences in health outcomes were all correlated with differences in the gut microbiome of these animals illustrating the important role being played by microbes in host health. More insight has also been gained into the role of microbiomes in river and lake water related to degradation of these ecosystem. Most recently our publication in Water Research shows that the elevated microbial indicators of fecal contamination in Lake Michigan beaches did not come from refuges in the beach sand or sediment. This suggests mitigation of contamination into these waters should focus on other sources. Results from all our studies have collectively highlighted that understanding microbiome composition and structure is useful for identifying impact of perturbations on an ecosystem and then strategies can be developed to optimize changes to restore or maintain the health of the ecosystem.

Publications

  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Kozik, A. J., C. H. Nakatsu, H. Chun, and Y. L. Jones-Hall. 2019. Comparison of the fecal, cecal, and mucus microbiome in male and female mice after TNBS-induced colitis. PLoS ONE 14(11): e0225079.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Lu, H., H. Yan, H. Masey O'Neill, C. Bradley, M. Bedford, P. Wilcock., C. Nakatsu, L. Adeola, K. Ajuwon. 2020. Effect of timing of postweaning xylanase supplementation on growth performance, nutrient digestibility, and fecal microbial composition in weanling pigs. Canadian Journal of Animal Science 100:27-36.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Nevers, M.B., M. Byappanahalli, C.H. Nakatsu, J. Kinzelman, M. Phanikumar, D.A. Shively and A.M. Spoljaric. 2020. Interaction of microbial communities and indicators in shoreline sand, sediment, and water. Water Research 178:115671
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Palacios, C., M.A. Trak-Fellermeier, C.M. P�rez, F. Huffman, Y. Hernandez Suarez, Z. Bursac, T.B. Gambon, C.H. Nakatsu and C.M. Weaver. 2020. Effect of Soluble Corn Fiber supplementation for 1 year on bone metabolism in children (MetA-Bone Trial): Rationale and design. Contemporary Clinical Trials. 95:106061
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Kinzelman, J., M.B. Nevers, M. Byappanahalli, D.A. Shively, S. Kurdas and C.H. Nakatsu. 2020. Utilization of multiple microbial tools to evaluate efficacy of restoration strategies to improve recreational water quality at a Lake Michigan beach (Racine, WI). Journal of Microbiological Methods 178:106049.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Sato, A.Y., Nakatsu, C.H., Cregor, M., Mcandrews, K., Pellegrini, G.G., Ferruzzi, M.G., Lila, M.A., Weaver, C.M., and Bellido, T.M. A Sex Dimorphic Mechanism Links Protection from Bone Loss and Promotion of Gut Microbiome Diversity Induced by a Nutritional Intervention. Annual Meeting of the American Society for Bone and Mineral Research.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Byappanahalli, M., M. Nevers, A. Spoljaric, D. Shively, K. Kelly, J. Kinzelman, P. Mantha, and C. Nakatsu. Bacterial communities in coastal waters along southern Lake Michigan: Influence of filter size on detection of community abundance, composition, and diversity. American Society for Microbiology Annual Meeting Abstracts.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Nevers, M.B., M. Byappanahalli, C.H. Nakatsu, J. Kinzelman, M. Phanikumar, D.A. Shively and A.M. Spoljaric. 2020. Bacterial communities and water quality indicators in southern Lake Michigan: Interactions among water, sand, and sediment matrices. American Society for Microbiology Annual Meeting Abstracts
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Palacios C, Trak-Fellermeier MA, P�rez CM, Huffman F, Hernandez Suarez Y, Bursac Z, Gambon TB, Nakatsu CH and Weaver CM Effect of Soluble Corn Fiber supplementation for 1 year on bone metabolism in children: MetA-Bone Trial Study Protocol-Rationale and Design. Annual Meeting of the American Society of Nutrition Abstracts.


Progress 10/01/18 to 09/30/19

Outputs
Target Audience:Target audiences include all individuals and industries interested in the well-being of the environment and/or health of humans and animals. For example, researchers, industries or members of the public who are interested in using or understanding the role of microbial communities to maintain and contribute to a healthy environment. With respect to human or animal health, those interested in improving health or preventing disease through the consumption of healthy diets, especially diets that include microbially fermented fibers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?A second year honors student from the Department of Biological Sciences has been conducting research in my laboratory on microbiomes for academic credits. One post-doctoral researcher came to the lab for training in microbiome analysis methods. Informal teaching and mentoring, mainly in microbial community analysis, was provided to undergraduate and graduate students, and researchers from the programs of other collaborators. How have the results been disseminated to communities of interest?Dissemination of findings to the community includes publications in topic relevant journals, presentation at conferences and invited presentations given to academic, government and industrial research groups. For example, research results for this last year have been published or accepted for publication in the journals: Soil Biology and Biochemistry, Journal of Applied Soil Ecology, Frontiers in Microbiology, PLoS ONE and Canadian Journal of Animal Science. What do you plan to do during the next reporting period to accomplish the goals?Continue on the same lines of research

Impacts
What was accomplished under these goals? Microbial communities associated with degraded compared to healthy environments differed and using various statistical analyses taxa contributing to these differences were identified. Nutritional perturbations tested regardless of the ecosystem resulted in changes to community diversity. Correlated with these changes in microbial community were changes to measured functions in the ecosystem. In a study of cover crop impact on microbiomes, significant determinants of soil microbial community composition were decomposition degree-days, cover crop treatment (vetch versus cereal rye), and residue management treatment (till versus no-till). Microbial functional differences were evident in activity of enzymes related to nitrogen and carbon metabolism involved in cover crop decomposition. Research also continues on examining the impact of polyphenol rich foods on microbiomes. Foods rich in polyphenols that being studied are grapes, blueberries and plums. A preliminary study adding grape powder to the diet of mice changed the microbial community and increased the concentrations of metabolites associated with health benefits. A study characterizing the microbiomes in river and lake water showed spatial and temporal differences in microbiome composition related to degradation of the ecosystem. The microbial community composition river indicated there were inputs of waste from human and agricultural sources but during the summer months these microbes were not transported into the lake. All these results collectively highlight that understanding microbiome composition and structure is useful for identifying impact of perturbations on an ecosystem and then strategies can be developed to optimize changes to restore or maintain the health of the ecosystem.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Zhao, Y., C. Nakatsu, and Q. Jiang. A grape powder attenuates colonic inflammation, inhibits colitis-associated colorectal cancer development and causes favorable changes of gut microbiota in mice. American Society for Nutrition Annual Meeting Abstracts, Baltimore, MA (June 2019).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Negrini, K., T. Jenkins, C. Means; L. Thompson, S. H. Johnson, R. M. Rodriquiz, C. Nakatsu, W. C. Wetsel, D. Little. Chronic social defeat stress induces changes to the osteoarthritis (OA) phenotype in mice compared to destabilization of the medical meniscus or sham surgery alone. Orthopaedic Research Society Annual Meeting Abstracts, Austin, TX (February 2019).
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Frank, G. S. C. H. Nakatsu, M. A. Jenkins. 2018. Soil chemistry and microbial community functional responses to invasive shrub removal in mixed hardwood forest. Journal Applied Soil Ecology 131:75-88
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Nevins, C., C.H. Nakatsu, and S. Armstrong. 2018. Characterization of microbial community response to cover crop decomposition. Soil Biology and Biochemistry 127:39-49.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Nakatsu, C.H., M. Byappanahalli, and M. Nevers. 2019. Bacterial community 16S rRNA gene sequencing characterizes riverine microbial impact on Lake Michigan. Frontiers in Microbiology 10:996
  • Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Lu, H., H. Yan, H. Masey O'Neill, C. Bradley, M. Bedford, P. Wilcock., C. Nakatsu, L. Adeola, K. Ajuwon. 2019. Effect of timing of postweaning xylanase supplementation on growth performance, nutrient digestibility, and fecal microbial composition in weanling pigs. Canadian Journal of Animal Science


Progress 10/01/17 to 09/30/18

Outputs
Target Audience:Individuals and industries interested in the well-being of the environment and/or health of humans and animals. For example, researchers, industries or members of the public who are interested in using or understanding the role of microbial communities to maintain and contribute to a healthy environment. With respect to human or animal health, those interested in improving health or preventing disease through the consumption of healthy diets, especially diets that include microbially fermented fibers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?One PhD level graduate student whom I co-advised with Dr. Jones-Hall, successfully defended and received her Ph.D. I also mentoring a non-thesis MS student in Department of Agronomy who successfully completed her program in May 2018. A first year honors student from the Department of Biological Sciences began research in my lab this fall. Informal teaching and mentoring, mainly in microbial community analysis, was provided to graduate students and researchers from the programs of other collaborators. How have the results been disseminated to communities of interest?Dissemination of findings to the community includes publications in topic relevant journals, presentation at conferences and invited presentations given to academic, government and industrial research groups What do you plan to do during the next reporting period to accomplish the goals?Continue on the same lines of research

Impacts
What was accomplished under these goals? Numerous approaches are being used to gain a better understanding of the role microorganisms in the environment. My laboratory has worked extensively to apply new molecular genetic tools for the interrogation of various environments. This has led to collaboration with researchers both within and outside of Purdue. Within the Agronomy Department I am collaborating on a cover crop project with Assistant Professor, Shalamar Armstrong. My contribution to this project is to determine differences in soil microbiome composition/structure in relation to different cover crops and their decomposition. Results showing changes to these communities associated with cover crop decomposition were presented at the 2017 ASA/CSSA/SSSA annual meetings by an MS student, Clayton Nevins. This work has now been published in Soil Biology and Biochemistry. In addition to soil microbial community analysis my group has a number of different collaborations to determine the influence of diet/disease on intestinal microbiomes. In collaborative project that I have continued with Yava Jones-Hall, in the Veterinary School, on the role of the microbiome in Crohn's Disease and our co-advised Ph.D. student Ariangela Kozik graduated in May 2018. Her work showed differences in the microbiome associated with sex, age and genotype of mice used as models for Crohn's Disease. A major collaboration outside of Purdue is with scientists at the USGS. I have continued research on the impact of invasive plant species on rhizospheres microbial communities with collaborators Noel Palvolic and Kurt Kowalchuk. Results of this study has shown differences rhizospheres microbiomes of invasive vs native plants collected from various locations in Indiana and Michigan. Also, a collaborative project with the USGS Lake Michigan has continued with the research group led by Murulee Byappanahalli and Meredith Nevers. A paper on this work was recently submitted to ES&T.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Almeida, V. V., H. Yan, C. H. Nakatsu and K. M. Ajuwon. 2018. Investigation of carry-over effect of prior fiber consumption on diet-induced obesity susceptibility and metabolic health indicators in Ossabaw Pigs. Journal of Animal Physiology and Animal Nutrition 102:1053-1061. (doi:10.1111/jpn.12900).
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Kozik, A. J., C. H. Nakatsu, H. Chun, and Y. L. Jones-Hall. 2017. Age, sex and TNF associated differences in the gut microbiota of mice and their impact on acute TNBS colitis. Experimental and Molecular Pathology 103(3):311-319. doi: 10.1016/j.yexmp.2017.11.014).
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Zhang, X., J-R Xu and C. H Nakatsu. 2017. Draft genome sequence of Pseudomonas fluorescens strain TR3, a potential biocontrol agent against the rice blast fungus Magnaporthe oryzae. Genome Announcements 5(47): e01332-17. doi: 10.1128/genomeA.01332-17
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Hillman, E.T., H. Lu, T. Yao, and C. H. Nakatsu. 2017. Microbial ecology along the gastrointestinal tract. Microbes Environ. 32(4):300-313. doi: 10.1264/jsme2.ME17017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Nakatsu, C.H., A. Kumar, M. Maiz, M. Datta and C. Weaver. Impact of dietary blueberries on the gut microbiome and age-related bone loss. The 15th International Symposium on Microbial Ecology Abstracts. Leipzig, Germany (August 2018).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Nevins, C., C. H. Nakatsu and S. Armstrong. Soil microbial community dynamics over the growing season of a corn agroecosystem after winter cover cropping. .American Society of Agronomy Annual Meeting Abstracts, Tampa, FL. (November 2017).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Nevins, C., C. H. Nakatsu and S. Armstrong. Soil biological parameters at corn growth stages as impacted by cover crops. .American Society of Agronomy Annual Meeting Abstracts, Tampa, FL. (November 2017)


Progress 10/01/16 to 09/30/17

Outputs
Target Audience:Target audiences include all individuals and industries interested in the well-being of the environment and/or health of humans and animals. For example, researchers, industries or members of the public who are interested in using or understanding the role of microbial communities to maintain and contribute to a healthy environment. With respect to human or animal health, those interested in improving health or preventing disease through the consumption of healthy diets, especially diets that include microbially fermented fibers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?I am co-advising one PhD level graduate student, who is just beginning her fifth year in the PULSe program. I am also mentoring a non-thesis MS student in Department of Agronomy and a first year honors student from the Department of Biological Sciences. Informal teaching and mentoring, mainly in microbial community analysis, was provided to graduate students and researchers from the programs of other collaborators. During the summer of 2017 worked on research planning, data analysis and manuscripts with researchers at the US-Geological Survey Lake Michigan Ecological Research Station. How have the results been disseminated to communities of interest?Dissemination of findings to the community includes publications in topic relevant journals, presentation at conferences and invited presentations given to academic, government and industrial research groups. What do you plan to do during the next reporting period to accomplish the goals?Continue on the same lines of research that has been successfully followed this year.

Impacts
What was accomplished under these goals? My laboratory has worked extensively to apply new molecular genetic tools for the interrogation of various environments. This has led to collaboration with researchers both within and outside of Purdue. Within the Agronomy Department I am collaborating on a cover crop project with a recently hired Assistant Professor, Shalamar Armstrong. My contribution to this project is to determine differences in soil microbiome composition/structure in relation to different cover crops' and their decomposition. Results showing changes to these communities associated with cover crop decomposition were presented at the recent ASA/CSSA/SSSA annual meetings by an MS student, Clayton Nevins. In addition to soil microbial community analysis my group has a number of different collaborations to determine the influence of diet/disease on intestinal microbiomes. In collaborative project that I have continued with Yava Jones-Hall, in the Veterinary School, on the role of the microbiome in Crohn's Disease and our co-advised Ph.D. student Ariangela Kozik presented some of her research at the Experimental Biology conference this year. Her work showed differences in the microbiome associated with sex, age and genotype of mice used as models for Crohn's Disease. A major collaboration outside of Purdue is with scientists at the USGS. I have continued research on the impact of invasive plant species on rhizospheres microbial communities with collaborators Noel Palvolic and Kurt Kowalchuk. Results of this study has shown differences rhizospheres microbiomes of invasive vs native plants collected from various locations in Indiana and Michigan. Also, a collaborative project with the USGS Lake Michigan has continued with the research group led by Murulee Byappanahalli and Meredith Nevers.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Tuncil, Y. E., C. H. Nakatsu, A. E. Kazem, S. Arioglu-Tuncil, B. Reuhs, E. C. Martens, B. R. Hamaker. 2017. Delayed utilization of fast-fermenting soluble dietary fibers by human gut microbiota is achieved when presented in a mixture. Journal of Functional Foods 32:347-357.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Lu, H., H. Yan, R. Potu, M. G. Ward, C. C. Pelkman, O. Adeola, C. H. Nakatsu and K. M. Ajuwon. 2017. Effects of dietary resistant starch content on metabolic status, milk composition, and microbial profile in lactating sows and on offspring performance. Journal of Animal Physiology and Animal Nutrition 101:190-200.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Kozik, A. J., C. H. Nakatsu, H. Chun, and Y. L. Jones-Hall. Sex, age and TNF influence the gut microbiota in a mouse model of TNBS colitis. Meeting of the Federation for American Society of Experimental Biology. FASEB J. Chicago, IL
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Smith, T., A. J. Kozik, C. H. Nakatsu, and Y. L. Jones-Hall. Pro-inflammatory and anti-inflammatory cytokine expression in Tnf-/- and WT mice with chronic colitis. Meeting of the Federation for American Society of Experimental Biology. FASEB J. Chicago, IL
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Smith, T., A. J. Kozik, C. H. Nakatsu, Y. L. Jones-Hall, and. Local and systemic cytokine expression in Tnf -/- and WT mice with chronic TNBS colitis. Annual Biomedical Research Conference for Minority Students (ABRCMS). Tampa, FL