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1.  Potential Contribution of Anammox to Nitrogen Loss from Paddy Soils in Southern China 
The anaerobic oxidation of ammonium (anammox) process has been observed in diverse terrestrial ecosystems, while the contribution of anammox to N2 production in paddy soils is not well documented. In this study, the anammox activity and the abundance and diversity of anammox bacteria were investigated to assess the anammox potential of 12 typical paddy soils collected in southern China. Anammox bacteria related to “Candidatus Brocadia” and “Candidatus Kuenenia” and two novel unidentified clusters were detected, with “Candidatus Brocadia” comprising 50% of the anammox population. The prevalence of the anammox was confirmed by the quantitative PCR results based on hydrazine synthase (hzsB) genes, which showed that the abundance ranged from 1.16 × 104 to 9.65 × 104 copies per gram of dry weight. The anammox rates measured by the isotope-pairing technique ranged from 0.27 to 5.25 nmol N per gram of soil per hour in these paddy soils, which contributed 0.6 to 15% to soil N2 production. It is estimated that a total loss of 2.50 × 106 Mg N per year is linked to anammox in the paddy fields in southern China, which implied that ca. 10% of the applied ammonia fertilizers is lost via the anammox process. Anammox activity was significantly correlated with the abundance of hzsB genes, soil nitrate concentration, and C/N ratio. Additionally, ammonia concentration and pH were found to be significantly correlated with the anammox bacterial structure.
doi:10.1128/AEM.02664-14
PMCID: PMC4292472  PMID: 25416768
2.  The ocean sampling day consortium 
Kopf, Anna | Bicak, Mesude | Kottmann, Renzo | Schnetzer, Julia | Kostadinov, Ivaylo | Lehmann, Katja | Fernandez-Guerra, Antonio | Jeanthon, Christian | Rahav, Eyal | Ullrich, Matthias | Wichels, Antje | Gerdts, Gunnar | Polymenakou, Paraskevi | Kotoulas, Giorgos | Siam, Rania | Abdallah, Rehab Z | Sonnenschein, Eva C | Cariou, Thierry | O’Gara, Fergal | Jackson, Stephen | Orlic, Sandi | Steinke, Michael | Busch, Julia | Duarte, Bernardo | Caçador, Isabel | Canning-Clode, João | Bobrova, Oleksandra | Marteinsson, Viggo | Reynisson, Eyjolfur | Loureiro, Clara Magalhães | Luna, Gian Marco | Quero, Grazia Marina | Löscher, Carolin R | Kremp, Anke | DeLorenzo, Marie E | Øvreås, Lise | Tolman, Jennifer | LaRoche, Julie | Penna, Antonella | Frischer, Marc | Davis, Timothy | Katherine, Barker | Meyer, Christopher P | Ramos, Sandra | Magalhães, Catarina | Jude-Lemeilleur, Florence | Aguirre-Macedo, Ma Leopoldina | Wang, Shiao | Poulton, Nicole | Jones, Scott | Collin, Rachel | Fuhrman, Jed A | Conan, Pascal | Alonso, Cecilia | Stambler, Noga | Goodwin, Kelly | Yakimov, Michael M | Baltar, Federico | Bodrossy, Levente | Van De Kamp, Jodie | Frampton, Dion MF | Ostrowski, Martin | Van Ruth, Paul | Malthouse, Paul | Claus, Simon | Deneudt, Klaas | Mortelmans, Jonas | Pitois, Sophie | Wallom, David | Salter, Ian | Costa, Rodrigo | Schroeder, Declan C | Kandil, Mahrous M | Amaral, Valentina | Biancalana, Florencia | Santana, Rafael | Pedrotti, Maria Luiza | Yoshida, Takashi | Ogata, Hiroyuki | Ingleton, Tim | Munnik, Kate | Rodriguez-Ezpeleta, Naiara | Berteaux-Lecellier, Veronique | Wecker, Patricia | Cancio, Ibon | Vaulot, Daniel | Bienhold, Christina | Ghazal, Hassan | Chaouni, Bouchra | Essayeh, Soumya | Ettamimi, Sara | Zaid, El Houcine | Boukhatem, Noureddine | Bouali, Abderrahim | Chahboune, Rajaa | Barrijal, Said | Timinouni, Mohammed | El Otmani, Fatima | Bennani, Mohamed | Mea, Marianna | Todorova, Nadezhda | Karamfilov, Ventzislav | ten Hoopen, Petra | Cochrane, Guy | L’Haridon, Stephane | Bizsel, Kemal Can | Vezzi, Alessandro | Lauro, Federico M | Martin, Patrick | Jensen, Rachelle M | Hinks, Jamie | Gebbels, Susan | Rosselli, Riccardo | De Pascale, Fabio | Schiavon, Riccardo | dos Santos, Antonina | Villar, Emilie | Pesant, Stéphane | Cataletto, Bruno | Malfatti, Francesca | Edirisinghe, Ranjith | Silveira, Jorge A Herrera | Barbier, Michele | Turk, Valentina | Tinta, Tinkara | Fuller, Wayne J | Salihoglu, Ilkay | Serakinci, Nedime | Ergoren, Mahmut Cerkez | Bresnan, Eileen | Iriberri, Juan | Nyhus, Paul Anders Fronth | Bente, Edvardsen | Karlsen, Hans Erik | Golyshin, Peter N | Gasol, Josep M | Moncheva, Snejana | Dzhembekova, Nina | Johnson, Zackary | Sinigalliano, Christopher David | Gidley, Maribeth Louise | Zingone, Adriana | Danovaro, Roberto | Tsiamis, George | Clark, Melody S | Costa, Ana Cristina | El Bour, Monia | Martins, Ana M | Collins, R Eric | Ducluzeau, Anne-Lise | Martinez, Jonathan | Costello, Mark J | Amaral-Zettler, Linda A | Gilbert, Jack A | Davies, Neil | Field, Dawn | Glöckner, Frank Oliver
GigaScience  2015;4:27.
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
doi:10.1186/s13742-015-0066-5
PMCID: PMC4473829  PMID: 26097697
Ocean sampling day; OSD; Biodiversity; Genomics; Health Index; Bacteria; Microorganism; Metagenomics; Marine; Micro B3; Standards
3.  Athletic equipment microbiota are shaped by interactions with human skin 
Microbiome  2015;3:25.
Background
Americans spend the vast majority of their lives in built environments. Even traditionally outdoor pursuits, such as exercising, are often now performed indoors. Bacteria that colonize these indoor ecosystems are primarily derived from the human microbiome. The modes of human interaction with indoor surfaces and the physical conditions associated with each surface type determine the steady-state ecology of the microbial community.
Results
Bacterial assemblages associated with different surfaces in three athletic facilities, including floors, mats, benches, free weights, and elliptical handles, were sampled every other hour (8 am to 6 pm) for 2 days. Surface and equipment type had a stronger influence on bacterial community composition than the facility in which they were housed. Surfaces that were primarily in contact with human skin exhibited highly dynamic bacterial community composition and non-random co-occurrence patterns, suggesting that different host microbiomes—shaped by selective forces—were being deposited on these surfaces through time. However, bacterial assemblages found on the floors and mats changed less over time, and species co-occurrence patterns appeared random, suggesting more neutral community assembly.
Conclusions
These longitudinal patterns highlight the dramatic turnover of microbial communities on surfaces in regular contact with human skin. By uncovering these longitudinal patterns, this study promotes a better understanding of microbe-human interactions within the built environment.
Electronic supplementary material
The online version of this article (doi:10.1186/s40168-015-0088-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s40168-015-0088-3
PMCID: PMC4480904  PMID: 26113975
Gym microbiome; Athletic equipment; Microbiology; Niche communities; Next-generation sequencing
4.  Lifestyle Evolution in Cyanobacterial Symbionts of Sponges 
mBio  2015;6(3):e00391-15.
ABSTRACT
The “Candidatus Synechococcus spongiarum” group includes different clades of cyanobacteria with high 16S rRNA sequence identity (~99%) and is the most abundant and widespread cyanobacterial symbiont of marine sponges. The first draft genome of a “Ca. Synechococcus spongiarum” group member was recently published, providing evidence of genome reduction by loss of genes involved in several nonessential functions. However, “Ca. Synechococcus spongiarum” includes a variety of clades that may differ widely in genomic repertoire and consequently in physiology and symbiotic function. Here, we present three additional draft genomes of “Ca. Synechococcus spongiarum,” each from a different clade. By comparing all four symbiont genomes to those of free-living cyanobacteria, we revealed general adaptations to life inside sponges and specific adaptations of each phylotype. Symbiont genomes shared about half of their total number of coding genes. Common traits of “Ca. Synechococcus spongiarum” members were a high abundance of DNA modification and recombination genes and a reduction in genes involved in inorganic ion transport and metabolism, cell wall biogenesis, and signal transduction mechanisms. Moreover, these symbionts were characterized by a reduced number of antioxidant enzymes and low-weight peptides of photosystem II compared to their free-living relatives. Variability within the “Ca. Synechococcus spongiarum” group was mostly related to immune system features, potential for siderophore-mediated iron transport, and dependency on methionine from external sources. The common absence of genes involved in synthesis of residues, typical of the O antigen of free-living Synechococcus species, suggests a novel mechanism utilized by these symbionts to avoid sponge predation and phage attack.
IMPORTANCE
While the Synechococcus/Prochlorococcus-type cyanobacteria are widely distributed in the world’s oceans, a subgroup has established its niche within marine sponge tissues. Recently, the first genome of sponge-associated cyanobacteria, “Candidatus Synechococcus spongiarum,” was described. The sequencing of three representatives of different clades within this cyanobacterial group has enabled us to investigate intraspecies diversity, as well as to give a more comprehensive understanding of the common symbiotic features that adapt “Ca. Synechococcus spongiarum” to its life within the sponge host.
doi:10.1128/mBio.00391-15
PMCID: PMC4453008  PMID: 26037118
5.  Our unique microbial identity 
Genome Biology  2015;16(1):97.
A recent article examines the extent of individual variation in microbial identities and how this might determine disease susceptibility, therapeutic responses and recovery from clinical interventions.
Please see related article: http://dx.doi.org/10.1186/s13059-015-0646-9
doi:10.1186/s13059-015-0664-7
PMCID: PMC4430908  PMID: 25971745
6.  Forensic analysis of the microbiome of phones and shoes 
Microbiome  2015;3:21.
Background
Microbial interaction between human-associated objects and the environments we inhabit may have forensic implications, and the extent to which microbes are shared between individuals inhabiting the same space may be relevant to human health and disease transmission. In this study, two participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2-day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences.
Results
Samples taken from different surface types maintained significantly different microbial community structures. The impact of the floor microbial community on that of the shoe environments was strong and immediate, as evidenced by Procrustes analysis of shoe replicates and significant correlation between shoe and floor samples taken at the same time point. Supervised learning was highly effective at determining which participant had taken a given shoe or phone sample, and a Bayesian method was able to determine which participant had taken each shoe sample based entirely on its similarity to the floor samples. Both shoe and phone samples taken by conference participants clustered into distinct groups based on location, though much more so when an unweighted distance metric was used, suggesting sharing of low-abundance microbial taxa between individuals inhabiting the same space.
Conclusions
Correlations between microbial community sources and sinks allow for inference of the interactions between humans and their environment.
Electronic supplementary material
The online version of this article (doi:10.1186/s40168-015-0082-9) contains supplementary material, which is available to authorized users.
doi:10.1186/s40168-015-0082-9
PMCID: PMC4427962  PMID: 25969737
Forensic microbiology; Source-sink dynamics; Shoe microbiome; Phone microbiome; Microbial time series
7.  Distinct microbial communities associated with buried soils in the Siberian tundra 
The ISME Journal  2013;8(4):841-853.
Cryoturbation, the burial of topsoil material into deeper soil horizons by repeated freeze–thaw events, is an important storage mechanism for soil organic matter (SOM) in permafrost-affected soils. Besides abiotic conditions, microbial community structure and the accessibility of SOM to the decomposer community are hypothesized to control SOM decomposition and thus have a crucial role in SOM accumulation in buried soils. We surveyed the microbial community structure in cryoturbated soils from nine soil profiles in the northeastern Siberian tundra using high-throughput sequencing and quantification of bacterial, archaeal and fungal marker genes. We found that bacterial abundances in buried topsoils were as high as in unburied topsoils. In contrast, fungal abundances decreased with depth and were significantly lower in buried than in unburied topsoils resulting in remarkably low fungal to bacterial ratios in buried topsoils. Fungal community profiling revealed an associated decrease in presumably ectomycorrhizal (ECM) fungi. The abiotic conditions (low to subzero temperatures, anoxia) and the reduced abundance of fungi likely provide a niche for bacterial, facultative anaerobic decomposers of SOM such as members of the Actinobacteria, which were found in significantly higher relative abundances in buried than in unburied topsoils. Our study expands the knowledge on the microbial community structure in soils of Northern latitude permafrost regions, and attributes the delayed decomposition of SOM in buried soils to specific microbial taxa, and particularly to a decrease in abundance and activity of ECM fungi, and to the extent to which bacterial decomposers are able to act as their functional substitutes.
doi:10.1038/ismej.2013.219
PMCID: PMC3960545  PMID: 24335828
carbon storage; climate change; cryoturbation; microbial communities; permafrost-affected soil; soil organic matter (SOM)
8.  Social behavior and the microbiome 
eLife  null;4:e07322.
Social interactions influence the communities of microbes that live in wild baboons.
doi:10.7554/eLife.07322
PMCID: PMC4379491  PMID: 25826451
Papio cynocephalus; social behavior; gut microbiome; metagenomics; transmission; social network; other
9.  The Soil Microbiome Influences Grapevine-Associated Microbiota 
mBio  2015;6(2):e02527-14.
ABSTRACT
Grapevine is a well-studied, economically relevant crop, whose associated bacteria could influence its organoleptic properties. In this study, the spatial and temporal dynamics of the bacterial communities associated with grapevine organs (leaves, flowers, grapes, and roots) and soils were characterized over two growing seasons to determine the influence of vine cultivar, edaphic parameters, vine developmental stage (dormancy, flowering, preharvest), and vineyard. Belowground bacterial communities differed significantly from those aboveground, and yet the communities associated with leaves, flowers, and grapes shared a greater proportion of taxa with soil communities than with each other, suggesting that soil may serve as a bacterial reservoir. A subset of soil microorganisms, including root colonizers significantly enriched in plant growth-promoting bacteria and related functional genes, were selected by the grapevine. In addition to plant selective pressure, the structure of soil and root microbiota was significantly influenced by soil pH and C:N ratio, and changes in leaf- and grape-associated microbiota were correlated with soil carbon and showed interannual variation even at small spatial scales. Diazotrophic bacteria, e.g., Rhizobiaceae and Bradyrhizobium spp., were significantly more abundant in soil samples and root samples of specific vineyards. Vine-associated microbial assemblages were influenced by myriad factors that shape their composition and structure, but the majority of organ-associated taxa originated in the soil, and their distribution reflected the influence of highly localized biogeographic factors and vineyard management.
IMPORTANCE
Vine-associated bacterial communities may play specific roles in the productivity and disease resistance of their host plant. Also, the bacterial communities on grapes have the potential to influence the organoleptic properties of the wine, contributing to a regional terroir. Understanding that factors that influence these bacteria may provide insights into management practices to shape and craft individual wine properties. We show that soil serves as a key source of vine-associated bacteria and that edaphic factors and vineyard-specific properties can influence the native grapevine microbiome preharvest.
doi:10.1128/mBio.02527-14
PMCID: PMC4453523  PMID: 25805735
10.  Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients 
Microbial Ecology in Health and Disease  2015;26:10.3402/mehd.v26.26555.
Differences in the gut microbiota have been reported between individuals with autism spectrum disorders (ASD) and neurotypical controls, although direct evidence that changes in the microbiome contribute to causing ASD has been scarce to date. Here we summarize some considerations of experimental design that can help untangle causality in this complex system. In particular, large cross-sectional studies that can factor out important variables such as diet, prospective longitudinal studies that remove some of the influence of interpersonal variation in the microbiome (which is generally high, especially in children), and studies transferring microbial communities into germ-free mice may be especially useful. Controlling for the effects of technical variables, which have complicated efforts to combine existing studies, is critical when biological effect sizes are small. Large citizen-science studies with thousands of participants such as the American Gut Project have been effective at uncovering subtle microbiome effects in self-collected samples and with self-reported diet and behavior data, and may provide a useful complement to other types of traditionally funded and conducted studies in the case of ASD, especially in the hypothesis generation phase.
doi:10.3402/mehd.v26.26555
PMCID: PMC4355505  PMID: 25758371
autism; microbiology; microbiome; neurological
11.  Spatial and Temporal Variations in Indoor Environmental Conditions, Human Occupancy, and Operational Characteristics in a New Hospital Building 
PLoS ONE  2015;10(3):e0118207.
The dynamics of indoor environmental conditions, human occupancy, and operational characteristics of buildings influence human comfort and indoor environmental quality, including the survival and progression of microbial communities. A suite of continuous, long-term environmental and operational parameters were measured in ten patient rooms and two nurse stations in a new hospital building in Chicago, IL to characterize the indoor environment in which microbial samples were taken for the Hospital Microbiome Project. Measurements included environmental conditions (indoor dry-bulb temperature, relative humidity, humidity ratio, and illuminance) in the patient rooms and nurse stations; differential pressure between the patient rooms and hallways; surrogate measures for human occupancy and activity in the patient rooms using both indoor air CO2 concentrations and infrared doorway beam-break counters; and outdoor air fractions in the heating, ventilating, and air-conditioning systems serving the sampled spaces. Measurements were made at 5-minute intervals over consecutive days for nearly one year, providing a total of ∼8×106 data points. Indoor temperature, illuminance, and human occupancy/activity were all weakly correlated between rooms, while relative humidity, humidity ratio, and outdoor air fractions showed strong temporal (seasonal) patterns and strong spatial correlations between rooms. Differential pressure measurements confirmed that all patient rooms were operated at neutral pressure. The patient rooms averaged about 100 combined entrances and exits per day, which suggests they were relatively lightly occupied compared to higher traffic environments (e.g., retail buildings) and more similar to lower traffic office environments. There were also clear differences in several environmental parameters before and after the hospital was occupied with patients and staff. Characterizing and understanding factors that influence these building dynamics is vital for hospital environments, where they can impact patient health and the survival and spread of healthcare associated infections.
doi:10.1371/journal.pone.0118207
PMCID: PMC4346405  PMID: 25729898
12.  Adenomatous polyps are driven by microbe-instigated focal inflammation and are controlled by IL-10 producing T-cells 
Cancer research  2013;73(19):5905-5913.
Interleukin-10 (IL-10) is elevated in cancer and is thought to contribute to immune tolerance and tumor growth. Defying these expectations, the adoptive transfer of IL-10 expressing T-cells to mice with polyposis attenuates microbial-induced inflammation and suppresses polyposis. To gain better insights into how IL-10 impacts polyposis, we genetically ablated IL-10 in T-cells in APCΔ468 mice and compared the effects of treatment with broad-spectrum antibiotics. We found that T-cells and Tregs were a major cellular source of IL-10 in both the healthy and polyp-bearing colon. Notably, T-cell-specific ablation of IL-10 produced pathologies that were identical to mice with a systemic deficiency in IL-10, in both cases increasing the numbers and growth of colon polyps. Eosinophils were found to densely infiltrate colon polyps, which were enriched similarly for microbiota associated previously with colon cancer. In mice receiving broad-spectrum antibiotics, we observed reductions in microbiota, inflammation, and polyposis. Together our findings establish that colon polyposis is driven by high densities of microbes that accumulate within polyps and trigger local inflammatory responses. Inflammation, local microbe densities, and polyp growth are suppressed by IL-10 derived specifically from T-cells and Tregs.
doi:10.1158/0008-5472.CAN-13-1511
PMCID: PMC4322779  PMID: 23955389
interleukin-10; polyposis; microbiota; inflammation; colon
13.  Satellite remote sensing data can be used to model marine microbial metabolite turnover 
The ISME Journal  2014;9(1):166-179.
Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters to create a system-scale model of marine microbial metabolism for 5904 grid cells (49 km2) in the Western English Chanel, across 3 years of weekly averages. Thirteen environmental variables predicted the relative abundance of 24 bacterial Orders and 1715 unique enzyme-encoding genes that encode turnover of 2893 metabolites. The genes' predicted relative abundance was highly correlated (Pearson Correlation 0.72, P-value <10−6) with their observed relative abundance in sequenced metagenomes. Predictions of the relative turnover (synthesis or consumption) of CO2 were significantly correlated with observed surface CO2 fugacity. The spatial and temporal variation in the predicted relative abundances of genes coding for cyanase, carbon monoxide and malate dehydrogenase were investigated along with the predicted inter-annual variation in relative consumption or production of ∼3000 metabolites forming six significant temporal clusters. These spatiotemporal distributions could possibly be explained by the co-occurrence of anaerobic and aerobic metabolisms associated with localized plankton blooms or sediment resuspension, which facilitate the presence of anaerobic micro-niches. This predictive model provides a general framework for focusing future sampling and experimental design to relate biogeochemical turnover to microbial ecology.
doi:10.1038/ismej.2014.107
PMCID: PMC4274419  PMID: 25072414
14.  Life in a World without Microbes 
PLoS Biology  2014;12(12):e1002020.
Life in a world without microbes Can a macrorganism survive without commensal microbes in a world of microbes? What would happen if all microbes on earth suddenly disappeared?
doi:10.1371/journal.pbio.1002020
PMCID: PMC4267716  PMID: 25513890
15.  DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure 
MicrobiologyOpen  2014;3(6):910-921.
The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of target DNA per microliter. Exoskeletal pulverization and tissue digestion increased the reliability of extractions, suggesting that these steps should be included in any study of insect-associated microorganisms that relies on obtaining microbial DNA from intact body segments. Although laboratory and analysis techniques should be standardized across diverse sample types as much as possible, minimal modifications such as these will increase the number of environments in which bacterial communities can be successfully studied.
doi:10.1002/mbo3.216
PMCID: PMC4263514  PMID: 25257543
16S rRNA; ants; DNA extraction; Earth Microbiome Project; host-associated bacteria; insects; microbiome
16.  Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways 
BMC Genomics  2014;15(1):1014.
Background
Sphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. In particular, strains which harbour the lin pathway genes mediating the degradation of hexachlorocyclohexane (HCH) isomers are of interest due to the widespread persistence of this contaminant. Here, we examined the evolution and diversification of the lin pathway under the selective pressure of HCH, by comparing the draft genomes of six newly-sequenced Sphingobium spp. (strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH dumpsites, with three existing genomes (S. indicum B90A, S. japonicum UT26S and Sphingobium sp. SYK6).
Results
Efficient HCH degraders phylogenetically clustered in a closely related group comprising of UT26S, B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies with ANI value >98%. Less than 10% of the total gene content was shared among all nine strains, but among the eight HCH-associated strains, that is all except SYK6, the shared gene content jumped to nearly 25%. Genes associated with nitrogen stress response and two-component systems were found to be enriched. The strains also housed many xenobiotic degradation pathways other than HCH, despite the absence of these xenobiotics from isolation sources. Additionally, these strains, although non-motile, but posses flagellar assembly genes. While strains HDIPO4 and IP26 contained the complete set of lin genes, DS20 was entirely devoid of lin genes (except linKLMN) whereas, LL03, P25 and RL3 were identified as lin deficient strains, as they housed incomplete lin pathways. Further, in HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and linA2 known for their different enantioselectivity.
Conclusion
The bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on degradation efficacy. Further, the diversity in the lin gene sequences and copy number, their arrangement with respect to IS6100 and evidence for potential plasmid content elucidate possible evolutionary acquisition mechanisms for this pathway. This study further opens the horizon for selection of bacterial strains for inclusion in an HCH bioremediation consortium and suggests that HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-1014) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-1014
PMCID: PMC4289293  PMID: 25418849
Hexachlorocyclohexane (HCH); Sphingobium; lin genes; Xenobiotic compounds
17.  Ecological Succession and Viability of Human-Associated Microbiota on Restroom Surfaces 
Human-associated bacteria dominate the built environment (BE). Following decontamination of floors, toilet seats, and soap dispensers in four public restrooms, in situ bacterial communities were characterized hourly, daily, and weekly to determine their successional ecology. The viability of cultivable bacteria, following the removal of dispersal agents (humans), was also assessed hourly. A late-successional community developed within 5 to 8 h on restroom floors and showed remarkable stability over weeks to months. Despite late-successional dominance by skin- and outdoor-associated bacteria, the most ubiquitous organisms were predominantly gut-associated taxa, which persisted following exclusion of humans. Staphylococcus represented the majority of the cultivable community, even after several hours of human exclusion. Methicillin-resistant Staphylococcus aureus (MRSA)-associated virulence genes were found on floors but were not present in assembled Staphylococcus pan-genomes. Viral abundances, which were predominantly enterophages, human papilloma virus, and herpesviruses, were significantly correlated with bacterial abundances and showed an unexpectedly low virus-to-bacterium ratio in surface-associated samples, suggesting that bacterial hosts are mostly dormant on BE surfaces.
doi:10.1128/AEM.03117-14
PMCID: PMC4277569  PMID: 25398865
18.  The role of macrobiota in structuring microbial communities along rocky shores 
PeerJ  2014;2:e631.
Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.
doi:10.7717/peerj.631
PMCID: PMC4203024  PMID: 25337459
16S; Rocky intertidal; Mytilus californianus; Nitrogen cycling; Tatoosh Island; Nitrification; Animal excretion; Tidepool; Ammonium; Host-microbe
19.  Influence of Acidic pH on Hydrogen and Acetate Production by an Electrosynthetic Microbiome 
PLoS ONE  2014;9(10):e109935.
Production of hydrogen and organic compounds by an electrosynthetic microbiome using electrodes and carbon dioxide as sole electron donor and carbon source, respectively, was examined after exposure to acidic pH (∼5). Hydrogen production by biocathodes poised at −600 mV vs. SHE increased>100-fold and acetate production ceased at acidic pH, but ∼5–15 mM (catholyte volume)/day acetate and>1,000 mM/day hydrogen were attained at pH ∼6.5 following repeated exposure to acidic pH. Cyclic voltammetry revealed a 250 mV decrease in hydrogen overpotential and a maximum current density of 12.2 mA/cm2 at −765 mV (0.065 mA/cm2 sterile control at −800 mV) by the Acetobacterium-dominated community. Supplying −800 mV to the microbiome after repeated exposure to acidic pH resulted in up to 2.6 kg/m3/day hydrogen (≈2.6 gallons gasoline equivalent), 0.7 kg/m3/day formate, and 3.1 kg/m3/day acetate ( = 4.7 kg CO2 captured).
doi:10.1371/journal.pone.0109935
PMCID: PMC4198145  PMID: 25333313
20.  Development of the preterm infant gut microbiome: a research priority 
Microbiome  2014;2:38.
The very low birth weight (VLBW) infant is at great risk for marked dysbiosis of the gut microbiome due to multiple factors, including physiological immaturity and prenatal/postnatal influences that disrupt the development of a normal gut flora. However, little is known about the developmental succession of the microbiota in preterm infants as they grow and mature. This review provides a synthesis of our understanding of the normal development of the infant gut microbiome and contrasts this with dysbiotic development in the VLBW infant. The role of human milk in normal gut microbial development is emphasized, along with the role of the gut microbiome in immune development and gastroenteric health. Current research provides evidence that the gut microbiome interacts extensively with many physiological systems and metabolic processes in the developing infant. However, to the best of our knowledge, there are currently no studies prospectively mapping the gut microbiome of VLBW infants through early childhood. This knowledge gap must be filled to inform a healthcare system that can provide for the growth, health, and development of VLBW infants. The paper concludes with speculation about how the VLBW infants’ gut microbiome might function through host-microbe interactions to contribute to the sequelae of preterm birth, including its influence on growth, development, and general health of the infant host.
doi:10.1186/2049-2618-2-38
PMCID: PMC4203464  PMID: 25332768
Preterm infants; VLBW; Gut microbiota; Health
21.  Science is innate! 
Genome Biology  2014;15(10):477.
doi:10.1186/s13059-014-0477-0
PMCID: PMC4318431  PMID: 25315295
22.  Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness 
mBio  2014;5(5):e01361-14.
ABSTRACT
We analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients. Bacteria associated with the genera Enterococcus and Staphylococcus and the family Enterobacteriaceae comprised the majority of these communities. The composition of cultured species from stool samples correlated to the 16S rRNA analysis and additionally revealed the emergence of Candida albicans and Candida glabrata in ~75% of cases. Four of 14 ICU patients harbored 2-member pathogen communities consisting of one Candida taxon and one bacterial taxon. Bacterial members displayed a high degree of resistance to multiple antibiotics. The virulence potential of the 2-member communities was examined in C. elegans during nutrient deprivation and exposure to opioids in order to mimic local conditions in the gut during critical illness. Under conditions of nutrient deprivation, the bacterial members attenuated the virulence of fungal members, leading to a “commensal lifestyle.” However, exposure to opioids led to a breakdown in this commensalism in 2 of the ultra-low-diversity communities. Application of a novel antivirulence agent (phosphate-polyethylene glycol [Pi-PEG]) that creates local phosphate abundance prevented opioid-induced virulence among these pathogen communities, thus rescuing the commensal lifestyle. To conclude, the gut microflora in critically ill patients can consist of ultra-low-diversity communities of multidrug-resistant pathogenic microbes. Local environmental conditions in gut may direct pathogen communities to adapt to either a commensal style or a pathogenic style.
IMPORTANCE
During critical illness, the normal gut microbiota becomes disrupted in response to host physiologic stress and antibiotic treatment. Here we demonstrate that the community structure of the gut microbiota during prolonged critical illness is dramatically changed such that in many cases only two-member pathogen communities remain. Most of these ultra-low-membership communities display low virulence when grouped together (i.e., a commensal lifestyle); individually, however, they can express highly harmful behaviors (i.e., a pathogenic lifestyle). The commensal lifestyle of the whole community can be shifted to a pathogenic one in response to host factors such as opioids that are released during physiologic stress and critical illness. This shift can be prevented by using compounds such as Pi-PEG15-20 that interrupt bacterial virulence expression. Taking the data together, this report characterizes the plasticity seen with respect to the choice between a commensal lifestyle and a pathogenic lifestyle among ultra-low-diversity pathogen communities that predominate in the gut during critical illness and offers novel strategies for prevention of sepsis.
doi:10.1128/mBio.01361-14
PMCID: PMC4173762  PMID: 25249279
23.  Towards effective probiotics for autism and other mental disorders? 
Cell  2013;155(7):1446-1448.
Hsaio and colleagues link gut microbes to autism spectrum disorders (ASD) in a mouse model. They show that ASD symptoms are triggered by compositional and structural shifts of microbes and associated metabolites, but symptoms are relieved by a B. fragilis probiotic. Thus probiotics may provide therapeutic strategies for mental disorders.
doi:10.1016/j.cell.2013.11.035
PMCID: PMC4166551  PMID: 24360269
24.  Intestinal anastomotic injury alters spatially defined microbiome composition and function 
Microbiome  2014;2:35.
Background
When diseased intestine (i.e., from colon cancer, diverticulitis) requires resection, its reconnection (termed anastomosis) can be complicated by non-healing of the newly joined intestine resulting in spillage of intestinal contents into the abdominal cavity (termed anastomotic leakage). While it is suspected that the intestinal microbiota have the capacity to both accelerate and complicate anastomotic healing, the associated genotypes and functions have not been characterized.
Results
Using 16S rRNA amplicon sequencing of samples collected on the day of surgery (postoperative day 0 (POD0)) and the 6th day following surgery (postoperative day 0 (POD6)), we analyzed the changes in luminal versus tissue-associated microbiota at anastomotic sites created in the colon of rats. Results indicated that anastomotic injury induced significant changes in the anastomotic tissue-associated microbiota with minimal differences in the luminal microbiota. The most striking difference was a 500-fold and 200-fold increase in the relative abundance of Enterococcus and Escherichia/Shigella, respectively. Functional profiling predicted the predominance of bacterial virulence-associated pathways in post-anastomotic tissues, including production of hemolysin, cytolethal toxins, fimbriae, invasins, cytotoxic necrotizing factors, and coccolysin.
Conclusion
Taken together, our results suggest that compositional and functional changes accompany anastomotic tissues and may potentially accelerate or complicate anastomotic healing.
doi:10.1186/2049-2618-2-35
PMCID: PMC4171717  PMID: 25250176
Colon anastomosis; 16S rRNA; PiCRUST; Bacterial composition; Predicted function; Anastomotic tissues; Luminal content
25.  The Earth Microbiome project: successes and aspirations 
BMC Biology  2014;12:69.
doi:10.1186/s12915-014-0069-1
PMCID: PMC4141107  PMID: 25184604

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