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  • 1
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    Sewage reflects the microbiomes of human populations (2015)
    American Society for Microbiology
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mBio 6 (2015): e02574-14, doi:10.1128/mBio.02574-14.
    Description: Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome.
    Description: Funding for this work was provided by the NIH grant R01AI091829-01A1 to S.L.M. and M.L.S.
    Repository Name: Woods Hole Open Access Server
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  • 2
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    Minimum entropy decomposition : unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences (2015)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 9 (2015): 968–979, doi:10.1038/ismej.2014.195.
    Description: Molecular microbial ecology investigations often employ large marker gene datasets, for example, ribosomal RNAs, to represent the occurrence of single-cell genomes in microbial communities. Massively parallel DNA sequencing technologies enable extensive surveys of marker gene libraries that sometimes include nearly identical sequences. Computational approaches that rely on pairwise sequence alignments for similarity assessment and de novo clustering with de facto similarity thresholds to partition high-throughput sequencing datasets constrain fine-scale resolution descriptions of microbial communities. Minimum Entropy Decomposition (MED) provides a computationally efficient means to partition marker gene datasets into ‘MED nodes’, which represent homogeneous operational taxonomic units. By employing Shannon entropy, MED uses only the information-rich nucleotide positions across reads and iteratively partitions large datasets while omitting stochastic variation. When applied to analyses of microbiomes from two deep-sea cryptic sponges Hexadella dedritifera and Hexadella cf. dedritifera, MED resolved a key Gammaproteobacteria cluster into multiple MED nodes that are specific to different sponges, and revealed that these closely related sympatric sponge species maintain distinct microbial communities. MED analysis of a previously published human oral microbiome dataset also revealed that taxa separated by less than 1% sequence variation distributed to distinct niches in the oral cavity. The information theory-guided decomposition process behind the MED algorithm enables sensitive discrimination of closely related organisms in marker gene amplicon datasets without relying on extensive computational heuristics and user supervision.
    Description: AME was supported by a G. Unger Vetlesen Foundation grant to the Marine Biological Laboratory and the Alfred P Sloan Foundation.
    Repository Name: Woods Hole Open Access Server
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  • 3
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    Ocean and coastal acidification off New England and Nova Scotia (2015)
    The Oceanography Society
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    Publication Date: 2022-05-25
    Description: Author Posting. © The Oceanography Society, 2015. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 28, no. 2 (2015): 182-197, doi:10.5670/oceanog.2015.41.
    Description: New England coastal and adjacent Nova Scotia shelf waters have a reduced buffering capacity because of significant freshwater input, making the region’s waters potentially more vulnerable to coastal acidification. Nutrient loading and heavy precipitation events further acidify the region’s poorly buffered coastal waters. Despite the apparent vulnerability of these waters, and fisheries’ and mariculture’s significant dependence on calcifying species, the community lacks the ability to confidently predict how the region’s ecosystems will respond to continued ocean and coastal acidification. Here, we discuss ocean and coastal acidification processes specific to New England coastal and Nova Scotia shelf waters and review current understanding of the biological consequences most relevant to the region. We also identify key research and monitoring needs to be addressed and highlight existing capacities that should be leveraged to advance a regional understanding of ocean and coastal acidification.
    Description: This project was supported in part by an appointment to the Internship/Research Participation Program at the Office of Water, US Environmental Protection Agency (EPA), administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the US Department of Energy and the EPA. JS acknowledges support from NASA grant from NNX14AL84G NASA-CCS.
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Supplemental files from “Metazoans of redoxcline sediments in Mediterranean deep-sea hypersaline anoxic basins” (Bernhard et al., submitted, BMC Biology). (2015)
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    Publication Date: 2022-05-25
    Description: Link provides access to supplemental tables and figures to our manuscript regarding metazoans of redoxcline sediments in Mediterranean deep-sea hypersaline anoxic basins (DHABs). Specimens shown in supplemental figures are loriciferans collected from control and lower halocline sediments of L'Atalante Basin and Discovery Basin. Further details appear in Bernhard et al. (submitted).
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Anvi’o : an advanced analysis and visualization platform for ‘omics data (2015)
    PeerJ
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PeerJ 3 (2015): e1319, doi:10.7717/peerj.1319.
    Description: Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex data. Here we introduce anvi’o, an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. Its extensible visualization approach distills multiple dimensions of information about each contig, offering a dynamic and unified work environment for data exploration, manipulation, and reporting. Using anvi’o, we re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations through de novo characterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data. Anvi’o is an open-source platform that empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.
    Description: AME was supported by the G. Unger Vetlesen Foundation. The project was supported by the Frank R. Lillie Research Innovation Award given by the University of Chicago and the Marine Biological Laboratory.
    Keywords: Metagenomics ; Assembly ; Genome binning ; Visualization ; SNP profiling ; Metatranscriptomics
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Benthic protists and fungi of Mediterranean deep hypsersaline anoxic basin redoxcline sediments (2015)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2014): 605, doi:10.3389/fmicb.2014.00605.
    Description: Some of the most extreme marine habitats known are the Mediterranean deep hypersaline anoxic basins (DHABs; water depth ∼3500 m). Brines of DHABs are nearly saturated with salt, leading many to suspect they are uninhabitable for eukaryotes. While diverse bacterial and protistan communities are reported from some DHAB water-column haloclines and brines, the existence and activity of benthic DHAB protists have rarely been explored. Here, we report findings regarding protists and fungi recovered from sediments of three DHAB (Discovery, Urania, L’ Atalante) haloclines, and compare these to communities from sediments underlying normoxic waters of typical Mediterranean salinity. Halocline sediments, where the redoxcline impinges the seafloor, were studied from all three DHABs. Microscopic cell counts suggested that halocline sediments supported denser protist populations than those in adjacent control sediments. Pyrosequencing analysis based on ribosomal RNA detected eukaryotic ribotypes in the halocline sediments from each of the three DHABs, most of which were fungi. Sequences affiliated with Ustilaginomycotina Basidiomycota were the most abundant eukaryotic signatures detected. Benthic communities in these DHABs appeared to differ, as expected, due to differing brine chemistries. Microscopy indicated that only a low proportion of protists appeared to bear associated putative symbionts. In a considerable number of cases, when prokaryotes were associated with a protist, DAPI staining did not reveal presence of any nuclei, suggesting that at least some protists were carcasses inhabited by prokaryotic scavengers.
    Description: K. Kormas was partially supported by the University of Thessaly through a sabbatical in 2013. Supported by NSF grants OCE-0849578 to Virginia P. Edgcomb and Joan M. Bernhard and OCE-1061391 to Joan M. Bernhard and Virginia P. Edgcomb.
    Keywords: Eukaryote ; DHABs ; Discovery ; Urania, L’ Atalante ; Diversity ; rRNA
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Testing the depth-differentiation hypothesis in a deepwater octocoral (2015)
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of The Royal Society for personal use, not for redistribution. The definitive version was published in Proceedings of the Royal Society B: Biological Sciences 282 (2015): 20150008, doi:10.1098/rspb.2015.0008.
    Description: The depth-differentiation hypothesis proposes that the bathyal region is a source of genetic diversity and an area where there is a high rate of species formation. Genetic differentiation should thus occur over relatively small vertical distances, particularly along the upper continental slope (200-1000 m) where oceanography varies greatly over small differences in depth. To test whether genetic differentiation within deepwater octocorals is greater over vertical rather than geographic distances, Callogorgia delta was targeted. This species commonly occurs throughout the northern Gulf of Mexico at depths ranging from 400-900 m. We found significant genetic differentiation (FST=0.042) across seven sites spanning 400 km of distance and 400 m of depth. A pattern of isolation by depth emerged, but geographic distance between sites may further limit gene flow. Water mass boundaries may serve to isolate populations across depth; however, adaptive divergence with depth is also a possible scenario. Microsatellite markers also revealed significant genetic differentiation (FST=0.434) between C. delta and a closely-related species, C. americana, demonstrating the utility of microsatellites in species delimitation of octocorals. Results provided support for the depth-differentiation hypothesis, strengthening the notion that factors co-varying with depth serve as isolation mechanisms in deep-sea populations.
    Description: Funding was provided by BOEM and NOAA-OER (BOEM contract #M08PC20038) for the Lophelia II project led by TDI-Brooks International. AMQ was funded by the Dr. Nancy Foster Scholarship program, Temple University Dissertation Completion Grant, and the Lerner-Gray grant for marine research.
    Description: 2016-04-22
    Keywords: Deep sea ; Population genetics ; Connectivity ; Adaptive divergence ; Octocoral ; Gulf of Mexico
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 8
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    A single genus in the gut microbiome reflects host preference and specificity (2015)
    Nature Publishing Group
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 9 (2015): 90–100, doi:10.1038/ismej.2014.97.
    Description: Delineating differences in gut microbiomes of human and animal hosts contributes towards understanding human health and enables new strategies for detecting reservoirs of waterborne human pathogens. We focused upon Blautia, a single microbial genus that is important for nutrient assimilation as preliminary work suggested host-related patterns within members of this genus. In our dataset of 57 M sequence reads of the V6 region of the 16S ribosomal RNA gene in samples collected from seven host species, we identified 200 high-resolution taxonomic units within Blautia using oligotyping. Our analysis revealed 13 host-specific oligotypes that occurred exclusively in fecal samples of humans (three oligotypes), swine (six oligotypes), cows (one oligotype), deer (one oligotype), or chickens (two oligotypes). We identified an additional 171 oligotypes that exhibited differential abundance patterns among all the host species. Blautia oligotypes in the human population obtained from sewage and fecal samples displayed remarkable continuity. Oligotypes from only 10 Brazilian human fecal samples collected from individuals in a rural village encompassed 97% of all Blautia oligotypes found in a Brazilian sewage sample from a city of three million people. Further, 75% of the oligotypes in Brazilian human fecal samples matched those in US sewage samples, implying that a universal set of Blautia strains may be shared among culturally and geographically distinct human populations. Such strains can serve as universal markers to assess human fecal contamination in environmental samples. Our results indicate that host-specificity and host-preference patterns of organisms within this genus are driven by host physiology more than dietary habits.
    Description: This study was funded by the NIH grant R01AI091829-01A1 to SLM.
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  • 9
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    Topological analyses in APP/PS1 mice reveal that astrocytes do not migrate to amyloid-β plaques (2015)
    National Academy of Sciences
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    Publication Date: 2015-12-07
    Description: Although the clustering of GFAP immunopositive astrocytes around amyloid-β plaques in Alzheimer’s disease has led to the widespread assumption that plaques attract astrocytes, recent studies suggest that astrocytes stay put in injury. Here we reexamine astrocyte migration to plaques, using quantitative spatial analysis and computer modeling to investigate the topology of astrocytes in 3D images obtained by two-photon microscopy of living APP/PS1 mice and WT littermates. In WT mice, cortical astrocyte topology fits a model in which a liquid of hard spheres exclude each other in a confined space. Plaques do not disturb this arrangement except at very large plaque loads, but, locally, cause subtle outward shifts of the astrocytes located in three tiers around plaques. These data suggest that astrocytes respond to plaque-induced neuropil injury primarily by changing phenotype, and hence function, rather than location.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    Extinction reverses olfactory fear-conditioned increases in neuron number and glomerular size (2015)
    National Academy of Sciences
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    Publication Date: 2015-09-29
    Description: Although much work has investigated the contribution of brain regions such as the amygdala, hippocampus, and prefrontal cortex to the processing of fear learning and memory, fewer studies have examined the role of sensory systems, in particular the olfactory system, in the detection and perception of cues involved in learning and memory. The primary sensory receptive field maps of the olfactory system are exquisitely organized and respond dynamically to cues in the environment, remaining plastic from development through adulthood. We have previously demonstrated that olfactory fear conditioning leads to increased odorant-specific receptor representation in the main olfactory epithelium and in glomeruli within the olfactory bulb. We now demonstrate that olfactory extinction training specific to the conditioned odor stimulus reverses the conditioning-associated freezing behavior and odor learning-induced structural changes in the olfactory epithelium and olfactory bulb in an odorant ligand-specific manner. These data suggest that learning-induced freezing behavior, structural alterations, and enhanced neural sensory representation can be reversed in adult mice following extinction training.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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