51
|
Sun X, Li B, Han F, Xiao E, Xiao T, Sun W. Impacts of Arsenic and Antimony Co-Contamination on Sedimentary Microbial Communities in Rivers with Different Pollution Gradients. MICROBIAL ECOLOGY 2019; 78:589-602. [PMID: 30725170 DOI: 10.1007/s00248-019-01327-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
Arsenic (As) and antimony (Sb) are both toxic metalloids that are of primary concern for human health. Mining activity has introduced elevated levels of arsenic and antimony into the rivers and has increased the risks of drinking water contamination in China. Due to their mobility, the majority of the metalloids originating from mining activities are deposited in the river sediments. Thus, depending on various geochemical conditions, sediment could either be a sink or source for As and Sb in the water column. Microbes are key mediators for biogeochemical transformation and can both mobilize or precipitate As and Sb. To further understand the microbial community responses to As and Sb contamination, sediment samples with different contamination levels were collected from three rivers. The result of the study suggested that the major portions of As and Sb were in strong association with the sediment matrix and considered nonbioavailable. These fractions, however, were also suggested to have profound influences on the microbial community composition. As and Sb contamination caused strong reductions in microbial diversity in the heavily contaminated river sediments. Microorganisms were more sensitive to As comparing to Sb, as revealed by the co-occurrence network and random forest predictions. Operational taxonomic units (OTUs) that were potentially involved in As and Sb metabolism, such as Anaerolinea, Sphingomonas, and Opitutus, were enriched in the heavily contaminated samples. In contrast, many keystone taxa, including members of the Hyphomicrobiaceae and Bradyrhizobiaceae families, were inhibited by metalloid contamination, which could further impair crucial environmental services provided by these members.
Collapse
Affiliation(s)
- Xiaoxu Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou, 510650, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou, 510650, China
| | - Feng Han
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou, 510650, China
| | - Enzong Xiao
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Tangfu Xiao
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou, 510650, China.
| |
Collapse
|
52
|
Reddy KR, Rai RK, Green SJ, Chetri JK. Effect of temperature on methane oxidation and community composition in landfill cover soil. J Ind Microbiol Biotechnol 2019; 46:1283-1295. [PMID: 31317292 DOI: 10.1061/(asce)ee.1943-7870.0001712] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/11/2019] [Indexed: 05/26/2023]
Abstract
Municipal solid waste (MSW) landfills are the third largest anthropogenic source of methane (CH4) emissions in the United States. The majority of CH4 generated in landfills is converted to carbon dioxide (CO2) by CH4-oxidizing bacteria (MOB) present in the landfill cover soil, whose activity is controlled by various environmental factors including temperature. As landfill temperature can fluctuate substantially seasonally, rates of CH4 oxidation can also vary, and this could lead to incomplete oxidation. This study aims at analyzing the effect of temperature on CH4 oxidation potential and microbial community structure of methanotrophs in laboratory-based studies of landfill cover soil and cultivated consortia. Soil and enrichment cultures were incubated at temperatures ranging from 6 to 70 °C, and rates of CH4 oxidation were measured, and the microbial community structure was analyzed using 16S rRNA gene amplicon sequencing and shotgun metagenome sequencing. CH4 oxidation occurred at temperatures from 6 to 50 °C in soil microcosm tests, and 6-40 °C in enrichment culture batch tests; maximum rates of oxidation were obtained at 30 °C. A corresponding shift in the soil microbiota was observed, with a transition from putative psychrophilic to thermophilic methanotrophs with increasing incubation temperature. A strong shift in methanotrophic community structure was observed above 30 °C. At temperatures up to 30 °C, methanotrophs from the genus Methylobacter were dominant in soils and enrichment cultures; at a temperature of 40 °C, putative thermophilic methanotrophs from the genus Methylocaldum become dominant. Maximum rate measurements of nearly 195 μg CH4 g-1 day-1 were observed in soil incubations, while observed maximum rates in enrichments were significantly lower, likely as a result of diffusion limitations. This study demonstrates that temperature is a critical factor affecting rates of landfill soil CH4 oxidation in vitro and that changing rates of CH4 oxidation are in part driven by changes in methylotroph community structure.
Collapse
Affiliation(s)
- Krishna R Reddy
- Department of Civil and Materials Engineering, University of Illinois at Chicago, 842 West Taylor Street, Chicago, IL, 60607, USA.
| | - Raksha K Rai
- Department of Civil and Materials Engineering, University of Illinois at Chicago, 842 West Taylor Street, Chicago, IL, 60607, USA
| | - Stefan J Green
- Department of Biological Sciences, Sequencing Core, Resources Center, University of Illinois at Chicago, 835 S. Wolcott, Chicago, IL, 60612, USA
| | - Jyoti K Chetri
- Department of Civil and Materials Engineering, University of Illinois at Chicago, 842 West Taylor Street, Chicago, IL, 60607, USA
| |
Collapse
|
53
|
McCary MA, Wise DH. Plant invader alters soil food web via changes to fungal resources. Oecologia 2019; 191:587-599. [PMID: 31529212 DOI: 10.1007/s00442-019-04510-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/09/2019] [Indexed: 10/26/2022]
Abstract
While aboveground impacts of invasive plants are well documented, their influence on soil food webs remains less understood. Previous research has revealed that bottom-up forces are widespread in soil food webs of woodlands. Thus, an invasive plant that negatively impacts the base of the food web will likely decrease primary consumers as well as their predators. We examined how a North American plant invader, garlic mustard (Alliaria petiolata), affects arthropod primary (springtails and oribatid mites) and secondary (predaceous mites) consumers of the soil food web via changes to fungal resources. We measured the abundances of plants, soil fungi, fungivores, and predators in garlic mustard-invaded and uninvaded 1-m2 plots in five Midwestern USA woodlands. We then conducted a mesocosm (0.25-m2 plots) experiment to tease apart the direct and indirect effects of garlic mustard by manipulating plant identity (garlic mustard vs. native plant), soil history (invaded vs. uninvaded), and fungicide application (fungicide vs. no fungicide). Our first study revealed that plots without garlic mustard had 2.8 and 1.4 × more fungi and fungivores, respectively. Predator densities did not differ. Fungal composition and structural equation modeling (SEM) revealed the garlic mustard effects on fungivores were correlated with fungal declines. The mesocosm experiment confirmed that the impacts were indirect, as fungicide plots harbored similar fungivore densities, whereas fungivore densities differed according to plant identity and soil history in the fungicide-free plots. Our results reveal that by altering soil fungal abundance, an invasive plant can indirectly affect primary consumers in soil food webs, but this indirect effect does not influence predators.
Collapse
Affiliation(s)
- Matthew A McCary
- Department of Biological Sciences, University of Illinois, Chicago, IL, 60607, USA. .,Institute for Environmental Science and Policy, University of Illinois, Chicago, IL, 60612, USA. .,Department of Entomology, University of Wisconsin, Madison, WI, 53706, USA.
| | - David H Wise
- Department of Biological Sciences, University of Illinois, Chicago, IL, 60607, USA.,Institute for Environmental Science and Policy, University of Illinois, Chicago, IL, 60612, USA
| |
Collapse
|
54
|
Schweitzer-Natan O, Ofek-Lalzar M, Sher D, Sukenik A. Particle-Associated Microbial Community in a Subtropical Lake During Thermal Mixing and Phytoplankton Succession. Front Microbiol 2019; 10:2142. [PMID: 31572346 PMCID: PMC6753980 DOI: 10.3389/fmicb.2019.02142] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/30/2019] [Indexed: 12/11/2022] Open
Abstract
Ecosystem dynamics in monomictic lakes are characterized by seasonal thermal mixing and stratification. These physical processes bring about seasonal variations in nutrients and organic matter fluxes, affecting the biogeochemical processes that occur in the water column. Physical and chemical dynamics are generally reflected in seasonal structural changes in the phytoplankton and bacterio-plankton community. In this study, we analyzed, using 16S rRNA amplicon sequencing, the structure of the bacterial community associated with large particles (>20 μm) in Lake Kinneret (Sea of Galilee, Israel), and its associations to phytoplankton populations. The study was carried out during late winter and early spring, a highly dynamic period in terms of thermal mixing, nutrient availability, and shifts in phytoplankton composition. Structural changes in the bacterioplankton population corresponded with limnological variations in the lake. In terms of the entire heterotrophic community, the structural patterns of particle-associated bacteria were mainly correlated with abiotic factors such as pH, ammonia, water temperature and nitrate. However, analysis of microbial taxon-specific correlations with phytoplankton species revealed a strong potential link between specific bacterial populations and the presence of different phytoplankton species, such as the cyanobacterium Microcystis, as well as the dinoflagellates Peridinium and Peridiniopsis. We found that Brevundimonas, a common freshwater genus, and Bdellovibrio, a well-known Gram-negative bacteria predator, were positively associated to Microcystis, suggesting a potentially important role of these three taxa in the microbial ecology of the lake. Our results show that the dynamics of environmental abiotic conditions, rather than specific phytoplankton assemblages, are the main factors positively correlated with changes in the community structure as a whole. Nevertheless, some specific bacteria may interact and be linked with specific phytoplankton, which may potentially control the dynamic patterns of the microbial community.
Collapse
Affiliation(s)
- Orna Schweitzer-Natan
- Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Haifa, Israel
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | | | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Assaf Sukenik
- Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Haifa, Israel
| |
Collapse
|
55
|
Murine Genetic Background Has a Stronger Impact on the Composition of the Gut Microbiota than Maternal Inoculation or Exposure to Unlike Exogenous Microbiota. Appl Environ Microbiol 2019; 85:AEM.00826-19. [PMID: 31350316 DOI: 10.1128/aem.00826-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/29/2019] [Indexed: 01/07/2023] Open
Abstract
The gut microbiota is a complex ecosystem, affected by both environmental factors and host genetics. Here, we aim at uncovering the bacterial taxa whose gut persistence is controlled by host genetic variation. We used a murine model based on inbred lines BALB/c and C57BL/6J and their F1 reciprocal hybrids (♀C57BL/6J × ♂BALB/c; ♀BALB/c × ♂C57BL/6J). To guarantee genetic similarity of F1 offspring, including the sex chromosomes, we used only female mice. Based on 16S rRNA gene sequencing, we found that the genetically different inbred lines present different microbiota, whereas their genetically identical F1 reciprocal hybrids presented similar microbiota. Moreover, the F1 microbial composition differed from that of both parental lines. Twelve taxa were shown to have genetically controlled gut persistence, while none were found to show maternal effects. Nine of these taxa were dominantly inherited by the C57BL/6J line. Cohousing of the parental inbred lines resulted in a temporary and minor shift in microbiota composition, which returned back to the former microbial composition following separation, indicating that each line tends to maintain a unique bacterial signature reflecting the line. Taken together, our findings indicate that mouse genetics has an effect on the microbial composition in the gut, which is greater than maternal effect and continuous exposure to different microbiota of the alternative line. Uncovering the bacterial taxa associated with host genetics and understanding their role in the gut ecosystem could lead to the development of genetically oriented probiotic products, as part of the personalized medicine approach.IMPORTANCE The gut microbiota play important roles for their host. The link between host genetics and their microbial composition has received increasing interest. Using a unique reciprocal cross model, generating genetically similar F1 hybrids with different maternal inoculation, we demonstrate the inheritance of gut persistence of 12 bacterial taxa. No taxa identified as maternally transmitted. Moreover, cohabitation of two genetically different inbred lines did not dramatically affect the microbiota composition. Taken together, our results demonstrate the importance of the genetic effect over maternal inoculation or effect of exposure to unlike exogenous microbiota. These findings may lead to the development of personalized probiotic products, specifically designed according to the genetic makeup.
Collapse
|
56
|
Hoffman JD, Yanckello LM, Chlipala G, Hammond TC, McCulloch SD, Parikh I, Sun S, Morganti JM, Green SJ, Lin AL. Dietary inulin alters the gut microbiome, enhances systemic metabolism and reduces neuroinflammation in an APOE4 mouse model. PLoS One 2019; 14:e0221828. [PMID: 31461505 PMCID: PMC6713395 DOI: 10.1371/journal.pone.0221828] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/15/2019] [Indexed: 12/22/2022] Open
Abstract
The apolipoprotein ε4 allele (APOE4) is the strongest genetic risk factor for Alzheimer's disease (AD). APOE4 carriers develop systemic metabolic dysfunction decades before showing AD symptoms. Accumulating evidence shows that the metabolic dysfunction accelerates AD development, including exacerbated amyloid-beta (Aβ) retention, neuroinflammation and cognitive decline. Therefore, preserving metabolic function early on may be critical to reducing the risk for AD. Here, we show that inulin increases beneficial microbiota and decreases harmful microbiota in the feces of young, asymptomatic APOE4 transgenic (E4FAD) mice and enhances metabolism in the cecum, periphery and brain, as demonstrated by increases in the levels of SCFAs, tryptophan-derived metabolites, bile acids, glycolytic metabolites and scyllo-inositol. We show that inulin also reduces inflammatory gene expression in the hippocampus. This knowledge can be utilized to design early precision nutrition intervention strategies that use a prebiotic diet to enhance systemic metabolism and may be useful for reducing AD risk in asymptomatic APOE4 carriers.
Collapse
Affiliation(s)
- Jared D. Hoffman
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
- Department of Pharmacology and Nutritional Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Lucille M. Yanckello
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
- Department of Pharmacology and Nutritional Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - George Chlipala
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Tyler C. Hammond
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky, United States of America
| | | | - Ishita Parikh
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
- Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Sydney Sun
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
| | - Josh M. Morganti
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky, United States of America
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky, United States of America
| | - Stefan J. Green
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Ai-Ling Lin
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, United States of America
- Department of Pharmacology and Nutritional Science, University of Kentucky, Lexington, Kentucky, United States of America
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky, United States of America
- F. Joseph Halcomb III, M.D. Department of Biomedical Engineering, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
| |
Collapse
|
57
|
Seasonal diversity of the bacterial communities associated with petroglyphs sites from the Negev Desert, Israel. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01509-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
58
|
Jiang P, Green SJ, Chlipala GE, Turek FW, Vitaterna MH. Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight. MICROBIOME 2019; 7:113. [PMID: 31399081 PMCID: PMC6689164 DOI: 10.1186/s40168-019-0724-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 07/23/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Space environment imposes a range of challenges to mammalian physiology and the gut microbiota, and interactions between the two are thought to be important in mammalian health in space. While previous findings have demonstrated a change in the gut microbial community structure during spaceflight, specific environmental factors that alter the gut microbiome and the functional relevance of the microbiome changes during spaceflight remain elusive. METHODS We profiled the microbiome using 16S rRNA gene amplicon sequencing in fecal samples collected from mice after a 37-day spaceflight onboard the International Space Station. We developed an analytical tool, named STARMAPs (Similarity Test for Accordant and Reproducible Microbiome Abundance Patterns), to compare microbiome changes reported here to other relevant datasets. We also integrated the gut microbiome data with the publically available transcriptomic data in the liver of the same animals for a systems-level analysis. RESULTS We report an elevated microbiome alpha diversity and an altered microbial community structure that were associated with spaceflight environment. Using STARMAPs, we found the observed microbiome changes shared similarity with data reported in mice flown in a previous space shuttle mission, suggesting reproducibility of the effects of spaceflight on the gut microbiome. However, such changes were not comparable with those induced by space-type radiation in Earth-based studies. We found spaceflight led to significantly altered taxon abundance in one order, one family, five genera, and six species of microbes. This was accompanied by a change in the inferred microbial gene abundance that suggests an altered capacity in energy metabolism. Finally, we identified host genes whose expression in the liver were concordantly altered with the inferred gut microbial gene content, particularly highlighting a relationship between host genes involved in protein metabolism and microbial genes involved in putrescine degradation. CONCLUSIONS These observations shed light on the specific environmental factors that contributed to a robust effect on the gut microbiome during spaceflight with important implications for mammalian metabolism. Our findings represent a key step toward a better understanding the role of the gut microbiome in mammalian health during spaceflight and provide a basis for future efforts to develop microbiota-based countermeasures that mitigate risks to crew health during long-term human space expeditions.
Collapse
Affiliation(s)
- Peng Jiang
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL USA
| | - Stefan J. Green
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL USA
| | - George E. Chlipala
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL USA
| | - Fred W. Turek
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL USA
| | - Martha Hotz Vitaterna
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL USA
| |
Collapse
|
59
|
Gołębiewski M, Tretyn A. Generating amplicon reads for microbial community assessment with next‐generation sequencing. J Appl Microbiol 2019; 128:330-354. [DOI: 10.1111/jam.14380] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 12/12/2022]
Affiliation(s)
- M. Gołębiewski
- Plant Physiology and Biotechnology Nicolaus Copernicus University Toruń Poland
- Centre for Modern Interdisciplinary Technologies Nicolaus Copernicus University Toruń Poland
| | - A. Tretyn
- Plant Physiology and Biotechnology Nicolaus Copernicus University Toruń Poland
- Centre for Modern Interdisciplinary Technologies Nicolaus Copernicus University Toruń Poland
| |
Collapse
|
60
|
Reddy KR, Rai RK, Green SJ, Chetri JK. Effect of temperature on methane oxidation and community composition in landfill cover soil. J Ind Microbiol Biotechnol 2019; 46:1283-1295. [PMID: 31317292 DOI: 10.1007/s10295-019-02217-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/11/2019] [Indexed: 11/30/2022]
Abstract
Municipal solid waste (MSW) landfills are the third largest anthropogenic source of methane (CH4) emissions in the United States. The majority of CH4 generated in landfills is converted to carbon dioxide (CO2) by CH4-oxidizing bacteria (MOB) present in the landfill cover soil, whose activity is controlled by various environmental factors including temperature. As landfill temperature can fluctuate substantially seasonally, rates of CH4 oxidation can also vary, and this could lead to incomplete oxidation. This study aims at analyzing the effect of temperature on CH4 oxidation potential and microbial community structure of methanotrophs in laboratory-based studies of landfill cover soil and cultivated consortia. Soil and enrichment cultures were incubated at temperatures ranging from 6 to 70 °C, and rates of CH4 oxidation were measured, and the microbial community structure was analyzed using 16S rRNA gene amplicon sequencing and shotgun metagenome sequencing. CH4 oxidation occurred at temperatures from 6 to 50 °C in soil microcosm tests, and 6-40 °C in enrichment culture batch tests; maximum rates of oxidation were obtained at 30 °C. A corresponding shift in the soil microbiota was observed, with a transition from putative psychrophilic to thermophilic methanotrophs with increasing incubation temperature. A strong shift in methanotrophic community structure was observed above 30 °C. At temperatures up to 30 °C, methanotrophs from the genus Methylobacter were dominant in soils and enrichment cultures; at a temperature of 40 °C, putative thermophilic methanotrophs from the genus Methylocaldum become dominant. Maximum rate measurements of nearly 195 μg CH4 g-1 day-1 were observed in soil incubations, while observed maximum rates in enrichments were significantly lower, likely as a result of diffusion limitations. This study demonstrates that temperature is a critical factor affecting rates of landfill soil CH4 oxidation in vitro and that changing rates of CH4 oxidation are in part driven by changes in methylotroph community structure.
Collapse
Affiliation(s)
- Krishna R Reddy
- Department of Civil and Materials Engineering, University of Illinois at Chicago, 842 West Taylor Street, Chicago, IL, 60607, USA.
| | - Raksha K Rai
- Department of Civil and Materials Engineering, University of Illinois at Chicago, 842 West Taylor Street, Chicago, IL, 60607, USA
| | - Stefan J Green
- Department of Biological Sciences, Sequencing Core, Resources Center, University of Illinois at Chicago, 835 S. Wolcott, Chicago, IL, 60612, USA
| | - Jyoti K Chetri
- Department of Civil and Materials Engineering, University of Illinois at Chicago, 842 West Taylor Street, Chicago, IL, 60607, USA
| |
Collapse
|
61
|
Hydrocarbon-Degrading Microbial Communities Are Site Specific, and Their Activity Is Limited by Synergies in Temperature and Nutrient Availability in Surface Ocean Waters. Appl Environ Microbiol 2019; 85:AEM.00443-19. [PMID: 31126938 DOI: 10.1128/aem.00443-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/16/2019] [Indexed: 11/20/2022] Open
Abstract
The objective of this study was to quantify the potential for hydrocarbon biodegradation in surface waters of three sites, representing geographic regions of major oil exploration (Beaufort Sea in the Arctic, northern Gulf of Mexico [GOM], and southern GOM), in a systematic experimental design that incorporated gradients in temperature and the availability of major nutrients. Surface seawater was amended in microcosms with Macondo surrogate oil to simulate an oil slick, and microcosms were incubated, with or without nutrient amendment, at temperatures ranging from 4 to 38ºC. Using respiration rate as a proxy, distinct temperature responses were observed in surface seawater microcosms based on geographic origin; biodegradation was nearly always more rapid in the Arctic site samples than in the GOM samples. Nutrient amendment enhanced respiration rates by a factor of approximately 6, stimulated microbial growth, and generally elevated the taxonomic diversity of microbial communities within the optimal temperature range for activity at each site, while diversity remained the same or was lower at temperatures deviating from optimal conditions. Taken together, our results advance the understanding of how bacterioplankton communities from different geographic regions respond to oil perturbation. A pulsed disturbance of oil is proposed to favor copiotrophic r-strategists that are adapted to pointed seasonal inputs of phytoplankton carbon, displaying carbon and nutrient limitations, rather than oil exposure history. Further understanding of the ecological mechanisms underpinning the complex environmental controls of hydrocarbon degradation is required for improvement of predictive models of the fate and transport of spilled oil in marine environments.IMPORTANCE The risk of an oil spill accident in pristine regions of the world's oceans is increasing due to the development and transport of crude oil resources, especially in the Arctic region, as a result of the opening of ice-free transportation routes, and there is currently no consensus regarding the complex interplay among the environmental controls of petroleum hydrocarbon biodegradation for predictive modeling. We examined the hydrocarbon biodegradation potential of bacterioplankton from three representative geographic regions of oil exploration. Our results showed that rates of aerobic respiration coupled to hydrocarbon degradation in surface ocean waters are controlled to a large extent by effects of temperature and nutrient limitation; hydrocarbon exposure history did not appear to have a major impact. Further, the relationship between temperature and biodegradation rates is linked to microbial community structure, which is specific to the geographic origin.
Collapse
|
62
|
Keshri J, Chen Y, Pinto R, Kroupitski Y, Weinberg ZG, Sela Saldinger S. Bacterial Dynamics of Wheat Silage. Front Microbiol 2019; 10:1532. [PMID: 31354651 PMCID: PMC6632545 DOI: 10.3389/fmicb.2019.01532] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 06/19/2019] [Indexed: 11/13/2022] Open
Abstract
Knowledge regarding bacterial dynamics during crop ensiling is important for understanding of the fermentation process and may facilitate the production of nutritious and stable silage. The objective of this study was to analyze the bacterial dynamics associated with whole crop wheat silage with and without inoculants. Whole crop wheat was ensiled in laboratory silos, with and without Lactobacillus inoculants (L. plantarum, L. buchneri), for 3 months. Untreated and L. plantarum-treated silages were sampled at several times during ensiling, while L. buchneri-treated silage was sampled only at 3 months. Bacterial composition was studied using next generation sequencing approach. Dominant bacteria, before ensiling, were Pantoea (34.7%), Weissella (28.4%) and Pseudomonas (10.4%), Exiguobacterium (7.8%), and Paenibacillus (3.4%). Exogenous inoculants significantly affected bacterial composition and dynamics during ensiling. At 3 months of ensiling, Lactobacillus dominated the silage bacterial population and reached an abundance of 59.5, 92.5, and 98.2% in untreated, L. plantarum- and L. buchneri-treated silages, respectively. The bacterial diversity of the mature silage was lower in both treated silages compared to untreated silage. Functional profiling of the bacterial communities associated with the wheat ensiling demonstrated that the abundant pathways of membrane transporters, carbohydrate and amino acids metabolisms followed different pattern of relative abundance in untreated and L. plantarum-treated silages. Only three pathways, namely base-excision repair, pyruvate metabolism and transcription machinery, were significantly different between untreated and L. buchneri-treated silages upon maturation. Lactic acid content was higher in L. plantarum-treated silage compared to untreated and L. buchneri-treated silage. Still, the pH of both treated silages was lower in the two Lactobacillus-treated silages compared to untreated silage. Aerobic stability test demonstrated that L. plantarum-, but not L. buchneri-supplement, facilitated silage deterioration. The lower aerobic stability of the L. plantarum-treated silage may be attributed to lower content of acetic acid and other volatile fatty acids which inhibit aerobic yeasts and molds. Indeed, high yeast count was recorded, following exposure to air, only in L. plantarum-treated silage, supporting this notion. Analysis of bacterial community of crop silage can be used for optimization of the ensiling process and the selection of appropriate inoculants for improving aerobic stability.
Collapse
Affiliation(s)
- Jitendra Keshri
- Department of Food Science, Institute for Postharvest and Food Sciences, Agriculture Research Organization Volcani Center, Rishon LeZion, Israel
| | - Yaira Chen
- Department of Food Science, Institute for Postharvest and Food Sciences, Agriculture Research Organization Volcani Center, Rishon LeZion, Israel
| | - Riky Pinto
- Department of Food Science, Institute for Postharvest and Food Sciences, Agriculture Research Organization Volcani Center, Rishon LeZion, Israel
| | - Yulia Kroupitski
- Department of Food Science, Institute for Postharvest and Food Sciences, Agriculture Research Organization Volcani Center, Rishon LeZion, Israel
| | - Zwi G Weinberg
- Department of Food Science, Institute for Postharvest and Food Sciences, Agriculture Research Organization Volcani Center, Rishon LeZion, Israel
| | - Shlomo Sela Saldinger
- Department of Food Science, Institute for Postharvest and Food Sciences, Agriculture Research Organization Volcani Center, Rishon LeZion, Israel
| |
Collapse
|
63
|
Keshri J, Krouptiski Y, Abu-Fani L, Achmon Y, Bauer TS, Zarka O, Maler I, Pinto R, Sela Saldinger S. Dynamics of bacterial communities in alfalfa and mung bean sprouts during refrigerated conditions. Food Microbiol 2019; 84:103261. [PMID: 31421775 DOI: 10.1016/j.fm.2019.103261] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 06/07/2019] [Accepted: 07/05/2019] [Indexed: 02/08/2023]
Abstract
Sprouts are considered a healthy ready-to-eat food and has gained popularity in recent years. The objective of the present study was to determine the dynamics of sprouts' microbiome during cold storage to the end of their shelf-life at home. The microbiological quality of fresh alfalfa (Medicago sativa) and mung bean (Vigna radiata) sprouts from two commercial brands was tested and the number of APC ranges from 5.0 to 8.7 log CFU/g in alfalfa and 6.7 to 9.3 log CFU/g in mung bean sprouts. In the case of alfalfa, but not mung beans, there were differences in the mean numbers of APC between the two brands. The number of coliform bacteria ranges from 4.3 to 7.7 log CFU/g in alfalfa and 4.1 to 8.1 log CFU/g in mung bean sprouts. Four independent batches of sprouts were used for DNA preparation and were sampled immediately after purchase and once a week during subsequent storage in refrigerator until the end of their shelf-life. Microbial population of the sprouts was determined using next generation sequencing of 16S rRNA amplicons. Alfalfa sprouts were dominated by Pseudomonas throughout the storage time with relative abundance of >60% at 3 weeks. Fresh mung bean sprouts were dominated by both Pseudomonas and Pantoea, but Pantoea became the dominant taxa after 2 weeks of storage, with >46% of relative abundance. The bacterial communities associated with sprouts were largely dependent on the sprout type, and less dependent on the brand. The species richness and diversity declined during storage and the development of spoilage. Among the 160 genera identified on sprouts, 23 were reported to contain known spoilage-associated species and 30 genera comprise potential human pathogenic species. This study provides new insight into the microbiome dynamics of alfalfa and mung bean sprouts during cold storage.
Collapse
Affiliation(s)
- Jitendra Keshri
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel; College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Yulia Krouptiski
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel
| | - Lareen Abu-Fani
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel
| | - Ygal Achmon
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel; Department of Biotechnology and Food Engineering, Guangdong Technion Israel Institute of Technology, Shantou, China
| | - Tal Stern Bauer
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel; Department of Biochemistry and Food Science, Hebrew University of Jerusalem, Israel
| | - Omri Zarka
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel
| | - Ilana Maler
- The Laboratory of Food Microbiology, Kimron Veterinary Institute, P.O. Box 12, Bet Dagan, 50250, Israel
| | - Riky Pinto
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel
| | - Shlomo Sela Saldinger
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel.
| |
Collapse
|
64
|
Naqib A, Poggi S, Green SJ. Deconstructing the Polymerase Chain Reaction II: an improved workflow and effects on artifact formation and primer degeneracy. PeerJ 2019; 7:e7121. [PMID: 31231597 PMCID: PMC6573857 DOI: 10.7717/peerj.7121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/12/2019] [Indexed: 11/30/2022] Open
Abstract
Polymerase chain reaction (PCR) amplification of complex microbial genomic DNA templates with degenerate primers can lead to distortion of the underlying community structure due to inefficient primer-template interactions leading to bias. We previously described a method of deconstructed PCR (“PEX PCR”) to separate linear copying and exponential amplification stages of PCR to reduce PCR bias. In this manuscript, we describe an improved deconstructed PCR (“DePCR”) protocol separating linear and exponential stages of PCR and allowing higher throughput of sample processing. We demonstrate that the new protocol shares the same benefits of the original and show that the protocol dramatically and significantly decreases the formation of chimeric sequences during PCR. By employing PCR with annealing temperature gradients, we further show that there is a strong negative correlation between annealing temperature and the evenness of primer utilization in a complex pool of degenerate primers. Shifting primer utilization patterns mirrored shifts in observed microbial community structure in a complex microbial DNA template. We further employed the DePCR method to amplify the same microbial DNA template independently with each primer variant from a degenerate primer pool. The non-degenerate primers generated a broad range of observed microbial communities, but some were highly similar to communities observed with degenerate primer pools. The same experiment conducted with standard PCR led to consistently divergent observed microbial community structure. The DePCR method is simple to perform, is limited to PCR mixes and cleanup steps, and is recommended for reactions in which degenerate primer pools are used or when mismatches between primers and template are possible.
Collapse
Affiliation(s)
- Ankur Naqib
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States of America.,Rush University, Chicago, IL, United States of America
| | - Silvana Poggi
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States of America.,Northwestern University, Chicago, IL, United States of America
| | - Stefan J Green
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States of America
| |
Collapse
|
65
|
Sedghi L, Byron C, Jennings R, Chlipala GE, Green SJ, Silo-Suh L. Effect of Dietary Fiber on the Composition of the Murine Dental Microbiome. Dent J (Basel) 2019; 7:dj7020058. [PMID: 31159370 PMCID: PMC6630570 DOI: 10.3390/dj7020058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/25/2019] [Accepted: 05/13/2019] [Indexed: 11/16/2022] Open
Abstract
The oral cavity houses a diverse consortium of microorganisms, heavily influenced by host diet, that can mediate dental health and disease. While the impact of dietary carbohydrates to the dental microbiome has been well-documented, the effect of fiber as a mechanical influence on the dental microbiome is unexplored. We performed 16S rRNA gene analysis to investigate the response of the dental microbiome to the presence of increased fiber in terms of microbial taxonomic abundance and diversity. Dental microbial community structure was significantly different in mice fed a diet supplemented with increased fiber and/or sugar. Fiber significantly affected measures of beta diversity at the phylum and genus levels, and a strong interactive effect on alpha diversity was observed between sugar and fiber at the phylum level. The addition of fiber also induced significant variation in relative taxonomic abundance. This study demonstrates that fiber can promote significant variations in the mouse dental microbiome.
Collapse
Affiliation(s)
- Lea Sedghi
- Department of BioMedical Sciences, School of Medicine, Mercer University, Macon, GA 31207, USA.
| | - Craig Byron
- Department of Biology, Mercer University, Macon, GA 31207, USA.
| | - Ryan Jennings
- Department of Biology, Frostburg State University, Frostburg, MD 21532-2303, USA.
| | - George E Chlipala
- Research Resources Center, University of Illinois at Chicago, Chicago, IL 60612-3748, USA.
| | - Stefan J Green
- Research Resources Center, University of Illinois at Chicago, Chicago, IL 60612-3748, USA.
| | - Laura Silo-Suh
- Department of BioMedical Sciences, School of Medicine, Mercer University, Macon, GA 31207, USA.
| |
Collapse
|
66
|
Qi C, Hountras P, Pickens CO, Walter JM, Kruser JM, Singer BD, Seed P, Green SJ, Wunderink RG. Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing. J Med Microbiol 2019; 68:996-1002. [PMID: 31136295 DOI: 10.1099/jmm.0.000968] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE In this pilot study, we used shotgun metagenome sequencing (SMS) strategy on bronchoalveolar lavage (BAL) samples from hospitalized patients with suspected ventilate-associated pneumonia (VAP) in order to explore its potential for improving detection of ventilator-associated-pneumonia (VAP) etiology. METHODOLOGY In total, 67BAL samples from patients with VAP were tested with SMS strategy for detection of respiratory pathogens. Results of SMS and routine respiratory culture were compared. RESULTS SMS detected all pathogens recovered by cultivation approaches. In addition, putative pathogens other than the organisms recovered by culture were detected by SMS in culture-positive samples. In 40 of 45 (89 %) culture-negative samples, a potential pathogen was detected by SMS. CONCLUSION This proof-of-concept study demonstrates that SMS is able to detect bacterial, fungal and viral organisms in BAL, including culture-negative cases.
Collapse
Affiliation(s)
- Chao Qi
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Peter Hountras
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chiagozie Ononye Pickens
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - James M Walter
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jacqueline M Kruser
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Patrick Seed
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Ann and Robert H. Lurie Childrens Hospital, Chicago IL, USA.,Stanley Manne Children's Research Institute, Chicago IL, USA
| | - Stefan J Green
- Research Resources Center, University of Illinois at Chicago, Chicago IL, USA
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| |
Collapse
|
67
|
Xiao L, Engen PA, Leusink-Muis T, van Ark I, Stahl B, Overbeek SA, Garssen J, Naqib A, Green SJ, Keshavarzian A, Folkerts G, van't Land B. The Combination of 2'-Fucosyllactose with Short-Chain Galacto-Oligosaccharides and Long-Chain Fructo-Oligosaccharides that Enhance Influenza Vaccine Responses Is Associated with Mucosal Immune Regulation in Mice. J Nutr 2019; 149:856-869. [PMID: 31050747 PMCID: PMC6499104 DOI: 10.1093/jn/nxz006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/27/2018] [Accepted: 01/10/2019] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND A critical role for host-microbe interactions and establishment of vaccine responses has been postulated. Human milk oligosaccharides, of which 2'-fucosyllactose (2'FL) is the most prevalent, are known to alter host-associated microbial communities and play a critical role in the immunologic development of breastfed infants. OBJECTIVES Dietary supplementation with a combination of 2'FL and prebiotic short-chain (sc) galacto-oligosaccharides (GOS) and long-chain (lc) fructo-oligosaccharides (FOS) was employed to examine human milk oligosaccharide effects on immune responsiveness, within a murine influenza vaccination model. METHODS Female mice (6 wk old, C57Bl/6JOlaHsd) were fed either control diet (CON) or scGOS/lcFOS/2'FL-containing diet (GF2F) for 45 d. After starting dietary intervention (day 14), mice received a primary influenza vaccination (day 0) followed by a booster vaccination (day 21), after which ear challenges were conducted to measure vaccine-specific delayed type hypersensitivity (DTH). Serum immunoglobulin (Ig) levels, fecal and cecal microbial community structure, short-chain fatty acids, host intestinal gene expression and cellular responses in the mesenteric lymph nodes (MLNs) were also measured. RESULTS Relative to CON, mice fed the GF2F diet had increased influenza vaccine-specific DTH responses (79.3%; P < 0.01), higher levels of both IgG1 (3.2-fold; P < 0.05) and IgG2a (1.2-fold; P < 0.05) in serum, and greater percentages of activated B cells (0.3%; P < 0.05), regulatory T cells (1.64%; P < 0.05), and T-helper 1 cells (2.2%; P < 0.05) in their MLNs. GF2F-fed mice had elevated cecal butyric (P < 0.05) and propionic (P < 0.05) acid levels relative to CON, which correlated to DTH responses (R2 = 0.22; P = 0.05 and R2 = 0.39; P < 0.01, respectively). Specific fecal microbial taxa altered in GF2F diet fed mice relative to CON were significantly correlated with the DTH response and IgG2a level increases. CONCLUSIONS Dietary GF2F improved influenza vaccine-specific T-helper 1 responses and B cell activation in MLNs and enhanced systemic IgG1 and IgG2a concentrations in mice. These immunologic changes are correlated with microbial community structure and metabolites.
Collapse
Affiliation(s)
- Ling Xiao
- Utrecht University, Faculty of Science, Department of Pharmaceutical Sciences, Division of Pharmacology, Utrecht, The Netherlands
| | - Phillip A Engen
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL USA
| | - Thea Leusink-Muis
- Utrecht University, Faculty of Science, Department of Pharmaceutical Sciences, Division of Pharmacology, Utrecht, The Netherlands
| | - Ingrid van Ark
- Utrecht University, Faculty of Science, Department of Pharmaceutical Sciences, Division of Pharmacology, Utrecht, The Netherlands
| | - Bernd Stahl
- Danone Nutricia Research, Departments of Immunology/Human Milk Research & Analytical Science, Utrecht, The Netherlands
| | - Saskia A Overbeek
- Utrecht University, Faculty of Science, Department of Pharmaceutical Sciences, Division of Pharmacology, Utrecht, The Netherlands,Danone Nutricia Research, Departments of Immunology/Human Milk Research & Analytical Science, Utrecht, The Netherlands
| | - Johan Garssen
- Utrecht University, Faculty of Science, Department of Pharmaceutical Sciences, Division of Pharmacology, Utrecht, The Netherlands,Danone Nutricia Research, Departments of Immunology/Human Milk Research & Analytical Science, Utrecht, The Netherlands
| | - Ankur Naqib
- Sequencing Core, Research Resources Center,University of Illinois at Chicago, Chicago, IL USA
| | - Stefan J Green
- Sequencing Core, Research Resources Center,University of Illinois at Chicago, Chicago, IL USA,Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL USA
| | - Ali Keshavarzian
- Utrecht University, Faculty of Science, Department of Pharmaceutical Sciences, Division of Pharmacology, Utrecht, The Netherlands,Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL USA,Department of Pharmacology, Division of Physiology, Rush University Medical Center, Chicago, IL USA
| | - Gert Folkerts
- Utrecht University, Faculty of Science, Department of Pharmaceutical Sciences, Division of Pharmacology, Utrecht, The Netherlands
| | - Belinda van't Land
- Danone Nutricia Research, Departments of Immunology/Human Milk Research & Analytical Science, Utrecht, The Netherlands,University Medical Center Utrecht, The Wilhelmina Children's Hospital, Laboratory of Translational Immunology, Utrecht, The Netherlands,Address correspondence to BL (e-mail: )
| |
Collapse
|
68
|
Campen R, Kowalski J, Lyons WB, Tulaczyk S, Dachwald B, Pettit E, Welch KA, Mikucki JA. Microbial diversity of an Antarctic subglacial community and high-resolution replicate sampling inform hydrological connectivity in a polar desert. Environ Microbiol 2019; 21:2290-2306. [PMID: 30927377 DOI: 10.1111/1462-2920.14607] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 11/30/2022]
Abstract
Antarctic subglacial environments host microbial ecosystems and are proving to be geochemically and biologically diverse. The Taylor Glacier, Antarctica, periodically expels iron-rich brine through a conduit sourced from a deep subglacial aquifer, creating a dramatic red surface feature known as Blood Falls. We used Illumina MiSeq sequencing to describe the core microbiome of this subglacial brine and identified previously undetected but abundant groups including the candidate bacterial phylum Atribacteria and archaeal phylum Pacearchaeota. Our work represents the first microbial characterization of samples collected from within a glacier using a melt probe, and the only Antarctic subglacial aquatic environment that, to date, has been sampled twice. A comparative analysis showed the brine community to be stable at the operational taxonomic unit level of 99% identity over a decade. Higher resolution sequencing enabled deconvolution of the microbiome of subglacial brine from mixtures of materials collected at the glacier surface. Diversity patterns between this brine and samples from the surrounding landscape provide insight into the hydrological connectivity of subglacial fluids to the surface polar desert environment. Understanding subice brines collected on the surfaces of thick ice covers has implications for analyses of expelled materials that may be sampled on icy extraterrestrial worlds.
Collapse
Affiliation(s)
- Richard Campen
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | | | | | - Slawek Tulaczyk
- University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Bernd Dachwald
- Faculty of Aerospace Engineering, FH Aachen University of Applied Sciences, Aachen, Germany
| | - Erin Pettit
- College of Earth, Ocean, and Atmospheric Science, Oregon State University, Corvallis, OR, 97331, USA
| | | | - Jill A Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| |
Collapse
|
69
|
Goglio A, Marzorati S, Rago L, Pant D, Cristiani P, Schievano A. Microbial recycling cells: First steps into a new type of microbial electrochemical technologies, aimed at recovering nutrients from wastewater. BIORESOURCE TECHNOLOGY 2019; 277:117-127. [PMID: 30660962 DOI: 10.1016/j.biortech.2019.01.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
The aim of this work were to study terracotta-based porous air-water separators (4 mm thickness) in microbial recycling cells (MRCs) fed with cow manure (CM), swine manure (SM) and dairy wastewater (DW). Over 125 days, besides the removal of 60-90% of soluble-COD, considerable fractions of the main macronutrients (C, N, P, K, Fe, Mn, Ca, Mg) were removed from the wastewater and deposited on the terracotta separators as both inorganic salts and biomass deposits. Water evaporation at air-water interface as well as the high cathodic pH (10-12), induced by oxygen reduction to OH-, were the predominant factors leading to precipitation. The separators were saturated of up to 10 g per kg of terracotta of the main macronutrients, with negligible concentrations of the main inorganic contaminants. These materials could be directly reused as nutrients-enriched solid conditioners for agricultural soils.
Collapse
Affiliation(s)
- Andrea Goglio
- e-Bio Center, Department of Environmental Science and Policy, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Stefania Marzorati
- e-Bio Center, Department of Environmental Science and Policy, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Laura Rago
- e-Bio Center, Department of Environmental Science and Policy, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Deepak Pant
- Separation & Conversion Technology, Flemish Institute for Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium
| | - Pierangela Cristiani
- Ricerca del Sistema Energetico, Via Rubattino 54, 20134 Milano, Italy; e-Bio Center, Department of Environmental Science and Policy, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Andrea Schievano
- e-Bio Center, Department of Environmental Science and Policy, University of Milan, Via Celoria 2, 20133 Milan, Italy.
| |
Collapse
|
70
|
Cohen Y, Pasternak Z, Johnke J, Abed‐Rabbo A, Kushmaro A, Chatzinotas A, Jurkevitch E. Bacteria and microeukaryotes are differentially segregated in sympatric wastewater microhabitats. Environ Microbiol 2019; 21:1757-1770. [DOI: 10.1111/1462-2920.14548] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 01/20/2019] [Accepted: 01/28/2019] [Indexed: 01/22/2023]
Affiliation(s)
- Yossi Cohen
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem Rehovot, 76100 Israel
| | - Zohar Pasternak
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem Rehovot, 76100 Israel
| | - Julia Johnke
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research – UFZ Permoserstrasse 15, Leipzig, 04318 Germany
| | - Alfred Abed‐Rabbo
- Faculty of ScienceBethlehem University, Palestinian National Authority, Bethlehem, Israel
| | - Ariel Kushmaro
- Avram and Stella Goldstein‐Goren, The Department of Biotechnology Engineering, Faculty of Engineering SciencesBen‐Gurion University of the Negev P.O. Box 653, Beer‐Sheva Israel
- The Ilse Katz Centre for Meso and Nanoscale Science and TechnologyBen‐Gurion University of the Negev Beer‐Sheva Israel
| | - Antonis Chatzinotas
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research – UFZ Permoserstrasse 15, Leipzig, 04318 Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Deutscher Platz 5e, Leipzig, 04103 Germany
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and EnvironmentThe Hebrew University of Jerusalem Rehovot, 76100 Israel
| |
Collapse
|
71
|
Zolti A, Green SJ, Ben Mordechay E, Hadar Y, Minz D. Root microbiome response to treated wastewater irrigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 655:899-907. [PMID: 30481716 DOI: 10.1016/j.scitotenv.2018.11.251] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/12/2018] [Accepted: 11/17/2018] [Indexed: 06/09/2023]
Abstract
With increasing fresh water (FW) scarcity, the use of treated wastewater (TWW) for crop irrigation is expanding globally. Besides clear benefits, some undesired long-term effects of irrigation with this low quality water on plant performance have been reported. As the rhizosphere microbiome can mediate plant-soil interactions, an examination of the response of these organisms to TWW is necessary to understand the full effects of water quality. In the current study, the effects of irrigation water quality on the microbial community structure of soil and roots as well as edaphic properties and plant performance were evaluated. We compared soil and roots microbiomes of two different plant species (tomato and lettuce), each grown in two distinct soils, and irrigated with either FW or TWW. Irrigation with TWW significantly increase soil pH, EC, K, Na and DOC, and decrease plant fruit and shoot weight, relatively to samples irrigated with FW. We calculated the effect size of plant species, soil type, and irrigation water quality on microbial community structure in soil and root. In the roots, plant species and irrigation water were the dominant factors in shaping both total (DNA based) and active (RNA based) microbial communities, with both factors contributing similarly to the observed microbial population. Soil type and irrigation water were the dominant factors shaping the total microbial community in the soil and were of similar magnitude. Irrigation water quality is demonstrated to be a major force in shaping root-associated microbiome, leading to altered microbial community structure in the critical juncture between plant and soil.
Collapse
Affiliation(s)
- Avihai Zolti
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization - Volcani Center, Rishon Lezion 7528809, Israel; Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Stefan J Green
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Evyatar Ben Mordechay
- Department of Soil and Water Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization - Volcani Center, Rishon Lezion 7528809, Israel.
| |
Collapse
|
72
|
Naqib A, Jeon T, Kunstman K, Wang W, Shen Y, Sweeney D, Hyde M, Green SJ. PCR effects of melting temperature adjustment of individual primers in degenerate primer pools. PeerJ 2019; 7:e6570. [PMID: 30863685 PMCID: PMC6404654 DOI: 10.7717/peerj.6570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/05/2019] [Indexed: 01/07/2023] Open
Abstract
Deep sequencing of small subunit ribosomal RNA (SSU rRNA) gene amplicons continues to be the most common approach for characterization of complex microbial communities. PCR amplifications of conserved regions of SSU rRNA genes often employ degenerate pools of primers to enable targeting of a broad spectrum of organisms. One little noticed feature of such degenerate primer sets is the potential for a wide range of melting temperatures between the primer variants. The melting temperature variation of primers in a degenerate pool could lead to variable amplification efficiencies and PCR bias. Thus, we sought to adjust the melting temperature of each primer variant individually. Individual primer modifications were used to reduce theoretical melting temperature variation between primers, as well as to introduce inter-cluster nucleotide diversity during Illumina sequencing of primer regions. We demonstrate here the suitability of such primers for microbial community analysis. However, no substantial differences in microbial community structure were revealed when using primers with adjusted melting temperatures, though the optimal annealing temperature decreased.
Collapse
Affiliation(s)
- Ankur Naqib
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Trisha Jeon
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Kevin Kunstman
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Weihua Wang
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Yiding Shen
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Dagmar Sweeney
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Marieta Hyde
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Stefan J Green
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States of America
| |
Collapse
|
73
|
Rago L, Zecchin S, Villa F, Goglio A, Corsini A, Cavalca L, Schievano A. Bioelectrochemical Nitrogen fixation (e-BNF): Electro-stimulation of enriched biofilm communities drives autotrophic nitrogen and carbon fixation. Bioelectrochemistry 2019; 125:105-115. [DOI: 10.1016/j.bioelechem.2018.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 10/28/2022]
|
74
|
Rennstam Rubbmark O, Sint D, Horngacher N, Traugott M. A broadly applicable COI primer pair and an efficient single-tube amplicon library preparation protocol for metabarcoding. Ecol Evol 2018; 8:12335-12350. [PMID: 30619549 PMCID: PMC6308894 DOI: 10.1002/ece3.4520] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/06/2018] [Accepted: 06/10/2018] [Indexed: 12/25/2022] Open
Abstract
The nucleotide variation in the cytochrome c oxidase subunit I (COI) gene makes it ideal for assigning sequences to species. However, this variability also makes it difficult to design truly universal primers. Here, we present the forward primer "Sauron-S878," specifically designed to facilitate library preparation for metabarcoding. This primer is modified to improve the coverage of terrestrial species compared to the primer mCOIintF, optimized for aquatic systems, which raised the in silico coverage from 74.4% to 98.3% of available NCBI sequences (perfect match in 3' region, up to three mismatches in remaining primer). When paired with the reverse primer "jgHCO2198" (fragment length ~313 bp), these primers amplified 98.4% of 255 tested DNA extracts from various taxa, which are better than many other common COI barcoding primers. Furthermore, a single-tube protocol was developed, wherein these primers amplify the target gene, and attach MIDs and Illumina sequencing adapters in one reaction. This eliminates the need for re-amplification or enzymatic ligation during library preparation while keeping the flexibility to modularly combine primers and MIDs. Using the single-tube approach, three replicates of three mock samples were sequenced on a MiSeq platform with no adverse effects compared to commercial Nextera indexing kits. From this run, 75% of all included taxa could be recovered, with no considerable bias among taxonomic groups. Despite the fact that 98.4% of the extracts were confirmed to amplify in vitro, this number was lower than expected. A reason for this discrepancy was a clear link between the relative concentration of a specific DNA type in the template and the number of returned reads for this DNA. We would argue that such a bias may be especially problematic in metabarcoding where samples usually contain trace DNA in unknown amounts. However, how this affects the completeness of metabarcoding results has yet been poorly investigated.
Collapse
Affiliation(s)
- Oskar Rennstam Rubbmark
- Mountain Agriculture Research UnitInstitute of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Daniela Sint
- Mountain Agriculture Research UnitInstitute of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Nina Horngacher
- Mountain Agriculture Research UnitInstitute of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Michael Traugott
- Mountain Agriculture Research UnitInstitute of EcologyUniversity of InnsbruckInnsbruckAustria
| |
Collapse
|
75
|
Behdad A, Zhou XY, Gao J, Raparia K, Dittman D, Green SJ, Qi C, Betz B, Bryar P, Chen Q, Chen YH. High Frequency of MYD88 L265P Mutation in Primary Ocular Adnexal Marginal Zone Lymphoma and Its Clinicopathologic Correlation: A Study From a Single Institution. Arch Pathol Lab Med 2018; 143:483-493. [PMID: 30444439 DOI: 10.5858/arpa.2018-0092-oa] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The pathogenesis of primary ocular adnexal marginal zone lymphoma (POAMZL) remains unclear. The reported associations with Chlamydia psittaci infection and MYD88 mutations are highly variable. OBJECTIVE.— To examine MYD88 L265P mutation in ocular marginal zone lymphomas and correlate with clinicopathologic features and Chlamydia infection. DESIGN.— Presence of MYD88 L265P mutation and Chlamydia infection in lymphoma was analyzed by using sensitive polymerase chain reaction (PCR) methods. RESULTS.— The MYD88 L265P mutation was identified in 8 of 22 POAMZLs (36%), including 2 of 3 cases in which PCR failed to detect clonal IGH gene rearrangement; none of the 4 secondary marginal zone lymphomas were positive. Test results for Chlamydia were negative in all cases. Patients with and without the MYD88 mutation had similar clinicopathologic features. CONCLUSIONS.— The MYD88 mutational analysis provides important information in diagnostic workup of POAMZL. The frequent MYD88 mutation suggests a critical role of this aberration in the pathogenesis of POAMZL and may serve as a therapeutic target for patients with progressive disease.
Collapse
Affiliation(s)
- Amir Behdad
- From the Departments of Pathology (Drs Behdad, Gao, and Raparia; Mr Dittman; Drs Qi, Q Chen, and Y-H Chen) and Ophthalmology (Dr Bryar), Northwestern Memorial Hospital, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Wayne State University School of Medicine, Detroit, Michigan (Dr Zhou); Research Resources Center, University of Illinois at Chicago, Chicago (Dr Green); Department of Pathology, University of Michigan, Ann Arbor (Dr Betz). Dr Zhou is currently at the Department of Ophthalmology, Bascom-Palmer Eye Institute, Miami, Florida. Dr Raparia is currently at the Department of Pathology, Kaiser Permanente, Santa Clara, California
| | - Xiao Yi Zhou
- From the Departments of Pathology (Drs Behdad, Gao, and Raparia; Mr Dittman; Drs Qi, Q Chen, and Y-H Chen) and Ophthalmology (Dr Bryar), Northwestern Memorial Hospital, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Wayne State University School of Medicine, Detroit, Michigan (Dr Zhou); Research Resources Center, University of Illinois at Chicago, Chicago (Dr Green); Department of Pathology, University of Michigan, Ann Arbor (Dr Betz). Dr Zhou is currently at the Department of Ophthalmology, Bascom-Palmer Eye Institute, Miami, Florida. Dr Raparia is currently at the Department of Pathology, Kaiser Permanente, Santa Clara, California
| | - Juehua Gao
- From the Departments of Pathology (Drs Behdad, Gao, and Raparia; Mr Dittman; Drs Qi, Q Chen, and Y-H Chen) and Ophthalmology (Dr Bryar), Northwestern Memorial Hospital, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Wayne State University School of Medicine, Detroit, Michigan (Dr Zhou); Research Resources Center, University of Illinois at Chicago, Chicago (Dr Green); Department of Pathology, University of Michigan, Ann Arbor (Dr Betz). Dr Zhou is currently at the Department of Ophthalmology, Bascom-Palmer Eye Institute, Miami, Florida. Dr Raparia is currently at the Department of Pathology, Kaiser Permanente, Santa Clara, California
| | - Kirtee Raparia
- From the Departments of Pathology (Drs Behdad, Gao, and Raparia; Mr Dittman; Drs Qi, Q Chen, and Y-H Chen) and Ophthalmology (Dr Bryar), Northwestern Memorial Hospital, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Wayne State University School of Medicine, Detroit, Michigan (Dr Zhou); Research Resources Center, University of Illinois at Chicago, Chicago (Dr Green); Department of Pathology, University of Michigan, Ann Arbor (Dr Betz). Dr Zhou is currently at the Department of Ophthalmology, Bascom-Palmer Eye Institute, Miami, Florida. Dr Raparia is currently at the Department of Pathology, Kaiser Permanente, Santa Clara, California
| | - David Dittman
- From the Departments of Pathology (Drs Behdad, Gao, and Raparia; Mr Dittman; Drs Qi, Q Chen, and Y-H Chen) and Ophthalmology (Dr Bryar), Northwestern Memorial Hospital, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Wayne State University School of Medicine, Detroit, Michigan (Dr Zhou); Research Resources Center, University of Illinois at Chicago, Chicago (Dr Green); Department of Pathology, University of Michigan, Ann Arbor (Dr Betz). Dr Zhou is currently at the Department of Ophthalmology, Bascom-Palmer Eye Institute, Miami, Florida. Dr Raparia is currently at the Department of Pathology, Kaiser Permanente, Santa Clara, California
| | - Stefan J Green
- From the Departments of Pathology (Drs Behdad, Gao, and Raparia; Mr Dittman; Drs Qi, Q Chen, and Y-H Chen) and Ophthalmology (Dr Bryar), Northwestern Memorial Hospital, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Wayne State University School of Medicine, Detroit, Michigan (Dr Zhou); Research Resources Center, University of Illinois at Chicago, Chicago (Dr Green); Department of Pathology, University of Michigan, Ann Arbor (Dr Betz). Dr Zhou is currently at the Department of Ophthalmology, Bascom-Palmer Eye Institute, Miami, Florida. Dr Raparia is currently at the Department of Pathology, Kaiser Permanente, Santa Clara, California
| | - Chao Qi
- From the Departments of Pathology (Drs Behdad, Gao, and Raparia; Mr Dittman; Drs Qi, Q Chen, and Y-H Chen) and Ophthalmology (Dr Bryar), Northwestern Memorial Hospital, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Wayne State University School of Medicine, Detroit, Michigan (Dr Zhou); Research Resources Center, University of Illinois at Chicago, Chicago (Dr Green); Department of Pathology, University of Michigan, Ann Arbor (Dr Betz). Dr Zhou is currently at the Department of Ophthalmology, Bascom-Palmer Eye Institute, Miami, Florida. Dr Raparia is currently at the Department of Pathology, Kaiser Permanente, Santa Clara, California
| | - Bryan Betz
- From the Departments of Pathology (Drs Behdad, Gao, and Raparia; Mr Dittman; Drs Qi, Q Chen, and Y-H Chen) and Ophthalmology (Dr Bryar), Northwestern Memorial Hospital, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Wayne State University School of Medicine, Detroit, Michigan (Dr Zhou); Research Resources Center, University of Illinois at Chicago, Chicago (Dr Green); Department of Pathology, University of Michigan, Ann Arbor (Dr Betz). Dr Zhou is currently at the Department of Ophthalmology, Bascom-Palmer Eye Institute, Miami, Florida. Dr Raparia is currently at the Department of Pathology, Kaiser Permanente, Santa Clara, California
| | - Paul Bryar
- From the Departments of Pathology (Drs Behdad, Gao, and Raparia; Mr Dittman; Drs Qi, Q Chen, and Y-H Chen) and Ophthalmology (Dr Bryar), Northwestern Memorial Hospital, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Wayne State University School of Medicine, Detroit, Michigan (Dr Zhou); Research Resources Center, University of Illinois at Chicago, Chicago (Dr Green); Department of Pathology, University of Michigan, Ann Arbor (Dr Betz). Dr Zhou is currently at the Department of Ophthalmology, Bascom-Palmer Eye Institute, Miami, Florida. Dr Raparia is currently at the Department of Pathology, Kaiser Permanente, Santa Clara, California
| | - Qing Chen
- From the Departments of Pathology (Drs Behdad, Gao, and Raparia; Mr Dittman; Drs Qi, Q Chen, and Y-H Chen) and Ophthalmology (Dr Bryar), Northwestern Memorial Hospital, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Wayne State University School of Medicine, Detroit, Michigan (Dr Zhou); Research Resources Center, University of Illinois at Chicago, Chicago (Dr Green); Department of Pathology, University of Michigan, Ann Arbor (Dr Betz). Dr Zhou is currently at the Department of Ophthalmology, Bascom-Palmer Eye Institute, Miami, Florida. Dr Raparia is currently at the Department of Pathology, Kaiser Permanente, Santa Clara, California
| | - Yi-Hua Chen
- From the Departments of Pathology (Drs Behdad, Gao, and Raparia; Mr Dittman; Drs Qi, Q Chen, and Y-H Chen) and Ophthalmology (Dr Bryar), Northwestern Memorial Hospital, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Wayne State University School of Medicine, Detroit, Michigan (Dr Zhou); Research Resources Center, University of Illinois at Chicago, Chicago (Dr Green); Department of Pathology, University of Michigan, Ann Arbor (Dr Betz). Dr Zhou is currently at the Department of Ophthalmology, Bascom-Palmer Eye Institute, Miami, Florida. Dr Raparia is currently at the Department of Pathology, Kaiser Permanente, Santa Clara, California
| |
Collapse
|
76
|
Habtom H, Pasternak Z, Matan O, Azulay C, Gafny R, Jurkevitch E. Applying microbial biogeography in soil forensics. Forensic Sci Int Genet 2018; 38:195-203. [PMID: 30447564 DOI: 10.1016/j.fsigen.2018.11.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 10/10/2018] [Accepted: 11/07/2018] [Indexed: 11/28/2022]
Abstract
The ubiquity, heterogeneity and transferability of soil makes it useful as evidence in criminal investigations, especially using new methods that survey the microbial DNA it contains. However, to be used effectively and reliably, more needs to be learned about the natural distribution patterns of microbial communities in soil. In this study we examine these patterns in detail, at local to regional scales (2 m-260 km), across an environmental gradient in three different soil types. Geographic location was found to be more important than soil type in determining the microbial community composition: communities from the same site but different soil types, although significantly different from each other, were still much more similar to each other than were communities from the same soil type but from different sites. At a local scale (25-1000 m), distance-decay relationships were observed in all soil types: the farther apart two soil communities were located, even in the same soil type, the more they differed. At regional-scale distances (1-260 km), differences between communities did not increase with increased geographic distance between them, and the dominant factor determining the community profile was the physico-chemical environment, most notably annual precipitation (R2 = 0.69), soil sodium (R2 = 0.49) and soil ammonium (R2 = 0.47) levels. We introduce a likelihood-ratio framework for quantitative evaluation of soil microbial DNA profile evidence in casework. In conclusion, these profiles, along with detailed knowledge of natural soil microbial biogeography, provide valuable forensic information on soil sample comparison and allow the determination of approximate source location on large (hundreds of km) spatial scales. Moreover, at small spatial scales it may enable pinpointing the source location of a sample to within at least 25 m, regardless of soil type and environmental conditions.
Collapse
Affiliation(s)
- Habteab Habtom
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zohar Pasternak
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Ofra Matan
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Chen Azulay
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ron Gafny
- Forensic Biology Laboratory, Division of Identification and Forensic Science, Israel Police, National Headquarters, Haim Bar-Lev Road, Jerusalem, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| |
Collapse
|
77
|
Maki KA, Diallo AF, Lockwood MB, Franks AT, Green SJ, Joseph PV. Considerations When Designing a Microbiome Study: Implications for Nursing Science. Biol Res Nurs 2018; 21:125-141. [PMID: 30409024 DOI: 10.1177/1099800418811639] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nurse scientists play an important role in studying complex relationships among human genetics, environmental factors, and the microbiome, all of which can contribute to human health and disease. Therefore, it is essential that they have the tools necessary to execute a successful microbiome research study. The purpose of this article is to highlight important methodological factors for nurse scientists to consider when designing a microbiome study. In addition to considering factors that influence host-associated microbiomes (i.e., microorganisms associated with organisms such as humans, mice, and rats), this manuscript highlights study designs and methods for microbiome analysis. Exemplars are presented from nurse scientists who have incorporated microbiome methods into their program of research. This review is intended to be a resource to guide nursing-focused microbiome research and highlights how study of the microbiome can be incorporated to answer research questions.
Collapse
Affiliation(s)
- Katherine A Maki
- 1 Department of Biobehavioral Health Science, College of Nursing, University of Illinois at Chicago, Chicago, IL, USA
| | - Ana F Diallo
- 2 Institute of Inclusion, Inquiry and Innovation, Richmond Health and Wellness Clinics, Virginia Commonwealth University School of Nursing, Richmond, VA, USA
| | - Mark B Lockwood
- 1 Department of Biobehavioral Health Science, College of Nursing, University of Illinois at Chicago, Chicago, IL, USA
| | - Alexis T Franks
- 3 Sensory Science and Metabolism Unit, Biobehavioral Branch, Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Stefan J Green
- 4 Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Paule V Joseph
- 3 Sensory Science and Metabolism Unit, Biobehavioral Branch, Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| |
Collapse
|
78
|
Cornejo-Castillo FM, Muñoz-Marín MDC, Turk-Kubo KA, Royo-Llonch M, Farnelid H, Acinas SG, Zehr JP. UCYN-A3, a newly characterized open ocean sublineage of the symbiotic N 2 -fixing cyanobacterium Candidatus Atelocyanobacterium thalassa. Environ Microbiol 2018; 21:111-124. [PMID: 30255541 DOI: 10.1111/1462-2920.14429] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 09/06/2018] [Accepted: 09/22/2018] [Indexed: 12/01/2022]
Abstract
The symbiotic unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is one of the most abundant and widespread nitrogen (N2 )-fixing cyanobacteria in the ocean. Although it remains uncultivated, multiple sublineages have been detected based on partial nitrogenase (nifH) gene sequences, including the four most commonly detected sublineages UCYN-A1, UCYN-A2, UCYN-A3 and UCYN-A4. However, very little is known about UCYN-A3 beyond the nifH sequences from nifH gene diversity surveys. In this study, single cell sorting, DNA sequencing, qPCR and CARD-FISH assays revealed discrepancies involving the identification of sublineages, which led to new information on the diversity of the UCYN-A symbiosis. 16S rRNA and nifH gene sequencing on single sorted cells allowed us to identify the 16S rRNA gene of the uncharacterized UCYN-A3 sublineage. We designed new CARD-FISH probes that allowed us to distinguish and observe UCYN-A2 in a coastal location (SIO Pier; San Diego) and UCYN-A3 in an open ocean location (Station ALOHA; Hawaii). Moreover, we reconstructed about 13% of the UCYN-A3 genome from Tara Oceans metagenomic data. Finally, our findings unveil the UCYN-A3 symbiosis in open ocean waters suggesting that the different UCYN-A sublineages are distributed along different size fractions of the plankton defined by the cell-size ranges of their prymnesiophyte hosts.
Collapse
Affiliation(s)
- Francisco M Cornejo-Castillo
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.,Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Maria Del Carmen Muñoz-Marín
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.,Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - Kendra A Turk-Kubo
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Hanna Farnelid
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.,Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
| |
Collapse
|
79
|
Xu Z, Te SH, He Y, Gin KYH. The Characteristics and Dynamics of Cyanobacteria-Heterotrophic Bacteria Between Two Estuarine Reservoirs - Tropical Versus Sub-Tropical Regions. Front Microbiol 2018; 9:2531. [PMID: 30459732 PMCID: PMC6232297 DOI: 10.3389/fmicb.2018.02531] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 10/03/2018] [Indexed: 12/20/2022] Open
Abstract
In this study, Illumina MiSeq sequencing technique was employed to explore the characteristics and dynamics of cyanobacteria–heterotrophic bacteria between two estuarine reservoirs in sub-tropical (reservoir A in Shanghai) and tropical (reservoir B in Singapore) regions. The results indicated that significant differences in bacterial community composition were found between two estuarine reservoirs, which influenced by varied environmental variables. The environmental heterogeneity in reservoir A was much higher, which indicated that the composition of bacterial community in reservoir A was more complex. In contrast, reservoir B provided a suitable and temperate water environment conditions for bacterial growth, which resulted in higher community diversity and less co-exclusion correlations. The molecular ecological network indicated that the presence of dominant bacterial community in each of the reservoir were significant different. These differences mainly reflected the responses of bacterial community to the variations of environmental variables. Although Synechococcus was the dominant cyanobacterial species in both reservoirs, it exhibited co-occurrence patterns with different heterotrophic bacteria between reservoirs. In addition, the cyanobacteria–heterotrophic bacteria interaction exhibited highly dynamic variations, which was affected by nutrition and survive space. Also, the co-occurrence of Microcystis and Pseudanabaena found in reservoir B implied that the non-N-fixing Microcystis accompanied with N-fixing Pseudanabeana occurrence in freshwater lakes, so as to better meet the demand for nitrogen source.
Collapse
Affiliation(s)
- Zheng Xu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Shu Harn Te
- NUS Environmental Research Institute (NERI), National University of Singapore, Singapore, Singapore
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute (NERI), National University of Singapore, Singapore, Singapore.,Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
| |
Collapse
|
80
|
Robidart JC, Magasin JD, Shilova IN, Turk-Kubo KA, Wilson ST, Karl DM, Scholin CA, Zehr JP. Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre. ISME JOURNAL 2018; 13:374-387. [PMID: 30254320 DOI: 10.1038/s41396-018-0280-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/26/2018] [Accepted: 08/26/2018] [Indexed: 11/09/2022]
Abstract
Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity in the surface ocean is constrained by nutrients which are supplied, in part, by mixing with deeper water. Little is known about the time scales, frequency, or impact of mixing on microbial communities. We combined in situ sampling using the Environmental Sample Processor and a small-scale mixing experiment with lower euphotic zone water to determine how individual populations respond to mixing. Transcriptional responses were measured using the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) microarray, which targets all three domains of life and viruses. The experiment showed that mixing substantially affects photosynthetic taxa as expected, but surprisingly also showed that populations respond differently to unfiltered deep water which contains particles (organisms and detritus) compared to filtered deep water that only contains nutrients and viruses, pointing to the impact of biological interactions associated with these events. Comparison between experimental and in situ population transcription patterns indicated that manipulated populations can serve as analogs for natural populations, and that natural populations may be frequently or continuously responding to nutrients from deeper waters. Finally, this study also shows that the microarray approach, which is complementary to metatranscriptomic sequencing, is useful for determining the physiological status of in situ microbial communities.
Collapse
Affiliation(s)
- J C Robidart
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.,National Oceanography Centre, Southampton, UK
| | - J D Magasin
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - I N Shilova
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.,Second Genome, South San Francisco, CA, USA
| | - K A Turk-Kubo
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - S T Wilson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - D M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - C A Scholin
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - J P Zehr
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.
| |
Collapse
|
81
|
Elfeki M, Alanjary M, Green SJ, Ziemert N, Murphy BT. Assessing the Efficiency of Cultivation Techniques To Recover Natural Product Biosynthetic Gene Populations from Sediment. ACS Chem Biol 2018; 13:2074-2081. [PMID: 29932624 DOI: 10.1021/acschembio.8b00254] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Despite decades of cultivating microorganisms for use in drug discovery, few attempts have been made to measure the extent to which common cultivation techniques have accessed existing chemical space. Metagenomic studies have shown that cultivable bacteria represent a fraction of those that exist in the environment, and that uncultivated populations in sediment have genes that encode for a high diversity of novel natural product (NP) biosynthetic enzymes. Quantifying these genes in both sediment and cultivatable bacterial populations allows us to assess how much diversity is present on nutrient agar and is critical to guiding the trajectory of future NP discovery platforms. Herein, we employed next-generation amplicon sequencing to assess the NP biosynthetic gene populations present in two Lake Huron sediment samples, and compared these with populations from their corresponding cultivatable bacteria. We highlight three findings from our study: (1) after cultivation, we recovered between 7.7% and 23% of three common types of NP biosynthetic genes from the original sediment population; (2) between 76.3% and 91.5% of measured NP biosynthetic genes from nutrient agar have yet to be characterized in known biosynthetic gene cluster databases, indicating that readily cultivatable bacteria harbor the potential to produce new NPs; and (3) even though the predominant taxa present on nutrient media represented some of the major producers of bacterial NPs, the sediment harbored a significantly greater pool of NP biosynthetic genes that could be mined for structural novelty, and these likely belong to taxa that typically have not been represented in microbial drug discovery libraries.
Collapse
Affiliation(s)
| | - Mohammad Alanjary
- German Centre for Infection Research (DZIF), Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | | | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | | |
Collapse
|
82
|
Farnelid H, Turk-Kubo K, Ploug H, Ossolinski JE, Collins JR, Van Mooy BAS, Zehr JP. Diverse diazotrophs are present on sinking particles in the North Pacific Subtropical Gyre. ISME JOURNAL 2018; 13:170-182. [PMID: 30116043 PMCID: PMC6299005 DOI: 10.1038/s41396-018-0259-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/03/2018] [Accepted: 07/26/2018] [Indexed: 11/09/2022]
Abstract
Sinking particles transport carbon and nutrients from the surface ocean into the deep sea and are considered hot spots for bacterial diversity and activity. In the oligotrophic oceans, nitrogen (N2)-fixing organisms (diazotrophs) are an important source of new N but the extent to which these organisms are present and exported on sinking particles is not well known. Sinking particles were collected every 6 h over a 2-day period using net traps deployed at 150 m in the North Pacific Subtropical Gyre. The bacterial community and composition of diazotrophs associated with individual and bulk sinking particles was assessed using 16S rRNA and nifH gene amplicon sequencing. The bacterial community composition in bulk particles remained remarkably consistent throughout time and space while large variations of individually picked particles were observed. This difference suggests that unique biogeochemical conditions within individual particles may offer distinct ecological niches for specialized bacterial taxa. Compared to surrounding seawater, particle samples were enriched in different size classes of globally significant N2-fixing cyanobacteria including Trichodesmium, symbionts of diatoms, and the unicellular cyanobacteria Crocosphaera and UCYN-A. The particles also contained nifH gene sequences of diverse non-cyanobacterial diazotrophs suggesting that particles could be loci for N2 fixation by heterotrophic bacteria. The results demonstrate that diverse diazotrophs were present on particles and that new N may thereby be directly exported from surface waters on sinking particles.
Collapse
Affiliation(s)
- Hanna Farnelid
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA. .,Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
| | - Kendra Turk-Kubo
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Helle Ploug
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Justin E Ossolinski
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - James R Collins
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.,MIT/WHOI Joint Program in Oceanography, University of Washington, Seattle, WA, USA.,School of Oceanography and eScience Institute, University of Washington, Seattle, WA, USA
| | - Benjamin A S Van Mooy
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California at Santa Cruz, Santa Cruz, CA, USA
| |
Collapse
|
83
|
Sicsic R, Goshen T, Dutta R, Kedem-Vaanunu N, Kaplan-Shabtai V, Pasternak Z, Gottlieb Y, Shpigel NY, Raz T. Microbial communities and inflammatory response in the endometrium differ between normal and metritic dairy cows at 5-10 days post-partum. Vet Res 2018; 49:77. [PMID: 30068391 PMCID: PMC6071394 DOI: 10.1186/s13567-018-0570-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/16/2018] [Indexed: 01/06/2023] Open
Abstract
Post-partum metritis is among the most prevalent disease in dairy cows affecting animal welfare and inflicting considerable economic loses. While post-partum contamination of the uterus is rife in dairy cows, only a fraction of these animals will develop metritis. Our main objective was to compare the bacterial communities and the inflammatory response in the endometrium of healthy and metritic dairy cows. Holstein-Friesian cows (n = 35) were sampled immediately following clinical classification as healthy (n = 21), suffering from metritis (n = 13) or septic metritis (n = 1), based on veterinary examination at 5-10 days post-partum. Polymorphonuclear cells (PMN) percentage in endometrial cytology was significantly higher in cows with metritis. Full-thickness uterine biopsy analysis revealed that the luminal epithelium in inter-caruncle areas was preserved in healthy cows, but in metritis it was compromised, with marked PMN infiltration particularly in the apical endometrium. Gram staining revealed that bacterial load and spatial distribution was associated with disease severity. 16S-rDNA bacterial community analysis revealed unique endometrial bacterial community composition in metritic cows, as compared to more diverse communities among healthy cows. The most abundant phyla in healthy cows were Proteobacteria (31.8 ± 9.3%), Firmicutes (27.9 ± 8.4%) and Bacteroidetes (19.7 ± 7.2%), while Bacteroidetes (60.3 ± 10.3%), Fusobacteria (13.4 ± 5.9%) and Firmicutes (10.5 ± 3.3%) were most abundant in the endometrial mucosa of metritic cows. Relative abundance of Bacteroidetes (19.7 ± 7.2% vs. 60.3 ± 10.3%), Fusobacteria (7.5 ± 5.2% vs. 13.4 ± 5.9%) and Proteobacteria (31.8 ± 9.3% vs. 7.3 ± 5.6%) phyla differed significantly between healthy and metritic cows. In summary, endometrial PMN abundance, spatial distribution and bacterial communities differed between healthy and metritic dairy cows at early post-partum.
Collapse
Affiliation(s)
- Ron Sicsic
- Koret School of Veterinary Medicine, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tamir Goshen
- Koret School of Veterinary Medicine, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- Hachaklait, Mutual Society for Veterinary Services, Caesarea Industrial Park, Caesarea, Israel
| | - Rahul Dutta
- Koret School of Veterinary Medicine, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Noa Kedem-Vaanunu
- Koret School of Veterinary Medicine, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Veronica Kaplan-Shabtai
- Koret School of Veterinary Medicine, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zohar Pasternak
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yuval Gottlieb
- Koret School of Veterinary Medicine, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Nahum Y. Shpigel
- Koret School of Veterinary Medicine, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tal Raz
- Koret School of Veterinary Medicine, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| |
Collapse
|
84
|
Turk-Kubo KA, Connell P, Caron D, Hogan ME, Farnelid HM, Zehr JP. In Situ Diazotroph Population Dynamics Under Different Resource Ratios in the North Pacific Subtropical Gyre. Front Microbiol 2018; 9:1616. [PMID: 30090092 PMCID: PMC6068237 DOI: 10.3389/fmicb.2018.01616] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/28/2018] [Indexed: 11/13/2022] Open
Abstract
Major advances in understanding the diversity, distribution, and activity of marine N2-fixing microorganisms (diazotrophs) have been made in the past decades, however, large gaps in knowledge remain about the environmental controls on growth and mortality rates. In order to measure diazotroph net growth rates and microzooplankton grazing rates on diazotrophs, nutrient perturbation experiments and dilution grazing experiments were conducted using free-floating in situ incubation arrays in the vicinity of Station ALOHA in March 2016. Net growth rates for targeted diazotroph taxa as well as Prochlorococcus, Synechococcus and photosynthetic picoeukaryotes were determined under high (H) and low (L) nitrate:phosphate (NP) ratio conditions at four depths in the photic zone (25, 45, 75, and 100 m) using quantitative PCR and flow cytometry. Changes in the prokaryote community composition in response to HNP and LNP treatments were characterized using 16S rRNA variable region tag sequencing. Microzooplankton grazing rates on diazotrophs were measured using a modified dilution technique at two depths in the photic zone (15 and 125 m). Net growth rates for most of the targeted diazotrophs after 48 h were not stimulated as expected by LNP conditions, rather enhanced growth rates were often measured in HNP treatments. Interestingly, net growth rates of the uncultivated prymnesiophyte symbiont UCYN-A1 were stimulated in HNP treatments at 75 and 100 m, suggesting that N used for growth was acquired through continuing to fix N2 in the presence of nitrate. Net growth rates for UCYN-A1, UCYN-C, Crocosphaera sp. (UCYN-B) and the diatom symbiont Richelia (associated with Rhizosolenia) were uniformly high at 45 m (up to 1.6 ± 0.5 d-1), implying that all were growing optimally at the onset of the experiment at that depth. Differences in microzooplankton grazing rates on UCYN-A1 and UCYN-C in 15 m waters indicate that the grazer assemblage preyed preferentially on UCYN-A1. Deeper in the water column (125 m), both diazotrophs were grazed at substantial rates, suggesting grazing pressure may increase with depth in the photic zone. Constraining in situ diazotroph growth and mortality rates are important steps for improving parameterization for diazotrophs in global ecosystem models.
Collapse
Affiliation(s)
- Kendra A. Turk-Kubo
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Paige Connell
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - David Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Mary E. Hogan
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Hanna M. Farnelid
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Jonathan P. Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
| |
Collapse
|
85
|
Mahdavinia M, Engen PA, LoSavio PS, Naqib A, Khan RJ, Tobin MC, Mehta A, Kota R, Preite NZ, Codispoti CD, Tajudeen BA, Schleimer RP, Green SJ, Keshavarzian A, Batra PS. The nasal microbiome in patients with chronic rhinosinusitis: Analyzing the effects of atopy and bacterial functional pathways in 111 patients. J Allergy Clin Immunol 2018; 142:287-290.e4. [PMID: 29452201 PMCID: PMC6890201 DOI: 10.1016/j.jaci.2018.01.033] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/30/2017] [Accepted: 01/24/2018] [Indexed: 10/18/2022]
Affiliation(s)
- Mahboobeh Mahdavinia
- Department of Internal Medicine, Allergy/Immunology Division, Rush University Medical Center, Chicago, Ill.
| | - Phillip A Engen
- Department of Internal Medicine, Division of Gastroenterology, Hepatology and Nutrition, Rush University Medical Center, Chicago, Ill
| | - Phillip S LoSavio
- Department of Otorhinolaryngology-Head and Neck Surgery and Rush Sinus Program, Rush University Medical Center, Chicago, Ill
| | - Ankur Naqib
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Ill
| | - Rafsa J Khan
- Department of Internal Medicine, Allergy/Immunology Division, Rush University Medical Center, Chicago, Ill
| | - Mary C Tobin
- Department of Internal Medicine, Allergy/Immunology Division, Rush University Medical Center, Chicago, Ill
| | - Arpita Mehta
- Department of Internal Medicine, Allergy/Immunology Division, Rush University Medical Center, Chicago, Ill
| | - Raj Kota
- Department of Internal Medicine, Allergy/Immunology Division, Rush University Medical Center, Chicago, Ill
| | - Nailliw Z Preite
- Department of Internal Medicine, Allergy/Immunology Division, Rush University Medical Center, Chicago, Ill; Department of Internal Medicine, Division of Gastroenterology, Hepatology and Nutrition, Rush University Medical Center, Chicago, Ill
| | - Christopher D Codispoti
- Department of Internal Medicine, Allergy/Immunology Division, Rush University Medical Center, Chicago, Ill
| | - Bobby A Tajudeen
- Department of Otorhinolaryngology-Head and Neck Surgery and Rush Sinus Program, Rush University Medical Center, Chicago, Ill
| | - Robert P Schleimer
- Division of Allergy and Immunology, Internal Medicine Department, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Stefan J Green
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Ill; Department of Biological Sciences, University of Illinois at Chicago, Chicago, Ill
| | - Ali Keshavarzian
- Department of Internal Medicine, Division of Gastroenterology, Hepatology and Nutrition, Rush University Medical Center, Chicago, Ill
| | - Pete S Batra
- Department of Otorhinolaryngology-Head and Neck Surgery and Rush Sinus Program, Rush University Medical Center, Chicago, Ill
| |
Collapse
|
86
|
Yang F, Ding F, Chen H, He M, Zhu S, Ma X, Jiang L, Li H. DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2018; 2018:5160254. [PMID: 29849709 PMCID: PMC5937547 DOI: 10.1155/2018/5160254] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/11/2018] [Indexed: 02/06/2023]
Abstract
Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.
Collapse
Affiliation(s)
- Fan Yang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Fei Ding
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Hong Chen
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Mingqi He
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Shixin Zhu
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Xin Ma
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Li Jiang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Haifeng Li
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| |
Collapse
|
87
|
Environmental Controls of Oyster-Pathogenic Vibrio spp. in Oregon Estuaries and a Shellfish Hatchery. Appl Environ Microbiol 2018; 84:AEM.02156-17. [PMID: 29475863 PMCID: PMC5930336 DOI: 10.1128/aem.02156-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/25/2018] [Indexed: 12/24/2022] Open
Abstract
Vibrio spp. have been a persistent concern for coastal bivalve hatcheries, which are vulnerable to environmental pathogens in the seawater used for rearing larvae, yet the biogeochemical drivers of oyster-pathogenic Vibrio spp. in their planktonic state are poorly understood. Here, we present data tracking oyster-pathogenic Vibrio bacteria in Netarts Bay and Yaquina Bay in Oregon, USA, as well as in adjacent coastal waters and a local shellfish hatchery, through the 2015 upwelling season. Vibrio populations were quantified using a culture-independent approach of high-throughput Vibrio-specific 16S rRNA gene sequencing paired with droplet digital PCR, and abundances were analyzed in the context of local biogeochemistry. The most abundant putative pathogen in our samples was Vibrio coralliilyticus. Environmental concentrations of total Vibrio spp. and V. coralliilyticus were highest in Netarts Bay sediment samples and higher in seawater from Netarts Bay than from nearshore coastal waters or Yaquina Bay. In Netarts Bay, the highest V. coralliilyticus concentrations were observed during low tide, and abundances increased throughout the summer. We hypothesize that the warm shallow waters in estuarine mudflats facilitate the local growth of the V. coralliilyticus pathogen. Samples from larval oyster tanks in Whiskey Creek Shellfish Hatchery, which uses seawater pumped directly from Netarts Bay, contained significantly lower total Vibrio species concentrations, but roughly similar V. coralliilyticus concentrations, than did the bay water, resulting in a 30-fold increase in the relative abundance of the V. coralliilyticus pathogen in hatchery tanks. This suggests that the V. coralliilyticus pathogen is able to grow or persist under hatchery conditions. IMPORTANCE It has been argued that oyster-pathogenic Vibrio spp. have contributed to recent mortality events in U.S. shellfish hatcheries (R. A. Elston, H. Hasegawa, K. L. Humphrey, I. K. Polyak, and C. Häse, Dis Aquat Organ 82:119–134, 2008, https://doi.org/10.3354/dao01982); however, these events are often sporadic and unpredictable. The success of hatcheries is critically linked to the chemical and biological composition of inflowing seawater resources; thus, it is pertinent to understand the biogeochemical drivers of oyster-pathogenic Vibrio spp. in their planktonic state. Here, we show that Netarts Bay, the location of a local hatchery, is enriched in oyster-pathogenic V. coralliilyticus compared to coastal seawater, and we hypothesize that conditions in tidal flats promote the local growth of this pathogen. Furthermore, V. coralliilyticus appears to persist in seawater pumped into the local hatchery. These results improve our understanding of the ecology and environmental controls of the V. coralliilyticus pathogen and could be used to improve future aquaculture efforts, as multiple stressors impact hatchery success.
Collapse
|
88
|
Adami GR, Tangney CC, Tang JL, Zhou Y, Ghaffari S, Naqib A, Sinha S, Green SJ, Schwartz JL. Effects of green tea on miRNA and microbiome of oral epithelium. Sci Rep 2018; 8:5873. [PMID: 29651001 PMCID: PMC5897334 DOI: 10.1038/s41598-018-22994-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/03/2018] [Indexed: 02/07/2023] Open
Abstract
Consumption of green tea (GT) extracts or purified catechins has shown the ability to prevent oral and other cancers and inhibit cancer progression in rodent models, but the evidence for this in humans is mixed. Working with humans, we sought to understand the source of variable responses to GT by examining its effects on oral epithelium. Lingual epithelial RNA and lingual and gingival microbiota were measured before and after 4 weeks of exposure in tobacco smokers, whom are at high risk of oral cancer. GT consumption had on average inconsistent effects on miRNA expression in the oral epithelium. Only analysis that examined paired miRNAs, showing changed and coordinated expression with GT exposure, provided evidence for a GT effect on miRNAs, identifying miRNAs co-expressed with two hubs, miR-181a-5p and 301a-3p. An examination of the microbiome on cancer prone lingual mucosa, in contrast, showed clear shifts in the relative abundance of Streptococcus and Staphylococcus, and other genera after GT exposure. These data support the idea that tea consumption can consistently change oral bacteria in humans, which may affect carcinogenesis, but argue that GT effects on oral epithelial miRNA expression in humans vary between individuals.
Collapse
Affiliation(s)
- Guy R Adami
- Department of Oral Medicine & Diagnostic Sciences, Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, USA.
| | - Christy C Tangney
- Department of Clinical Nutrition, College of Health Sciences, Rush University Medical Center, 1700 W Van Buren St. Suite 425, Chicago, IL, USA
| | - Jessica L Tang
- Department of Oral Medicine & Diagnostic Sciences, Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, USA
| | - Yalu Zhou
- Department of Oral Medicine & Diagnostic Sciences, Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, USA
| | - Saba Ghaffari
- Department of Computer Science and Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, 2122 Siebel Center, 201N. Goodwin Ave, Urbana, IL, USA
| | - Ankur Naqib
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Saurabh Sinha
- Department of Computer Science and Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, 2122 Siebel Center, 201N. Goodwin Ave, Urbana, IL, USA
| | - Stefan J Green
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Joel L Schwartz
- Department of Oral Medicine & Diagnostic Sciences, Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, 801 South Paulina Street, Chicago, IL, USA
| |
Collapse
|
89
|
Common Hydraulic Fracturing Fluid Additives Alter the Structure and Function of Anaerobic Microbial Communities. Appl Environ Microbiol 2018; 84:AEM.02729-17. [PMID: 29453259 DOI: 10.1128/aem.02729-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/08/2018] [Indexed: 11/20/2022] Open
Abstract
The development of unconventional oil and gas (UOG) resources results in the production of large volumes of wastewater containing a complex mixture of hydraulic fracturing chemical additives and components from the formation. The release of these wastewaters into the environment poses potential risks that are poorly understood. Microbial communities in stream sediments form the base of the food chain and may serve as sentinels for changes in stream health. Iron-reducing organisms have been shown to play a role in the biodegradation of a wide range of organic compounds, and so to evaluate their response to UOG wastewater, we enriched anaerobic microbial communities from sediments collected upstream (background) and downstream (impacted) of an UOG wastewater injection disposal facility in the presence of hydraulic fracturing fluid (HFF) additives: guar gum, ethylene glycol, and two biocides, 2,2-dibromo-3-nitrilopropionamide (DBNPA) and bronopol (C3H6BrNO4). Iron reduction was significantly inhibited early in the incubations with the addition of biocides, whereas amendment with guar gum and ethylene glycol stimulated iron reduction relative to levels in the unamended controls. Changes in the microbial community structure were observed across all treatments, indicating the potential for even small amounts of UOG wastewater components to influence natural microbial processes. The microbial community structure differed between enrichments with background and impacted sediments, suggesting that impacted sediments may have been preconditioned by exposure to wastewater. These experiments demonstrated the potential for biocides to significantly decrease iron reduction rates immediately following a spill and demonstrated how microbial communities previously exposed to UOG wastewater may be more resilient to additional spills.IMPORTANCE Organic components of UOG wastewater can alter microbial communities and biogeochemical processes, which could alter the rates of essential natural attenuation processes. These findings provide new insights into microbial responses following a release of UOG wastewaters and are critical for identifying strategies for the remediation and natural attenuation of impacted environments.
Collapse
|
90
|
Rago L, Zecchin S, Marzorati S, Goglio A, Cavalca L, Cristiani P, Schievano A. A study of microbial communities on terracotta separator and on biocathode of air breathing microbial fuel cells. Bioelectrochemistry 2018; 120:18-26. [DOI: 10.1016/j.bioelechem.2017.11.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 11/10/2017] [Accepted: 11/10/2017] [Indexed: 11/16/2022]
|
91
|
Barengolts E, Green SJ, Eisenberg Y, Akbar A, Reddivari B, Layden BT, Dugas L, Chlipala G. Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease. PLoS One 2018; 13:e0194171. [PMID: 29596446 PMCID: PMC5875756 DOI: 10.1371/journal.pone.0194171] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 02/26/2018] [Indexed: 02/07/2023] Open
Abstract
Objective The gut microbiota is known to be related to type 2 diabetes (T2D), psychiatric conditions, and opioid use. In this study, we tested the hypothesis that variability in gut microbiota in T2D is associated with psycho-metabolic health. Methods A cross-sectional study was conducted among African American men (AAM) (n = 99) that were outpatients at a Chicago VA Medical Center. The main outcome measures included fecal microbiota ecology (by 16S rRNA gene sequencing), psychiatric disorders including opioid use, and circulating leptin and oxytocin as representative hormone biomarkers for obesity and psychological pro-social behavior. Results The study subjects had prevalent overweight/obesity (78%), T2D (50%) and co-morbid psychiatric (65%) and opioid use (45%) disorders. In the analysis of microbiota, the data showed interactions of opioids, T2D and metformin with Bifidobacterium and Prevotella genera. The differential analysis of Bifidobacterium stratified by opioids, T2D and metformin, showed significant interactions among these factors indicating that the effect of one factor was changed by the other (FDR-adjusted p [q] < 0.01). In addition, the pair-wise comparison showed that participants with T2D not taking metformin had a significant 6.74 log2 fold increase in Bifidobacterium in opioid users as compared to non-users (q = 2.2 x 10−8). Since metformin was not included in this pair-wise comparison, the significant ‘q’ suggested association of opioid use with Bifidobacterium abundance. The differences in Bifidobacterium abundance could possibly be explained by opioids acting as organic cation transporter 1 (OCT1) inhibitors. Analysis stratified by lower and higher leptin and oxytocin (divided by the 50th percentile) in the subgroup without T2D showed lower Dialister in High-Leptin vs. Low-Leptin (p = 0.03). Contrary, the opposite was shown for oxytocin, higher Dialister in High-Oxytocin vs. Low-Oxytocin (p = 0.04). Conclusions The study demonstrated for the first time that Bifidobacterium and Prevotella abundance was affected by interactions of T2D, metformin and opioid use. Also, in subjects without T2D Dialister abundance varied according to circulating leptin and oxytocin.
Collapse
Affiliation(s)
- Elena Barengolts
- Department of Medicine, University of Illinois Medical Center, Chicago, Illinois, United States of America
- Department of Medicine, Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
- * E-mail:
| | - Stefan J. Green
- DNA Services Facility, Research Resources Center, University of Illinois, Chicago, Illinois, United States of America
| | - Yuval Eisenberg
- Department of Medicine, University of Illinois Medical Center, Chicago, Illinois, United States of America
| | - Arfana Akbar
- Department of Medicine, University of Illinois Medical Center, Chicago, Illinois, United States of America
- Research and Development Division, Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
| | - Bharathi Reddivari
- Department of Medicine, University of Illinois Medical Center, Chicago, Illinois, United States of America
- Research and Development Division, Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
| | - Brian T. Layden
- Department of Medicine, University of Illinois Medical Center, Chicago, Illinois, United States of America
- Department of Medicine, Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
| | - Lara Dugas
- Department of Public Health Sciences, Loyola University, Maywood, Illinois, United States of America
| | - George Chlipala
- Core for Research Informatics, Research Resources Center, University of Illinois, Chicago, Illinois, United States of America
| |
Collapse
|
92
|
Gasc C, Peyret P. Hybridization capture reveals microbial diversity missed using current profiling methods. MICROBIOME 2018; 6:61. [PMID: 29587880 PMCID: PMC5870382 DOI: 10.1186/s40168-018-0442-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 03/13/2018] [Indexed: 06/07/2023]
Abstract
BACKGROUND Microorganisms comprise the majority of living organisms on our planet. For many years, exploration of the composition of microbial communities has been performed through the PCR-based study of the small subunit rRNA gene due to its high conservation across the domains of life. The application of this method has resulted in the discovery of many unexpected evolutionary lineages. However, amplicon sequencing is subject to numerous biases, with some taxa being missed, and is limited by the read length of second-generation sequencing platforms, which drastically reduces the phylogenetic resolution. RESULTS Here, we describe a hybridization capture strategy that allows the enrichment of 16S rRNA genes from metagenomic samples and enables an exhaustive identification and a complete reconstruction of the biomarker. Applying this approach to a microbial mock community and a soil sample, we demonstrated that hybridization capture is able to reveal greater microbial diversity than 16S rDNA amplicon sequencing and shotgun sequencing. The reconstruction of full-length 16S rRNA genes facilitated the improvement of phylogenetic resolution and the discovery of novel prokaryotic taxa. CONCLUSIONS Our results demonstrate that hybridization capture can lead to major breakthroughs in our understanding of microbial diversity, overcoming the limitations of conventional 16S rRNA gene studies. If applied to a broad range of environmental samples, this innovative approach could reveal the undescribed diversity of the still underexplored microbial communities and could provide a better understanding of ecosystem function.
Collapse
Affiliation(s)
- Cyrielle Gasc
- Université Clermont Auvergne, INRA, UMR 454 MEDIS, 28, place Henri Dunant, F-63000 Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRA, UMR 454 MEDIS, 28, place Henri Dunant, F-63000 Clermont-Ferrand, France
| |
Collapse
|
93
|
Keshri J, Chen Y, Pinto R, Kroupitski Y, Weinberg ZG, Sela S. Microbiome dynamics during ensiling of corn with and without Lactobacillus plantarum inoculant. Appl Microbiol Biotechnol 2018. [DOI: 10.1007/s00253-018-8903-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
94
|
The TLR9 agonist MGN1703 triggers a potent type I interferon response in the sigmoid colon. Mucosal Immunol 2018; 11:449-461. [PMID: 28766555 PMCID: PMC5796873 DOI: 10.1038/mi.2017.59] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/25/2017] [Indexed: 02/04/2023]
Abstract
Toll-like receptor 9 (TLR9) agonists are being developed for treatment of colorectal and other cancers, yet the impact of these drugs on human intestines remains unknown. This, together with the fact that there are additional potential indications for TLR9 agonist therapy (e.g., autoimmune and infectious diseases), led us to investigate the impact of MGN1703 (Lefitolimod) on intestinal homeostasis and viral persistence in HIV-positive individuals. Colonic sigmoid biopsies were collected (baseline and week four) from 11 HIV+ individuals on suppressive antiretroviral therapy, who received MGN1703 (60 mg s.c.) twice weekly for 4 weeks in a single-arm, phase 1b/2a study. Within sigmoid mucosa, global transcriptomic analyses revealed 248 modulated genes (false discovery rate<0.05) including many type I interferon (IFN)-stimulated genes. MGN1703 increased the frequencies of cells exhibiting MX1 (P=0.001) and ISG15 (P=0.014) protein expression. No changes were observed in neutrophil infiltration (myeloperoxidase; P=0.97). No systematic effect on fecal microbiota structure was observed (analysis of similarity Global R=-0.105; P=0.929). TLR9 expression at baseline was inversely proportional to the change in integrated HIV DNA during MGN1703 treatment (P=0.020). In conclusion, MGN1703 induced a potent type I IFN response, without a concomitant general inflammatory response, in the intestines.
Collapse
|
95
|
Gaby JC, Rishishwar L, Valderrama-Aguirre LC, Green SJ, Valderrama-Aguirre A, Jordan IK, Kostka JE. Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline. Appl Environ Microbiol 2018; 84:e01512-17. [PMID: 29180374 PMCID: PMC5795091 DOI: 10.1128/aem.01512-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/21/2017] [Indexed: 11/20/2022] Open
Abstract
The dinitrogenase reductase gene (nifH) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. The developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field.IMPORTANCE Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. The utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.
Collapse
Affiliation(s)
- John Christian Gaby
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Lavanya Rishishwar
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Lina C Valderrama-Aguirre
- Laboratory of Microorganismal Production (Bioinoculums), Department of Field Research in Sugarcane, Incauca S.A.S, Cali, Valle del Cauca, Colombia
- School of Natural Resources and Environmental Engineering, PhD Program in Sanitary and Environmental Engineering, Universidad del Valle, Cali, Valle del Cauca, Colombia
| | - Stefan J Green
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Augusto Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- Biomedical Research Institute, Universidad Libre, Cali, Valle del Cauca, Colombia
- Regenerar, Center of Excellence for Regenerative and Personalized Medicine, Valle del Cauca, Colombia
| | - I King Jordan
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Joel E Kostka
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| |
Collapse
|
96
|
Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance. Appl Environ Microbiol 2018; 84:AEM.02087-17. [PMID: 29180372 DOI: 10.1128/aem.02087-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/20/2017] [Indexed: 11/20/2022] Open
Abstract
Anthropogenic activities alter the structure and function of a bacterial community. Furthermore, bacterial communities structured by the conditions the anthropogenic activities present may consequently reduce their stability in response to an unpredicted acute disturbance. The present mesocosm-scale study exposed soil bacterial communities to different irrigation water types, including freshwater, fertilized freshwater, treated wastewater, and artificial wastewater, and evaluated their response to a disturbance caused by heat. These effectors may be considered deterministic and stochastic forces common in agricultural operations of arid and semiarid regions. Bacterial communities under conditions of high mineral and organic carbon availability (artificial wastewater) differed from the native bacterial community and showed a proteobacterial dominance. These bacterial communities had a lower resistance to the heat treatment disturbance than soils under conditions of low resource availability (high-quality treated wastewater or freshwater). The latter soil bacterial communities showed a higher abundance of operational taxonomic units (OTUs) classified as Bacilli These results were elucidated by soil under conditions of high resource availability, which lost higher degrees of functional potential and had a greater bacterial community composition change. However, the functional resilience, after the disturbance ended, was higher under a condition of high resource availability despite the bacterial community composition shift and the decrease in species richness. The functional resilience was directly connected to the high growth rates of certain Bacteroidetes and proteobacterial groups. A high stability was found in samples that supported the coexistence of both resistant OTUs and fast-growing OTUs.IMPORTANCE This report presents the results of a study employing a hypothesis-based experimental approach to reveal the forces involved in determining the stability of a soil bacterial community to disturbance. The resultant postdisturbance bacterial community composition dynamics and functionality were analyzed. The paper demonstrates the relatedness of community structure and stability under cultivation conditions prevalent in an arid area under irrigation with water of different qualities. The use of common agricultural practices to demonstrate these features has not been described before. The combination of a fundamental theoretical issue in ecology with common and concerning disturbances caused by agricultural practice makes this study unique. Furthermore, the results of the present study have applicable importance regarding soil conservation, as it enables a better characterization and monitoring of stressed soil bacterial communities and possible intervention to reduce the stress. It will also be of valued interest in coming years, as fresh water scarcity and the use of alternative water sources are expected to rise globally.
Collapse
|
97
|
Collado MC, Engen PA, Bandín C, Cabrera-Rubio R, Voigt RM, Green SJ, Naqib A, Keshavarzian A, Scheer FAJL, Garaulet M. Timing of food intake impacts daily rhythms of human salivary microbiota: a randomized, crossover study. FASEB J 2018; 32:2060-2072. [PMID: 29233857 DOI: 10.1096/fj.201700697rr] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The composition of the diet (what we eat) has been widely related to the microbiota profile. However, whether the timing of food consumption (when we eat) influences microbiota in humans is unknown. A randomized, crossover study was performed in 10 healthy normal-weight young women to test the effect of the timing of food intake on the human microbiota in the saliva and fecal samples. More specifically, to determine whether eating late alters daily rhythms of human salivary microbiota, we interrogated salivary microbiota in samples obtained at 4 specific time points over 24 h, to achieve a better understanding of the relationship between food timing and metabolic alterations in humans. Results revealed significant diurnal rhythms in salivary diversity and bacterial relative abundance ( i.e., TM7 and Fusobacteria) across both early and late eating conditions. More importantly, meal timing affected diurnal rhythms in diversity of salivary microbiota toward an inverted rhythm between the eating conditions, and eating late increased the number of putative proinflammatory taxa, showing a diurnal rhythm in the saliva. In a randomized, crossover study, we showed for the first time the impact of the timing of food intake on human salivary microbiota. Eating the main meal late inverts the daily rhythm of salivary microbiota diversity which may have a deleterious effect on the metabolism of the host.-Collado, M. C., Engen, P. A., Bandín, C., Cabrera-Rubio, R., Voigt, R. M., Green, S. J., Naqib, A., Keshavarzian, A., Scheer, F. A. J. L., Garaulet, M. Timing of food intake impacts daily rhythms of human salivary microbiota: a randomized, crossover study.
Collapse
Affiliation(s)
- María Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Phillip A Engen
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Cristina Bandín
- Department of Physiology, University of Murcia, Murcia Spain.,Murcian Institute of Biosanitary Research (IMIB)-Arrixaca, Murcia, Spain
| | - Raúl Cabrera-Rubio
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-Spanish National Research Council (IATA-CSIC), Valencia, Spain.,Alimentary Pharmabiotic Centre (APC) Microbiome Institute, University College Cork, Cork, Ireland.,Moorepark Teagasc Food Research Centre, Fermoy, Ireland
| | - Robin M Voigt
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Stefan J Green
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Ankur Naqib
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Ali Keshavarzian
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA.,Department of Pharmacology, Rush University Medical Center, Chicago, Illinois, USA.,Department of Physiology, Rush University Medical Center, Chicago, Illinois, USA.,Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Frank A J L Scheer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts, USA; and.,Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Marta Garaulet
- Department of Physiology, University of Murcia, Murcia Spain.,Murcian Institute of Biosanitary Research (IMIB)-Arrixaca, Murcia, Spain
| |
Collapse
|
98
|
Making and Sequencing Heavily Multiplexed, High-Throughput 16S Ribosomal RNA Gene Amplicon Libraries Using a Flexible, Two-Stage PCR Protocol. Methods Mol Biol 2018; 1783:149-169. [PMID: 29767361 DOI: 10.1007/978-1-4939-7834-2_7] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Deep sequencing of polymerase chain reaction (PCR)-amplified small subunit (16S or 18S) ribosomal RNA (rRNA) genes fragments is commonly employed to characterize the composition and structure of microbial communities. Preparing genomic DNA for sequencing of such gene fragments on Illumina sequencers can be performed in a straightforward, two-stage PCR method, described herein. The protocol described allows for up to 384 samples to be sequenced simultaneously, and provides great flexibility in choice of primers.
Collapse
|
99
|
Li J, Summerlin M, Nitiss KC, Nitiss JL, Hanakahi LA. TDP1 is required for efficient non-homologous end joining in human cells. DNA Repair (Amst) 2017; 60:40-49. [PMID: 29078113 DOI: 10.1016/j.dnarep.2017.10.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 11/29/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) can remove a wide variety of 3' and 5' terminal DNA adducts. Genetic studies in yeast identified TDP1 as a regulator of non-homologous end joining (NHEJ) fidelity in the repair of double-strand breaks (DSBs) lacking terminal adducts. In this communication, we show that TDP1 plays an important role in joining cohesive DSBs in human cells. To investigate the role of TDP1 in NHEJ in live human cells we used CRISPR/cas9 to produce TDP1-knockout (TDP1-KO) HEK-293 cells. As expected, human TDP1-KO cells were highly sensitive to topoisomerase poisons and ionizing radiation. Using a chromosomally-integrated NHEJ reporter substrate to compare end joining between wild type and TDP1-KO cells, we found that TDP1-KO cells have a 5-fold reduced ability to repair I-SceI-generated DSBs. Extracts prepared from TDP1-KO cells had reduced NHEJ activity in vitro, as compared to extracts from wild type cells. Analysis of end-joining junctions showed that TDP1 deficiency reduced end-joining fidelity, with a significant increase in insertion events, similar to previous observations in yeast. It has been reported that phosphorylation of TDP1 serine 81 (TDP1-S81) by ATM and DNA-PK stabilizes TDP1 and recruits TDP1 to sites of DNA damage. We found that end joining in TDP1-KO cells was partially restored by the non-phosphorylatable mutant TDP1-S81A, but not by the phosphomimetic TDP1-S81E. We previously reported that TDP1 physically interacted with XLF. In this study, we found that XLF binding by TDP1 was reduced 2-fold by the S81A mutation, and 10-fold by the S81E phosphomimetic mutation. Our results demonstrate a novel role for TDP1 in NHEJ in human cells. We hypothesize that TDP1 participation in human NHEJ is mediated by interaction with XLF, and that TDP1-XLF interactions and subsequent NHEJ events are regulated by phosphorylation of TDP1-S81.
Collapse
Affiliation(s)
- Jing Li
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 1601 Parkview Ave. Rockford, Chicago, IL, 61107, United States
| | - Matthew Summerlin
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 1601 Parkview Ave. Rockford, Chicago, IL, 61107, United States
| | - Karin C Nitiss
- Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, 1601 Parkview Ave. Rockford, Chicago, IL, 61107, United States
| | - John L Nitiss
- Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, 1601 Parkview Ave. Rockford, Chicago, IL, 61107, United States
| | - Leslyn A Hanakahi
- Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, 1601 Parkview Ave. Rockford, Chicago, IL, 61107, United States.
| |
Collapse
|
100
|
Hoffman JD, Parikh I, Green SJ, Chlipala G, Mohney RP, Keaton M, Bauer B, Hartz AMS, Lin AL. Age Drives Distortion of Brain Metabolic, Vascular and Cognitive Functions, and the Gut Microbiome. Front Aging Neurosci 2017; 9:298. [PMID: 28993728 PMCID: PMC5622159 DOI: 10.3389/fnagi.2017.00298] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 08/30/2017] [Indexed: 12/15/2022] Open
Abstract
Advancing age is the top risk factor for the development of neurodegenerative disorders, including Alzheimer's disease (AD). However, the contribution of aging processes to AD etiology remains unclear. Emerging evidence shows that reduced brain metabolic and vascular functions occur decades before the onset of cognitive impairments, and these reductions are highly associated with low-grade, chronic inflammation developed in the brain over time. Interestingly, recent findings suggest that the gut microbiota may also play a critical role in modulating immune responses in the brain via the brain-gut axis. In this study, our goal was to identify associations between deleterious changes in brain metabolism, cerebral blood flow (CBF), gut microbiome and cognition in aging, and potential implications for AD development. We conducted our study with a group of young mice (5-6 months of age) and compared those to old mice (18-20 months of age) by utilizing metabolic profiling, neuroimaging, gut microbiome analysis, behavioral assessments and biochemical assays. We found that compared to young mice, old mice had significantly increased levels of numerous amino acids and fatty acids that are highly associated with inflammation and AD biomarkers. In the gut microbiome analyses, we found that old mice had increased Firmicutes/Bacteroidetes ratio and alpha diversity. We also found impaired blood-brain barrier (BBB) function and reduced CBF as well as compromised learning and memory and increased anxiety, clinical symptoms often seen in AD patients, in old mice. Our study suggests that the aging process involves deleterious changes in brain metabolic, vascular and cognitive functions, and gut microbiome structure and diversity, all which may lead to inflammation and thus increase the risk for AD. Future studies conducting comprehensive and integrative characterization of brain aging, including crosstalk with peripheral systems and factors, will be necessary to define the mechanisms underlying the shift from normal aging to pathological processes in the etiology of AD.
Collapse
Affiliation(s)
- Jared D Hoffman
- Sanders-Brown Center on Aging, University of KentuckyLexington, KY, United States.,Depatment of Pharmacology and Nutritional Science, University of KentuckyLexington, KY, United States
| | - Ishita Parikh
- Sanders-Brown Center on Aging, University of KentuckyLexington, KY, United States
| | - Stefan J Green
- Research Resources Center, University of Illinois at ChicagoChicago, IL, United States
| | - George Chlipala
- Research Resources Center, University of Illinois at ChicagoChicago, IL, United States
| | | | | | - Bjoern Bauer
- Department of Pharmaceutical Sciences, University of KentuckyLexington, KY, United States
| | - Anika M S Hartz
- Sanders-Brown Center on Aging, University of KentuckyLexington, KY, United States.,Depatment of Pharmacology and Nutritional Science, University of KentuckyLexington, KY, United States
| | - Ai-Ling Lin
- Sanders-Brown Center on Aging, University of KentuckyLexington, KY, United States.,Depatment of Pharmacology and Nutritional Science, University of KentuckyLexington, KY, United States.,Department of Engineering, University of KentuckyLexington, KY, United States
| |
Collapse
|