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Objective Dysbiosis is a common feature in the pathogenesis of inflammatory bowel diseases (IBD). Environmental factors, such as vitamin D deficiency, seem to play a role in the intestinal inflammation of IBD. The aim of this study was to investigate whether vitamin D administration has an impact on the bacterial composition in Crohn's disease (CD) compared to healthy controls (HC). Methods A prospective, longitudinal, controlled interventional analysis was conducted in seven patients with CD in clinical remission and 10 HC to investigate the effect of orally administrated vitamin D on the intestinal bacterial composition using 16S ribosomal RNA gene amplicon sequencing. Clinical parameters were assessed. Results In contrast to HC, microbial communities of CD patients changed significantly during early vitamin D administration. However, a further increase in vitamin D level was associated with a reversal of this effect and additionally with a decrease in the bacterial richness in the CD microbiome. Specific species with a high abundancy were found during vitamin D administration in CD, but not in HC; the abundancy of Alistipes, Barnesiella, unclassified Porphyromonadaceae (both Actinobacteria), Roseburia, Anaerotruncus, Subdoligranulum and an unclassified Ruminococaceae (all Firmicutes) increased significantly after 1-week vitamin D administration in CD. Conclusions Vitamin D has a specific influence on the bacterial communities in CD, but not in HC. Administration of vitamin D may have a positive effect in CD by modulating the intestinal bacterial composition and also by increasing the abundance of potential beneficial bacterial strains.

Mn is one of the most abundant redox-sensitive metals on earth. Some microorganisms are known to use Mn(IV) oxide (MnO2) as electron acceptor for the oxidation of organic compounds or hydrogen (H2), but so far the use of sulfide (H2S) has been suggested but not proven. Here we report on a bacterial isolate which grows autotrophically and couples the reduction of MnO2 to the oxidation of H2S or thiosulfate (S2O32−) for energy generation. The isolate, originating from the Black Sea, is a species within the genus Sulfurimonas, which typically occurs with high cell numbers in the vicinity of sulfidic environments [Y. Han, M. Perner, Front. Microbiol. 6, 989 (2015)]. H2S and S2O32− are oxidized completely to sulfate (SO42−) without the accumulation of intermediates. In the culture, Mn(IV) reduction proceeds via Mn(III) and finally precipitation of Ca-rich Mn(II) carbonate [Mn(Ca)CO3]. In contrast to Mn-reducing bacteria, which use organic electron donors or H2, Fe oxides are not observed to support growth, which may either indicate an incomplete gene set or a different pathway for extracellular electron transfer.

Differences in salinity are boundaries that act as barriers for the dispersal of most aquatic organisms. This creates distinctive biota in freshwater and brackish water (mesohaline) environments. To test how saline boundaries influence the diversity and composition of host-associated microbiota, we analyzed the microbiome within the digestive tract of Theodoxus fluviatilis, an organism able to cross the freshwater and mesohaline boundary. Alpha-diversity measures of the microbiome in freshwater and brackish water were not significantly different. However, the composition of the bacterial community within freshwater T. fluviatilis differed significantly compared with mesohaline T. fluviatilis and typical bacteria could be determined for the freshwater and the mesohaline digestive tract microbiome. An artificial increase in salinity surrounding these freshwater snails resulted in a strong change in the bacterial community and typical marine bacteria became more pronounced in the digestive tract microbiome of freshwater T. fluviatilis. However, the composition of the digestive tract microbiome in freshwater snails did not converge to that found within mesohaline snails. Within mesohaline snails, no cardinal change was found after either an increase or decrease in salinity. In all samples, Pseudomonas, Pirellula, Flavobacterium, Limnohabitans, and Acinetobacter were among the most abundant bacteria. These bacterial genera were largely unaffected by changes in environmental conditions. As permanent residents in T. fluviatilis, they may support the digestion of the algal food in the digestive tract. Our results show that freshwater and mesohaline water host-associated microbiomes respond differently to changes in salinity. Therefore, the salinization of coastal freshwater environments due to a rise in sea level can influence the gut microbiome and its functions with currently unknown consequences for, e.g., nutritional physiology of the host. DH, CK, VK, KK, and HT were supported by the European Regional Development Fund/Estonian Research Council funded “Mobilitas Plus Top Researcher grant MOBTT24.” In addition, VK was supported by Estonian Research Council grant PUT1389. The project is also supported by the Baltic-German University Liaison Office and the German Academic Exchange Service (DAAD) with funds from the Foreign Office of the Federal Republic of Germany. Financial support was also provided by the German Research Foundation (DFG), RTG 2010. DH, CK, VK, KK, and HT were supported by the European Regional Development Fund/Estonian Research Council funded “Mobilitas Plus Top Researcher grant MOBTT24.” In addition, VK was supported by Estonian Research Council grant PUT1389. The project is also supported by the Baltic-German University Liaison Office and the German Academic Exchange Service (DAAD) with funds from the Foreign Office of the Federal Republic of Germany. Financial support was also provided by the German Research Foundation (DFG), RTG 2010.

In inflammatory bowel diseases (IBD), microbial communities often become imbalanced suggesting abnormal microbial-gut interactions. In this study, we analysed the mucosa-attached gut microbiota from 26 Crohn's disease (CD) patients using 16S rRNA gene amplicon sequencing. The samples were stratified according to their disease activity (Crohn's disease activity index, CDAI). The different disease activity categories had a comparable bacterial richness. Bacterial communities of patients in remission and intermediate CDAI (0-220) were relatively similar and dominated by the genus Bacteroides (>40%). The bacterial composition of patients assigned to a high CDAI category was dominated by Pelomonas (25%) and Flavobacterium (13%) but had a low relative abundance of Bacteroidetes (4%). This indicates the presence of specific abundant bacterial taxa at different CDAI levels. In addition, bacterial communities were also significantly influenced when a tumour necrosis factor (TNF)-α inhibitor was applied or by the local mucosal inflammation level. As a consequence, a shift of the microbial composition may also indicate a change of the disease activity in CD patients.

Enclosure experiments are frequently used to investigate the impact of changing environmental conditions on microbial assemblages. Yet, how the incuba- tion itself challenges complex bacterial communities is thus far unknown. In this study, metaproteomic profiling, 16S rRNA gene analyses, and cell counts were com- bined to evaluate bacterial communities derived from marine, mesohaline, and oli- gohaline conditions after long-term batch incubations. Early in the experiment, the three bacterial communities were highly diverse and differed significantly in their compositions. Manipulation of the enclosures with terrigenous dissolved organic car- bon resulted in notable differences compared to the control enclosures at this early phase of the experiment. However, after 55 days, bacterial communities in the ma- nipulated and the control enclosures under marine and mesohaline conditions were all dominated by gammaproteobacterium Spongiibacter. In the oligohaline enclo- sures, actinobacterial cluster I of the hgc group (hgc-I) remained abundant in the late phase of the incubation. Metaproteome analyses suggested that the ability to use outer membrane-based internal energy stores, in addition to the previously de- scribed grazing resistance, may enable the gammaproteobacterium Spongiibacter to prevail in long-time incubations. Under oligohaline conditions, the utilization of ex- ternal recalcitrant carbon appeared to be more important (hgc-I). Enclosure experi- ments with complex natural microbial communities are important tools to investi- gate the effects of manipulations. However, species-specific properties, such as individual carbon storage strategies, can cause manipulation-independent effects and need to be considered when interpreting results from enclosures. This study was financially supported by the SAW-funded ATKiM project, which provided funds to D. P. R. Herlemann, C. Meeske, K. Jürgens, S. Markert, and T. Schweder. D. P. R. Herlemann was also supported by the European Regional Develop- ment Fund/Estonian Research Council funded Mobilitas Plus Top Researcher grant MOBTT24. We thank the crew and captain of the RV Meteor (M86, M87) for support during the research cruise. The computations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) at the PDC Centre for High Performance Computing (PDC-HPC) and Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX). We thank Jana Matulla for excellent technical assis- tance and Stephan Fuchs for his help and advice in MS database construction. We also thank Stefan E. Heiden for valuable help with the CDD BLAST analyses. This study was financially supported by the SAW-funded ATKiM project, which provided funds to D. P. R. Herlemann, C. Meeske, K. Jürgens, S. Markert, and T. Schweder. D. P. R. Herlemann was also supported by the European Regional Develop- ment Fund/Estonian Research Council funded Mobilitas Plus Top Researcher grant MOBTT24. We thank the crew and captain of the RV Meteor (M86, M87) for support during the research cruise. The computations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) at the PDC Centre for High Performance Computing (PDC-HPC) and Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX). We thank Jana Matulla for excellent technical assis- tance and Stephan Fuchs for his help and advice in MS database construction. We also thank Stefan E. Heiden for valuable help with the CDD BLAST analyses.

The Black Sea is the world’s largest anoxic basin and a model system for studying processes across redox gradients. In between the oxic surface and the deeper sulfidic waters there is an unusually broad layer of 10–40 m, where neither oxygen nor sulfide are detectable. In this suboxic zone, dissolved phosphate profiles display a pronounced minimum at the upper and a maximum at the lower boundary, with a peak of particulate phosphorus in between, which was suggested to be caused by the sorption of phosphate on sinking particles of metal oxides. Here we show that bacterial polyphosphate inclusions within large magnetotactic bacteria related to the genus Magnetococcus contribute substantially to the observed phosphorus peak, as they contain 26–34% phosphorus compared to only 1–5% in metal-rich particles. Furthermore, we found increased gene expression for polyphosphate kinases by several groups of bacteria including Magnetococcaceae at the phosphate maximum, indicating active bacterial polyphosphate degradation. We propose that large magnetotactic bacteria shuttle up and down within the suboxic zone, scavenging phosphate at the upper and releasing it at the lower boundary. In contrast to a passive transport via metal oxides, this bacterial transport can quantitatively explain the observed phosphate profiles. We are grateful for the competent technical assistance of Ronny Baaske, Christian Burmeister, Christin Laudan and Christian Meeske. We are greatly indebted to Cindy Lee and Bo Barker Jørgensen for providing extremely helpful comments on an earlier version of the manuscript. Horst D. Schulz and René Friedland are acknowledged for stimulating discussions on the modeling approach. We thank the captain and the crew of the R/V “Maria S. Merian” for the excellent support on board and the DFG (MSM33) and BMBF (01DK12043) for financing the cruise. The particle analysis was funded by the BMBF (03F0663A). S.B. was funded by a BONUS BLUEPRINT project (03F0679A awarded to KJ; http://blueprint- project.org), supported by BONUS (Art 185), funded jointly by the EU and the German Federal Ministry of Education and Research (BMBF). T. S. was funded by the German research foundation (DFG) (awarded to K.J., JU 367/16-1). Metagenome sequencing was done at the Swedish National Genomics Infrastructure (NGI) at SciLifeLab (Sweden). We are grateful for the competent technical assistance of Ronny Baaske, Christian Burmeister, Christin Laudan and Christian Meeske. We are greatly indebted to Cindy Lee and Bo Barker Jørgensen for providing extremely helpful comments on an earlier version of the manuscript. Horst D. Schulz and René Friedland are acknowledged for stimulating discussions on the modeling approach. We thank the captain and the crew of the R/V “Maria S. Merian” for the excellent support on board and the DFG (MSM33) and BMBF (01DK12043) for financing the cruise. The particle analysis was funded by the BMBF (03F0663A). S.B. was funded by a BONUS BLUEPRINT project (03F0679A awarded to KJ; http://blueprint- project.org), supported by BONUS (Art 185), funded jointly by the EU and the German Federal Ministry of Education and Research (BMBF). T. S. was funded by the German research foundation (DFG) (awarded to K.J., JU 367/16-1). Metagenome sequencing was done at the Swedish National Genomics Infrastructure (NGI) at SciLifeLab (Sweden).

The role of bacteria in chronic rhinosinusitis (CRS) is still not well understood. Whole microbiome analysis adds new aspects to our current understanding that ismainly based on isolated bacteria. It is still unclear how the results of microbiome analysis and the classical culture based approaches interrelate. To address this, middle meatus swabs and tissue samples were obtained during sinus surgery in 5 patients with CRS with nasal polyps (CRSwNP), 5 patients with diffuse CRS without nasal polyps (CRSsNP), 5 patients with unilateral purulent maxillary CRS (upm CRS) and 3 patients with healthy sinus mucosa. Swabs were cultured, and associated bacteria were identified. Additionally, parts of each tissue sample also underwent culture approaches, and in parallel DNA was extracted for 16S rRNA gene amplicon-based microbiome analysis. From tissue samples 4.2 ± 1.2 distinct species per patient were cultured, from swabs 5.4 ± 1.6. The most frequently cultured species from the swabs were Propionibacterium acnes, Staphylococcus epidermidis, Corynebacterium spp. and Staphylococcus aureus. The 16S-RNA gene analysis revealed no clear differentiation of the bacterial community of healthy compared to CRS samples of unilateral purulent maxillary CRS and CRSwNP. However, the bacterial community of CRSsNP differed significantly from the healthy controls. In the CRSsNP samples Flavobacterium, Pseudomonas, Pedobacter, Porphyromonas, Stenotrophomonas, and Brevundimonas were significantly enriched compared to the healthy controls. Species isolated from culture did not generally correspond with the most abundant genera in microbiome analysis. Only Fusobacteria, Parvimonas, and Prevotella found in 2 unilateral purulent maxillary CRS samples by the cultivation dependent approach were also found in the cultivation independent approach in high abundance, suggesting a classic infectious pathogenesis of odontogenic origin in these two specific cases. Alterations of the bacterial community might be a more crucial factor for the development of CRSsNP compared to CRSwNP. Further studies are needed to investigate the relation between bacterial community characteristics and the development of CRSsNP. Purchase of the Illumina MiSeq was kindly supported by the EU-EFRE (European Funds for Regional Development) program and funds from the University Medicine Rostock. Purchase of the Illumina MiSeq was kindly supported by the EU-EFRE (European Funds for Regional Development) program and funds from the University Medicine Rostock.

Salinity has a strong impact on bacterial community composition such that freshwater bacterial communities are very different from those in seawater. By contrast, little is known about the composition and diversity of the bacterial community in the sediments (bacteriobenthos) at the freshwater-seawater transition (mesohaline conditions). In this study, partial 16S-rRNA sequences were used to investigate the bacterial community at five stations, representing almost freshwater (oligohaline) to marine conditions, in the Baltic Sea. Samples were obtained from the silty, top-layer (0–2.5 cm) sediments with mostly oxygenated conditions. The long water residence time characteristic of the Baltic Sea, was predicted to enable the development of autochthonous bacteriobenthos at mesohaline conditions. Our results showed that, similar to the water column, salinity is a major factor in structuring the bacteriobenthos and that there is no loss of bacterial richness at intermediate salinities. The bacterial communities of marine, mesohaline, and oligohaline sediments differed in terms of the relative rRNA abundances of the major bacterial phyla/classes. At mesohaline conditions typical marine and oligohaline operational taxonomic units (OTUs) were abundant. Putative unique OTUs in mesohaline sediments were present only at low abundances, suggesting that the mesohaline environment consists mainly of marine and oligohaline bacteria with a broad salinity tolerance. Our study provides a first overview of the diversity patterns and composition of bacteria in the sediments along the Baltic Sea salinity gradient as well as new insights into the bacteriobenthos at mesohaline conditions. The study was funded by the Leibniz Institute for Baltic Sea Research (IOW), KJ were funded by the DFG project MicroFun (JU367/15-1), JK by the Leibniz Association project TemBi (SAW-2011-IGB-2). The study was funded by the Leibniz Institute for Baltic Sea Research (IOW), KJ were funded by the DFG project MicroFun (JU367/15-1), JK by the Leibniz Association project TemBi (SAW-2011-IGB-2).

Major Baltic inflow (MBI) events carry highly saline water from the North Sea to the central Baltic Sea and thereby affect both its environmental conditions and its biota. While bacterioplankton communities in the Baltic Sea are strongly structured by salinity, how MBIs impact the composition and distribution of bacteria is unknown. The exceptional MBI in 2014, which brought saline and oxygenated water into the basins of the central Baltic Sea, enabled the linkage of microbiological investigations to hydrographic and modeling studies of this MBI. Using sequence data of 16S ribosomal RNA (rRNA) and 16S rRNA genes (rDNA), we analyzed bacterioplankton community composition in the inflowing water and in the uplifted former bottomwater at stations reached by the MBI. Bacterial diversity data were compared with respective data obtained from previous, non-inflow conditions. Changes in bacterial community composition following the 2014 MBI were mainly apparent at the genus level. A number of specific taxa were enriched in the inflowing water, with large changes in the rRNA/rDNA ratios indicating the different activity levels between of the water masses. The relative similarity of the bacterial communities in the inflowing and uplifted waters as well as the results from an inflow-simulating numerical model showed that the inflowing water did not originate directly from the North Sea but mostly from adjacent areas in the Baltic Sea. This suggested that the inflow event led to a series of shifts in Baltic Sea water masses among the Baltic Sea basins and a gradual mixing of the water bodies. Dramatic changes in the bacterial community composition occurred when the bottomwater inflow reached the anoxic, sulfidic deep basins, resulting in an uplifting of the formerly anoxic bacterial community, dominated by Epsilonproteobacteria. Our study of the impact of MBIs on bacterioplankton communities therefore highlights two relevant underlying mechanisms that impact the distribution and possibly also the activities of planktonic bacteria in the Baltic Sea: (1) the successive dilution of inflowing North Sea water with ambient waters and (2) the uplifting of former bottom-water communities to higher water strata. This work was funded by the Deutsche Forschungsgemeinschaft (DFG) (projects JU367/15-1, JU367/16-1 to KJ and LA1466/8- 1 to ML). DH was supported by the European Regional Development Fund and the Estonian Research Council Mobilitas Plus Top Researcher grant “MOBTT24.” UG was supported by the BMBF project “Hydrodynamic observations and simulations of munition in the sea,” a subproject of the collaborative project “Environmental monitoring for the delaboration of munitions in the sea” (Grant No. #03F0747C). This work was funded by the Deutsche Forschungsgemeinschaft (DFG) (projects JU367/15-1, JU367/16-1 to KJ and LA1466/8- 1 to ML). DH was supported by the European Regional Development Fund and the Estonian Research Council Mobilitas Plus Top Researcher grant “MOBTT24.” UG was supported by the BMBF project “Hydrodynamic observations and simulations of munition in the sea,” a subproject of the collaborative project “Environmental monitoring for the delaboration of munitions in the sea” (Grant No. #03F0747C).

Understanding the key processes that control bacterial community composition has enabled predictions of bacterial distribution and function within ecosystems. In this study, we used the Baltic Sea as a model system to quantify the phylogenetic signal of salinity and season with respect to bacterioplankton community composition. The abundances of 16S rRNA gene amplicon sequencing reads were analyzed from samples obtained from similar geographic locations in July and February along a brackish to marine salinity gradient in the Baltic Sea. While there was no distinct pattern of bacterial richness at different salinities, the number of bacterial phylotypes in winter was significantly higher than in summer. Bacterial community composition in brackish vs. marine conditions, and in July vs. February was significantly different. Non-metric multidimensional scaling showed that bacterial community composition was primarily separated according to salinity and secondly according to seasonal differences at all taxonomic ranks tested. Similarly, quantitative phylogenetic clustering implicated a phylogenetic signal for both salinity and seasonality. Our results support that global patterns of bacterial community composition with respect to salinity and season are the result of phylogenetically clustered ecological preferences with stronger imprints from salinity.

In response to global warming, increasing quantities of tDOM are transported through estuaries from land to the sea. In this study we investigated microbial responses to increased tDOM concentrations in three salinity regimes (salinity: 32, 7 and 3) characteristic of the Baltic Sea. Mesocosm experiments performed in May and November revealed low (0–6%) dissolved organic carbon (DOC) utilization. Molecular DOM analyses using ultra-high-resolution mass spectrometry identified the terrigenous signal in the tDOM manipulation, but the molecular changes in DOM levels over the course of the experiment were subtle. However, tDOM had significant stimulatory effects on bacterial production in the oligohaline mesocosms. The shift in the bacterial community composition was especially prominent in the tDOM-amended marine and mesohaline mesocosms, but not in the oligohaline mesocosms after 7 and 11 days of incubation. These results suggested the inherent ability of oligohaline bacterial communities to adapt to high tDOM concentrations and therefore to use tDOM. The higher rates of bacterial activity and DOC removal in mesocosms containing UV-pretreated tDOM supported the increased bioavailability of photoinduced, modified tDOM. The overall low rates of microbial tDOM utilization highlights the importance of abiotic factors in determining the distribution and dynamics of tDOM in estuaries. This article is protected by copyright. All rights reserved.

Kazachstania slooffiae is a porcine intestinal yeast whose role in the intestinal environment is largely unexplored. Therefore, the impact of K. slooffiae on growth performance, intestinal microbial metabolites and the microbiota of weaned piglets was investigated in this study. Forty-eight German Landrace pigs were weaned at day 27 or 28 of life and grouped into one control and three treatment groups. During the 5-week experiment, piglets had ad libitum access to feed and water. On days 5, 6 and 7 post weaning, pigs were orally supplemented with either placebo or K. slooffiae cells once a day. Faecal samples collected on days 5–8, 14, 21 and 28 post weaning were used for microbiological and chemical analyses. Between groups, there were no significant differences in the incidence of diarrhoea, pH and growth performance. Total yeasts and K. slooffiae correlated positively with total short-chain fatty acids, acetic, propionic, n -butyric, i- valeric and valeric acids, and negatively with pH. Pyrosequencing of the bacterial intestinal community revealed that K. slooffiae significantly affected the composition of the microbiota. The results of this study suggest that K. slooffiae may play an important role in the porcine digestive system, especially in the critical weaning period.

Salinity is a major factor controlling the distribution of biota in aquatic systems, and most aquatic multicellular organisms are either adapted to life in saltwater or freshwater conditions. Consequently, the saltwater-freshwater mixing zones in coastal or estuarine areas are characterized by limited faunal and floral diversity. Although changes in diversity and decline in species richness in brackish waters is well documented in aquatic ecology, it is unknown to what extent this applies to bacterial communities. Here, we report a first detailed bacterial inventory from vertical profiles of 60 sampling stations distributed along the salinity gradient of the Baltic Sea, one of world's largest brackish water environments, generated using 454 pyrosequencing of partial (400 bp) 16S rRNA genes. Within the salinity gradient, bacterial community composition altered at broad and finer-scale phylogenetic levels. Analogous to faunal communities within brackish conditions, we identified a bacterial brackish water community comprising a diverse combination of freshwater and marine groups, along with populations unique to this environment. As water residence times in the Baltic Sea exceed 3 years, the observed bacterial community cannot be the result of mixing of fresh water and saltwater, but our study represents the first detailed description of an autochthonous brackish microbiome. In contrast to the decline in the diversity of multicellular organisms, reduced bacterial diversity at brackish conditions could not be established. It is possible that the rapid adaptation rate of bacteria has enabled a variety of lineages to fill what for higher organisms remains a challenging and relatively unoccupied ecological niche.