Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies

Description and genome analysis of a novel archaeon isolated from a syntrophic pyrite-forming enrichment culture and reclassification of Methanospirillum hungatei strains GP1 and SK as Methanospirillum purgamenti sp. nov

The archaeal isolate J.3.6.1-F.2.7.3T was obtained from an anaerobic enrichment culture, where it may play an important role in methane production during pyrite formation. The new isolate formed a species-level clade with Methanospirillum hungatei strains GP1 and SK, which is separate from the type strain JF-1T. Cultivation-independent surveys indicate the occurrence of this phylogenetic group in sediments and anaerobic digesters. The abundance of this clade appears to be negatively affected by high nitrogen loads, indicating a sensitivity to certain nitrogen compounds that is not known in M. hungatei JF-1T. The relatively large core genome of this Methanospirillum clade is indicative of niche specialization and efficient control of horizontal gene transfer. Genes for nitrogenase and F420-dependent secondary alcohol dehydrogenase contribute to the metabolic versatility of this lineage. Characteristics of the new isolate such as the ability to utilize 2-propanol as an electron donor or the requirement for acetate as a carbon source are found also in the strains GP1 and SK, but not in the type strain M. hungatei JF-1T. Based on the genomic differences to related species, a new species within the genus Methanospirillum is proposed with the name M. purgamenti sp. nov. The determined phenotypic characteristics support this proposal and indicate a metabolic adaptation to a separate ecological niche.

Geographic and Ecological Diversity of Green Sulfur Bacteria in Hot Spring Mat Communities

Three strains of thermophilic green sulfur bacteria (GSB) are known; all are from microbial mats in hot springs in Rotorua, New Zealand (NZ) and belong to the species Chlorobaculum tepidum. Here, we describe diverse populations of GSB inhabiting Travel Lodge Spring (TLS) (NZ) and hot springs ranging from 36.1 °C to 51.1 °C in the Republic of the Philippines (PHL) and Yellowstone National Park (YNP), Wyoming, USA. Using targeted amplification and restriction fragment length polymorphism analysis, GSB 16S rRNA sequences were detected in mats in TLS, one PHL site, and three regions of YNP. GSB enrichments from YNP and PHL mats contained small, green, nonmotile rods possessing chlorosomes, chlorobactene, and bacteriochlorophyll c. Partial 16S rRNA gene sequences from YNP, NZ, and PHL mats and enrichments from YNP and PHL samples formed distinct phylogenetic clades, suggesting geographic isolation, and were associated with samples differing in temperature and pH, suggesting adaptations to these parameters. Sequences from enrichments and corresponding mats formed clades that were sometimes distinct, increasing the diversity detected. Sequence differences, monophyly, distribution patterns, and evolutionary simulation modeling support our discovery of at least four new putative moderately thermophilic Chlorobaculum species that grew rapidly at 40 °C to 44 °C.

Epichloë Endophytes Shape the Foliar Endophytic Fungal Microbiome and Alter the Auxin and Salicylic Acid Phytohormone Levels in Two Meadow Fescue Cultivars

Plants harbor a large diversity of endophytic microbes. Meadow fescue (Festuca pratensis) is a cool-season grass known for its symbiotic relationship with the systemic and vertically-via seeds-transmitted fungal endophyte Epichloë uncinata, yet its effects on plant hormones and the microbial community is largely unexplored. Here, we sequenced the endophytic bacterial and fungal communities in the leaves and roots, analyzing phytohormone concentrations and plant performance parameters in Epichloë-symbiotic (E+) and Epichloë-free (E-) individuals of two meadow fescue cultivars. The endophytic microbial community differed between leaf and root tissues independent of Epichloë symbiosis, while the fungal community was different in the leaves of Epichloë-symbiotic and Epichloë-free plants in both cultivars. At the same time, Epichloë symbiosis decreased salicylic acid and increased auxin concentrations in leaves. Epichloë-symbiotic plants showed higher biomass and higher seed mass at the end of the season. Our results demonstrate that Epichloë symbiosis alters the leaf fungal microbiota, which coincides with changes in phytohormone concentrations, indicating that Epichloë endophytes affect both plant immune responses and other fungal endophytes. Whether the effect of Epichloë endophytes on other fungal endophytes is connected to changes in phytohormone concentrations remains to be elucidated.

Honeybees affect floral microbiome composition in a central food source for wild pollinators in boreal ecosystems

Basic knowledge on dispersal of microbes in pollinator networks is essential for plant, insect, and microbial ecology. Thorough understanding of the ecological consequences of honeybee farming on these complex plant-pollinator-microbe interactions is a prerequisite for sustainable honeybee keeping. Most research on plant-pollinator-microbe interactions have focused on temperate agricultural systems. Therefore, information on a wild plant that is a seasonal bottleneck for pollinators in cold climate such as Salix phylicifolia is of specific importance. We investigated how floral visitation by insects influences the community structure of bacteria and fungi in Salix phylicifolia inflorescences under natural conditions. Insect visitors were experimentally excluded with net bags. We analyzed the microbiome and measured pollen removal in open and bagged inflorescences in sites where honeybees were foraging and in sites without honeybees. Site and plant individual explained most of the variation in floral microbial communities. Insect visitation and honeybees had a smaller but significant effect on the community composition of microbes. Honeybees had a specific effect on the inflorescence microbiome and, e.g., increased the relative abundance of operational taxonomic units (OTUs) from the bacterial order Lactobacillales. Site had a significant effect on the amount of pollen removed from inflorescences but this was not due to honeybees. Insect visitors increased bacterial and especially fungal OTU richness in the inflorescences. Pollinator visits explained 38% variation in fungal richness, but only 10% in bacterial richness. Our work shows that honeybee farming affects the floral microbiome in a wild plant in rural boreal ecosystems.

Hydrolytic enzyme screening and carotenoid production evaluation of halophilic archaea isolated from highly heavy metal-enriched solar saltern sediments

This paper aimed to screen the enzymatic activities and evaluate the carotenoid production level of twenty-two halophilic archaea isolated from Sfax solar saltern sediments. The molecular identification performed by sequencing the 16S rRNA genes showed that all strains have a high similarity degree (99.7-100%) with Halobacterium salinarum NRC-1. The strains were screened for the presence of eight hydrolase activities using agar plate-based assays. The most detected enzyme was gelatinase (77.27% of total strains), followed by protease (63.63%) and amylase activities (50%). The carotenoid production yields of the strains ranged between 2.027 and 14.880 mg/l. The UV-Visible spectroscopy of pigments revealed that it was a bacterioruberin type. When evaluated and compared to the standard β-carotene, the antioxidant capacities of these pigments showed a scavenging activity of more than 75% at a concentration of 5 μg/ml for three strains (AS16, AS17, and AS18). Then a sequence of one-step optimization processes was performed, using the one-factor-at-a-time approach, to define the optimum conditions for growth and carotenoid production of the highest carotenoid producing strain (AS17). Different environmental factors and nutritional conditions were tested. Variations in these factors were found to deeply influence growth and carotenoid production. A maximum carotenoid production (16.490 mg/l), higher than that of the control (14.880 mg/l), was observed at 37 °C, pH 7, 250 g/l of salinity, with 80% air phase in the flask at 110 rpm, in presence of light and in culture media containing (g/l) 10, yeast extract; 7.5, casamino acid; 20, MgSO4; 4, KCl; and 3, trisodium citrate.

Microbiomes and Planctomycete diversity in large-scale aquaria habitats

In commercial large-scale aquaria, controlling levels of nitrogenous compounds is essential for macrofauna health. Naturally occurring bacteria are capable of transforming toxic nitrogen species into their more benign counterparts and play important roles in maintaining aquaria health. Nitrification, the microbially-mediated transformation of ammonium and nitrite to nitrate, is a common and encouraged process for management of both commercial and home aquaria. A potentially competing microbial process that transforms ammonium and nitrite to dinitrogen gas (anaerobic ammonium oxidation [anammox]) is mediated by some bacteria within the phylum Planctomycetes. Anammox has been harnessed for nitrogen removal during wastewater treatment, as the nitrogenous end product is released into the atmosphere rather than in aqueous discharge. Whether anammox bacteria could be similarly utilized in commercial aquaria is an open question. As a first step in assessing the viability of this practice, we (i) characterized microbial communities from water and sand filtration systems for four habitats at the Tennessee Aquarium and (ii) examined the abundance and anammox potential of Planctomycetes using culture-independent approaches. 16S rRNA gene amplicon sequencing revealed distinct, yet stable, microbial communities and the presence of Planctomycetes (~1-15% of library reads) in all sampled habitats. Preliminary metagenomic analyses identified the genetic potential for multiple complete nitrogen metabolism pathways. However, no known genes diagnostic for the anammox reaction were found in this survey. To better understand the diversity of this group of bacteria in these systems, a targeted Planctomycete-specific 16S rRNA gene-based PCR approach was used. This effort recovered amplicons that share <95% 16S rRNA gene sequence identity to previously characterized Planctomycetes, suggesting novel strains within this phylum reside within aquaria.

How to Handle CT-Guided Abscess Drainages in Microbiological Analyses? Sterile Vials vs. Blood Culture Bottles for Transport and Processing

The aim of this investigation was to compare microbiological analyses of 100 computed tomography-guided drainages from infectious foci (thoracic, abdominal, musculoskeletal), transported and analyzed by two widely established techniques, that are (i) sterile vials or (ii) inoculated blood culture bottles. The mean number of detected microorganisms from blood culture (aerobic/anaerobic) or conventional method (sterile vial, solid and broth media) per specimen were comparable with 1.29 and 1.41, respectively (p = 1.0). The conventional method showed a trend towards shorter time-to-result (median 28.62 h) in comparison to blood culture incubation (median 43.55 h) (p = 0.0722). Of note, detection of anaerobes (13% vs. 36%) and the number of detected microorganisms in polymicrobial infections (2.76 vs. 3.26) differed significantly with an advantage towards conventional techniques (p = 0.0015; p = 0.035), especially in abdominal aspirations. Despite substantially overlapping results from both techniques, the conventional approach includes some benefits which justify its role as standard approach.

Development of fluorescence in situ hybridization (FISH) probes to detect and enumerate Gambierdiscus species

Ciguatera poisoning (CP) is a syndrome caused by the bioaccumulation of lipophilic ciguatoxins in coral reef fish and invertebrates, and their subsequent consumption by humans. These phycotoxins are produced by Gambierdiscus spp., tropical epiphytic dinoflagellates that live on a variety of macrophytes, as well as on dead corals and sand. Recent taxonomic studies have identified novel diversity within the Gambierdiscus genus, with at least 18 species and several sub-groups now identified, many of which co-occur and differ significantly in toxicity. The ability to accurately and quickly distinguish Gambierdiscus species in field samples and determine community composition and abundance is central to assessing CP risk, yet most Gambierdiscus species are indistinguishable using light microscopy, and other enumeration methods are semi-quantitative. In order to investigate the spatial and temporal dynamics of Gambierdiscus species and community toxicity, new tools for species identification and enumeration in field samples are needed. Here, fluorescence in situ hybridization (FISH) probes were designed for seven species commonly found in the Caribbean Sea and Pacific Ocean, permitting their enumeration in field samples using epifluorescence microscopy. This technique enables the assessment of community composition and accurate determination of cell abundances of individual species. Molecular probes detecting G. australes, G. belizeanus, G. caribaeus, G. carolinianus, G. carpenteri, and the G. silvae/G. polynesiensis clade were designed using alignments of large subunit ribosomal RNA (rRNA) sequences. These probes were tested for specificity and cross-reactivity through experiments in which field samples were spiked with known concentrations of Gambierdiscus cultures, and analyzed to confirm that Gambierdiscus can be successfully detected and enumerated by FISH in the presence of detritus and other organisms. These probes were then used to characterize Gambierdiscus community structure in field samples collected from the Florida Keys and Hawai'i, USA. The probes revealed the co-occurrence of multiple species at each location. Time-series FISH analyses of samples collected from the Florida Keys quantified seasonal shifts in community composition as well as fluctuations in overall Gambierdiscus cell abundance. Application of species-specific FISH probes provides a powerful new tool to those seeking to target individual Gambierdiscus species, including significant toxin-producers, in field populations. Moving forward, analysis of Gambierdiscus community composition across multiple environments and over time will also allow species dynamics to be linked to environmental parameters, improving our ability to understand and manage the current and changing risks of CP worldwide.

Resistance of a Halobacterium salinarum isolate from a solar saltern to cadmium, lead, nickel, zinc, and copper

The current study focuses on the tolerance of a strain of Halobacterium salinarum isolated from Sfax solar saltern (Tunisia) towards cadmium (Cd), lead (Pb), nickel (Ni), zinc (Zn), and copper (Cu) by using agar dilution methods in complex and minimal media. The results showed the least inhibitory metals based on Minimum Inhibitory Concentrations (MICs) were lead (MIC = 4.5 mM), cadmium (MIC = 4 mM), and nickel (MIC = 2.5 mM) in complex medium. The MICs of these metals were more inhibitory (MIC < 2 mM) in the other tested media. The archaeal strain revealed a high sensitivity for copper and zinc, with MICs below 0.5 mM for both metals. Growth kinetics in complex and minimal media showed the strain to be more sensitive to the metals in liquid media than in solid media. The growth kinetic assays indicated the presence of selected heavy metals resulted in a lower growth rate and lower total cell mass relative to the control. Despite that cadmium and lead are nonessential and have no nutrient value, they were the most tolerated metals by H. salinarum strain. In addition, pigment intensity in the strain was inhibited by the presence of the heavy metals relative to the control.

Specific and effective detection of anammox bacteria using PCR primers targeting the 16S rRNA gene and functional genes

Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the nitrogen cycle by coupling ammonium and nitrite to produce dinitrogen gas (N₂). Polymerase chain reaction (PCR) is a fast, simple, and sensitive method that is widely used to assess the diversity, abundance, and activity of the slow-growing bacteria. In this review, we summarize and evaluate the wide variety of PCR primers targeting the 16S rRNA gene and functional genes (hzo, nir, and hzs) of anammox bacteria for their effectiveness and efficiencies in detecting this group of bacteria in different sample types. Furthermore, the efficiencies of different universal high-throughput sequencing 16S rRNA gene primers in anammox bacteria investigations were also evaluated to provide a reference for primer selection. Based on our in silico evaluation results, none of the 16S rRNA gene primers could recover all of the known anammox bacteria, but multiple hzo and hzs gene primers could accomplish this task. However, uncertain copies (1-3 copies) of hzo genes were identified in the genomes, and the hydrazine oxidation reaction catalyzed by hydrazine oxidoreductases (HZOs) can also be catalyzed by other hydroxylamine oxidoreductases (HAOs) in anammox bacteria, which can potentially result in large deviations in hzo-based qPCR and RT-qPCR analyses and results. Therefore, the use of optimal primers targeting unique hzs genes are recommended, although the efficiencies of these newly designed primers need further verification in practical applications. This article provides comprehensive information for the effective and specific detection of anammox bacteria using specific primers targeting the 16S rRNA gene and functional genes and serves as a basis for future high-quality primer design.

Diversity of sediment associated Planctomycetes and its related phyla with special reference to anammox bacterial community in a high Arctic fjord

The fjords of west Spitsbergen Svalbard, Arctic Norway, are undergoing a transformation as the impact of nutrient rich warmer Atlantic water is significantly altering the primary production and subsequently the carbon pool. Members of the phylum Planctomycetes are ubiquitous in marine systems and are important in the mineralization of organic matter. Hence, the phylogenetic diversity and distribution pattern of Planctomycetes in the surface sediments of a high Arctic fjord, the Kongsfjorden were studied. Further, considering the release of ammonium as a part of mineralization, the diversity of bacterial community involved in anaerobic ammonium oxidation (anammox) was also evaluated. The highly diverse Planctomycetes community, which consisted mainly of uncultivated and uncharacterized Planctomycetes, was observed in the study area with a total of 162 OTUs. The major genera observed were Blastopirellula (13.3%), Gimesia (13%), Rhodopirellula (10%), Planctomicrobium (2%) and Thermogutta (1.6%). Functional prediction revealed the dominance of carbohydrate metabolism genes and the presence of gene clusters for production of secondary metabolites and xenobiotic degradation. Anammox bacterial sequences were detected from all the samples with a total of 52 OTUs. Most of the OTUs belonged to the genus Candidatus Scalindua and three distinct clusters were observed in the phylogenetic tree, (a) Ca. Scalindua brodae (49%), (b) Ca. Scalindua wagneri (31%) and (c) Ca. Scalindua marina (12%) based on their phylogenic distance. Our findings suggest the existence of highly diverse Planctomycetes and anammox bacterial community with regional variants in the sediments of Kongsfjorden.

Environmental factors determining distribution and activity of anammox bacteria in minerotrophic fen soils

In contrast to the pervasive occurrence of denitrification in soils, anammox (anaerobic ammonium oxidation) is a spatially restricted process that depends on specific ecological conditions. To identify the factors that constrain the distribution and activity of anammox bacteria in terrestrial environments, we investigated four different soil types along a catena with opposing ecological gradients of nitrogen and water content, from an amended pasture to an ombrotrophic bog. Anammox was detected by polymerase chain reaction (PCR) and quantitative PCR (qPCR) only in the nitrophilic wet meadow and the minerotrophic fen, in soil sections remaining water-saturated for most of the year and whose interstitial water contained inorganic nitrogen. Contrastingly, aerobic ammonia oxidizing microorganisms were present in all examined samples and outnumbered anammox bacteria usually by at least one order of magnitude. 16S rRNA gene sequencing revealed a relatively high diversity of anammox bacteria with one Ca. Brocadia cluster. Three additional clusters could not be affiliated to known anammox genera, but have been previously detected in other soil systems. Soil incubations using 15N-labeled substrates revealed that anammox processes contributed about <2% to total N2 formation, leaving nitrification and denitrification as the dominant N-removal mechanism in these soils that represent important buffer zones between agricultural land and ombrotrophic peat bogs.

Dynamics and environmental importance of anaerobic ammonium oxidation (anammox) bacteria in urban river networks

Anaerobic ammonium oxidation (anammox) is recognized as an important bioprocess for nitrogen removal, yet little is known about the associated microbial communities in urban river networks which are intensively disturbed by human activity. In the present study, we investigated the community composition and abundance of anammox bacteria in the urban river network of Shanghai, and explored their potential correlations with nitrogen removal activities and the environmental parameters. High biodiversity of anammox bacteria was detected in the sediment of urban river networks, including Candidatus Brocadia, Scalindua, Jettenia, and Kuenenia. Anammox bacterial abundance ranged from 3.7 × 10⁶ to 3.9 × 10⁷ copies g^-1 dry sediment based on 16S rRNA gene, which was strongly correlated to the metabolic activity of anammox bacteria (P < 0.01). A strong linkage between anammox bacteria and denitrifiers was detected (P < 0.05), implying a potential metabolic interdependence between these two nitrogen-removing microbes was existed in urban river networks. Sediment ammonium (NH₄⁺) made a significant contribution to the anammox bacterial community-environment relationship, while anammox bacterial abundance related significantly with sediment total organic carbon (TOC) and silt contents (P < 0.05). However, no statistically significant correlation was observed between cell-specific anammox rate and the measured environmental factors (P > 0.05). In general, the community composition and abundance of anammox bacteria in different hierarchies of the river network was homogeneous, without significant spatial variations (P > 0.05). These results provided an opportunity to further understand the microbial mechanism of nitrogen removal bioprocesses in urban river networks.

Molecular analysis of methanogen populations and their interactions within anaerobic sludge digesters

Knowledge of archaeal population structure, function and interactions is of great interest for a deeper understanding of the anaerobic digestion step in wastewater treatment process, that represents a bottle neck in the optimization of digesters performance. Although culture-independent techniques have enabled the exploration of archaeal population in such systems, their population dynamics and interactions still require further investigation. In the present study, 2646 almost full archaeal 16S rRNA gene sequences retrieved from 22 anaerobic digesters located worldwide were analyzed and classified into 83 Operational Taxonomic Units (OTUs) for Euryarchaeotes and 2 OTUs for Crenarchaeotes. Among the Euryarchaeotes, Methanosarcinales represent the predominant archaeal population (47.5% of total sequences), followed by the ARC I (WSA2) lineage (25.3%), Methanomicrobiales (19.9%) and Methanobacteriales (1.9%). Theses lineages are predominant in nine, five, two and one digesters respectively. However, the remaining 5 digesters show no predominance of any methanogenic group. According to the predominance of theses lineages, 5 digester profiles were distinguished. This study revealed a clear interaction between the 4 methanogenic lineages. A core of 12 OTUs represented by five, four, two and one OTU for Methanosarcinales, Methanomicrobiales, ARC I and Methanobacteriales respectively were quantitatively abundant in at least 50% of the analyzed digesters. 16S rRNA targeted hybridization oligonucleotide probes targeting the predominant OTUs are being developed to follow their population dynamics under various parameters.

Isolation and Selection of Potential Probiotic Bacteria from the Pig Gastrointestinal Tract

The present study aimed to isolate bacterial strains from the pig gastrointestinal tract that have antagonistic activity against potential pathogens and are able to produce antimicrobial compounds. That ability would be a first requirement for the strains' possible use as probiotics. Samples obtained from pig intestinal mucosa and contents were screened for the presence of antagonistic activity against pathogenic indicator strains of Escherichia coli, Salmonella, and Listeria by means of the double-layer technique. Samples displaying the largest inhibitory halos were further studied for the production of inhibitory substances using the agar diffusion and microtitration methods. The three most promising isolates were identified by sequencing of the 16S rRNA gene and showed highest affiliation to Lactobacillus salivarius. Optimal growth conditions and bacteriocin production were recorded in de Man, Rogosa, and Sharpe broth under anaerobic conditions at 37 °C. The antimicrobial substances were found to be sensitive to proteolytic enzymes but showed good stability at pH values below 6. Our findings suggest that these three intestinal strains are able to produce antimicrobial substances capable of inhibiting the growth of potential enteric pathogens and might have potential as probiotic feed additives for the prevention of gastrointestinal diseases.

A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms

BACKGROUND

Several fungi-specific primers target the 18S rRNA gene sequence, one of the prominent markers for fungal classification. The design of most primers goes back to the last decades. Since then, the number of sequences in public databases increased leading to the discovery of new fungal groups and changes in fungal taxonomy. However, no reevaluation of primers was carried out and relevant information on most primers is missing. With this study, we aimed to develop an 18S rRNA gene sequence primer toolkit allowing an easy selection of the best primer pair appropriate for different sequencing platforms, research aims (biodiversity assessment versus isolate classification) and target groups.

RESULTS

We performed an intensive literature research, reshuffled existing primers into new pairs, designed new Illumina-primers, and annealing blocking oligonucleotides. A final number of 439 primer pairs were subjected to in silico PCRs. Best primer pairs were selected and experimentally tested. The most promising primer pair with a small amplicon size, nu-SSU-1333-5'/nu-SSU-1647-3' (FF390/FR-1), was successful in describing fungal communities by Illumina sequencing. Results were confirmed by a simultaneous metagenomics and eukaryote-specific primer approach. Co-amplification occurred in all sample types but was effectively reduced by blocking oligonucleotides.

CONCLUSIONS

The compiled data revealed the presence of an enormous diversity of fungal 18S rRNA gene primer pairs in terms of fungal coverage, phylum spectrum and co-amplification. Therefore, the primer pair has to be carefully selected to fulfill the requirements of the individual research projects. The presented primer toolkit offers comprehensive lists of 164 primers, 439 primer combinations, 4 blocking oligonucleotides, and top primer pairs holding all relevant information including primer's characteristics and performance to facilitate primer pair selection.

Growth performance of piglets during the first two weeks of lactation affects the development of the intestinal microbiota

The aim of this study was to evaluate the effect of newborn piglet weight gain during the first 2 weeks of lactation on the luminal and mucosal microbiota of the ileum and colon. The microbiota from high-weight-gain (HWG) and low-weight-gain (LWG) 2-week-old piglets was characterized by amplicon length heterogeneity PCR (LH-PCR) and compared using diversity indices and multivariate statistical analyses. At birth, LWG piglets weighted in average 0.26 kg less than HWG piglets (p = .002). The weight difference between LWG and HWG piglets increased with time and reached 2.1 kg after 16 days of lactation (p < .0001). Based on these growth performance differences, estimated colostrum and milk intake was greater in HWG than in LWG piglets (p < .0001). Analysis of the LH-PCR data of the microbiota using non-metric multidimensional scaling (NMS) and blocked multiresponse permutation procedure (MRBP) revealed that the microbiota of the HWG and LWG piglets tended to differ in ileal mucosa (p = .097) and differed in colonic lumen (p = .024). The microbiota of HWG piglets had higher levels of Bacteroidetes, Bacteroides and Ruminoccocaceae, and lower proportions of Actinobacillus porcinus and Lactobacillus amylovorus when compared with those of LWG piglets. As the weight gain of nursing piglets is highly correlated with the amount of ingested colostrum and milk, the results strongly suggest that colostrum and milk intake in the first 2 weeks of life influenced the development of the gut microbiota.

Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis

Necrotising enterocolitis (NEC) and sepsis are serious diseases of preterm infants that can result in feeding intolerance, the need for bowel resection, impaired physiological and neurological development, and high mortality rates. Neonatal healthcare improvements have allowed greater survival rates in preterm infants leading to increased numbers at risk of developing NEC and sepsis. Gut bacteria play a role in protection from or propensity to these conditions and have therefore, been studied extensively using targeted 16S rRNA gene sequencing methods. However, exact epidemiology of these conditions remain unknown and the role of the gut microbiota in NEC remains enigmatic. Many studies have confounding variables such as differing clinical intervention strategies or major methodological issues such as the inability of 16S rRNA gene sequencing methods to determine viable from non-viable taxa. Identification of viable community members is important to identify links between the microbiota and disease in the highly unstable preterm infant gut. This is especially important as remnant DNA is robust and persists in the sampling environment following cell death. Chelation of such DNA prevents downstream amplification and inclusion in microbiota characterisation. This study validates use of propidium monoazide (PMA), a DNA chelating agent that is excluded by an undamaged bacterial membrane, to reduce bias associated with 16S rRNA gene analysis of clinical stool samples. We aim to improve identification of the viable microbiota in order to increase the accuracy of clinical inferences made regarding the impact of the preterm gut microbiota on health and disease. Gut microbiota analysis was completed on stools from matched twins (n = 16) that received probiotics. Samples were treated with PMA, prior to bacterial DNA extraction. Meta-analysis highlighted a significant reduction in bacterial diversity in 68.8% of PMA treated samples as well as significantly reduced overall rare taxa abundance. Importantly, overall abundances of genera associated with protection from and propensity to NEC and sepsis such as: Bifidobacterium; Clostridium, and Staphylococcus sp. were significantly different following PMA-treatment. These results suggest non-viable cell exclusion by PMA-treatment reduces bias in gut microbiota analysis from which clinical inferences regarding patient susceptibility to NEC and sepsis are made.

Bacteriocin-Producing Enterococcus faecium LCW 44: A High Potential Probiotic Candidate from Raw Camel Milk

Bacterial isolates from raw camel milk were screened for antibacterial activity using the agar diffusion assay. Ten isolates selected for their inhibition of Gram-positive bacteria were identified by 16S sequencing as Enterococcus faecium or durans. An isolate named E. faecium LCW 44 exhibited the broadest antibacterial spectrum with an inhibitory activity against several Gram-positive strains belonging to the genera Clostridium, Listeria, Staphylococcus, and Lactobacillus. E. faecium LCW 44 was shown to produce N-formylated enterocins L50A and L50B, as revealed by mass spectrometry and PCR analyses. This isolate did not harbor any of the virulence factors tested and was shown to be sensitive to all tested antibiotics. It showed high resistance to gastric and intestinal conditions (78 ± 4% survival). Its adhesion index was evaluated at 176 ± 86 and 24 ± 86 on Caco-2 cells and HT-29 cells, respectively, and it significantly reduced adhesion of Listeria monocytogenes by 65 and 49%, respectively. In Macfarlane broth (simulating the nutrient content of the colon), counts of L. monocytogenes were reduced by 2 log₁₀ cycles after 24 h in co-culture with E. faecium LCW 44, compared to the increase of 4 log₁₀ cycles when cultured alone. Comparison with a bacteriocin-non-producing mutant of E. faecium LCW 44 strongly suggests that inhibition of L. monocytogenes was due to bacteriocin production. Altogether, E. faecium LCW 44 thus has potential for use as a probiotic for humans and veterinary medicine.

Plants Assemble Species Specific Bacterial Communities from Common Core Taxa in Three Arcto-Alpine Climate Zones

Evidence for the pivotal role of plant-associated bacteria to plant health and productivity has accumulated rapidly in the last years. However, key questions related to what drives plant bacteriomes remain unanswered, among which is the impact of climate zones on plant-associated microbiota. This is particularly true for wild plants in arcto-alpine biomes. Here, we hypothesized that the bacterial communities associated with pioneer plants in these regions have major roles in plant health support, and this is reflected in the formation of climate and host plant specific endophytic communities. We thus compared the bacteriomes associated with the native perennial plants Oxyria digyna and Saxifraga oppositifolia in three arcto-alpine regions (alpine, low Arctic and high Arctic) with those in the corresponding bulk soils. As expected, the bulk soil bacterial communities in the three regions were significantly different. The relative abundances of Proteobacteria decreased progressively from the alpine to the high-arctic soils, whereas those of Actinobacteria increased. The candidate division AD3 and Acidobacteria abounded in the low Arctic soils. Furthermore, plant species and geographic region were the major determinants of the structures of the endophere communities. The plants in the alpine region had higher relative abundances of Proteobacteria, while plants from the low- and high-arctic regions were dominated by Firmicutes. A highly-conserved shared set of ubiquitous bacterial taxa (core bacteriome) was found to occur in the two plant species. Burkholderiales, Actinomycetales and Rhizobiales were the main taxa in this core, and they were also the main contributors to the differences in the endosphere bacterial community structures across compartments as well as regions. We postulate that the composition of this core is driven by selection by the two plants.

Survival and Metabolic Activity of Pediocin Producer Pediococcus acidilactici UL5: Its Impact on Intestinal Microbiota and Listeria monocytogenes in a Model of the Human Terminal Ileum

Pediococcus acidilactici UL5 is a promising probiotic candidate due to its high survival rate under gastric and duodenal conditions and to its ability to produce the antilisterial bacteriocin pediocin PA-1. Its survival, metabolic activity, and impact on Listeria monocytogenes in a continuous stirred tank reactor containing immobilized human intestinal microbiota were studied over a period of 32 days of feeding a nutrient medium simulating ileal chyme. The impact of P. acidilactici UL5 on different bacterial groups of intestinal origin as well as its survival and its impact on L. monocytogenes were quantified using quantitative polymerase chain reaction coupling with propidium monoazide (PMA-qPCR), which was shown to detect and quantify viable bacteria only. P. acidilactici UL5 and its non-pediocin-producing mutant had no effect on the microbiota, but the producing strain induced an increase in the production of acetic and propionic acids. P. acidilactici survived but appeared to be a poor competitor with intestinal microbiota, dropping by 1.3 and 2.8 log₁₀ after 8 h of fermentation to 10⁴ colony-forming units (cfu) mL^-1. A 1.64 log but non-significant reduction of Listeria was observed when P. acidilactici UL5 was added at 10⁸ cfu mL^-1. P. acidilactici UL5 isolated from the reactor after 3 days was still able to produce the active bacteriocin. These data demonstrate that P. acidilactici UL5 is capable of surviving transit through the ileum without losing its ability to produce pediocin PA-1 but seems to not be enough competitive with the great diversity of organisms found in the ileum.

Tidal pumping facilitates dissimilatory nitrate reduction in intertidal marshes

Intertidal marshes are alternately exposed and submerged due to periodic ebb and flood tides. The tidal cycle is important in controlling the biogeochemical processes of these ecosystems. Intertidal sediments are important hotspots of dissimilatory nitrate reduction and interacting nitrogen cycling microorganisms, but the effect of tides on dissimilatory nitrate reduction, including denitrification, anaerobic ammonium oxidation and dissimilatory nitrate reduction to ammonium, remains unexplored in these habitats. Here, we use isotope-tracing and molecular approaches simultaneously to show that both nitrate-reduction activities and associated functional bacterial abundances are enhanced at the sediment-tidal water interface and at the tide-induced groundwater fluctuating layer. This pattern suggests that tidal pumping may sustain dissimilatory nitrate reduction in intertidal zones. The tidal effect is supported further by nutrient profiles, fluctuations in nitrogen components over flood-ebb tidal cycles, and tidal simulation experiments. This study demonstrates the importance of tides in regulating the dynamics of dissimilatory nitrate-reducing pathways and thus provides new insights into the biogeochemical cycles of nitrogen and other elements in intertidal marshes.

Microbial community structure associated with the high loading anaerobic codigestion of olive mill and abattoir wastewaters

The effect of increasing the organic loading rates (OLRs) on the performance of the anaerobic codigestion of olive mill (OMW) and abattoir wastewaters (AW) was investigated under mesophilic and thermophilic conditions. The structure of the microbial community was also monitored. Increasing OLR to 9g of chemical oxygen demand (COD) L(-1)d(-1) affected significantly the biogas yield and microbial diversity at 35°C. However, at 55°C digester remained stable until OLR of 12g of CODL(-1)d(-1) with higher COD removal (80%) and biogas yield (0.52Lg(-1) COD removed). Significant differences in the bacterial communities were detected between mesophilic and thermophilic conditions. The dominant phyla detected in the digester at both phases were the Firmicutes, Actinobacteria, Bacteroidetes, Synergistetes and Spirochaete. However, Verrucomicrobia, Proteobacteria and the candidate division BRC1 were only detected at thermophilic conditions. The Methanobacteriales and the Thermoplasmales were found as a high predominant archaeal member in the anaerobic sludge.

Streptococcus bovis infectious endocarditis and occult gastrointestinal neoplasia: experience with 25 consecutive patients treated surgically

To assess the prevalence of gastrointestinal neoplasia in patients with Streptococcus bovis infectious endocarditis we performed a retrospective cohort analysis of all episodes of S. bovis infectious endocarditis treated at our institution between January 2000 through December 2014. Twenty-five patients were identified for this purpose. 12/25 patients received colonoscopy and 1/25 of the patients was assessed with CT colonography. Of the 13 who underwent colonic assessment, 11 were diagnosed with colonic neoplasms at different stages of development. In the absence of any strong contraindication, gastroenteroscopic evaluation in all patients diagnosed with S. bovis infectious endocarditis should be pursued.

Arthralgia and blood culture-negative endocarditis in middle Age Men suggest tropheryma whipplei infection: report of two cases and review of the literature

Background

Whipple’s disease is a rare, often multisystemic chronic infectious disease caused by the rod-shaped bacterium Tropheryma whipplei. Very rarely the heart is involved in the process of the disease, leading to culture-negative infective endocarditis. Up to 20 % of all infective endocarditis are blood culture-negative and therefore a diagnostic challenge. We present two unusual cases of culture-negative infective endocarditis encountered in two different patients with prior history of arthralgia. A history of rheumatic arthritis or even a transient arthralgia should put Tropheryma whipplei on the top of differentials in patients of this age group presenting with culture-negative infective endocarditis, especially in cases of therapy resistance to antirheumatic agents.

Case presentation

The first patient was a 55 year-old Caucasian male with culture-negative Whipple-related adhesive pericarditis and endocarditis of the aortic valve. Importantly, the patient reported a 15-year history of therapy resistant sero-negative migratory polyarthritis. Aortic valve endocarditis developed during treatment with tocilizumab. The second patient was a 65-year-old male patient with no prior history of the classic Whipple’s disease who presented with a culture-negative aortic valve endocarditis. His past medical history revealed episodes of transient arthralgia, which he was not treated for however, due to the self-limiting nature of the symptoms. Both patients underwent aortic valve replacement surgery. During surgery, pericardectomy was necessary in the first patient due to adhesive pericarditis. Post surgery both patients were started on long-term treatment with trimetoprim-sulfamethoxazol. At 1-year follow-up of both patients, echocardiographic and clinical assessment revealed no signs of persistent infection. Both men reported negative history of arthralgia during the one year period post surgery.

Conclusion

Tropheryma whipplei culture negative-infective endocarditis is an emerging clinical entity, predominantly found in middle-aged and older men with a history of arthralgia. These data highlight the need for ruling out Whipple’s disease in patients with a history of arthralgia prior to initiation of biological agents in treatment of rheumatoid arthritis. There is also a need to assess for Tropheryma whipplei in all patients with culture- negative infective endocarditis.

Nosocomial infection due to Enterococcus cecorum identified by MALDI-TOF MS and Vitek 2 from a blood culture of a septic patient

We report the case of a nosocomial infection due to Enterococcus cecorum isolated from a blood culture of a 75-year-old septic male patient. Matrix-assisted laser desorption–ionization time-of-flight mass spectrometry (MALDI-TOF MS) and Vitek 2 succeeded in identification of the isolate.

Profiling of Indigenous Microbial Community Dynamics and Metabolic Activity During Enrichment in Molasses-Supplemented Crude Oil-Brine Mixtures for Improved Understanding of Microbial Enhanced Oil Recovery

Anaerobic incubations using crude oil and brine from a North Sea reservoir were conducted to gain increased understanding of indigenous microbial community development, metabolite production, and the effects on the oil-brine system after addition of a complex carbon source, molasses, with or without nitrate to boost microbial growth. Growth of the indigenous microbes was stimulated by addition of molasses. Pyrosequencing showed that specifically Anaerobaculum, Petrotoga, and Methanothermococcus were enriched. Addition of nitrate favored the growth of Petrotoga over Anaerobaculum. The microbial growth caused changes in the crude oil-brine system: formation of oil emulsions, and reduction of interfacial tension (IFT). Reduction in IFT was associated with microbes being present at the oil-brine interphase. These findings suggest that stimulation of indigenous microbial growth by addition of molasses has potential as microbial enhanced oil recovery (MEOR) strategy in North Sea oil reservoirs.

Co-occurence of Crenarchaeota, Thermoplasmata and methanogens in anaerobic sludge digesters

16S rRNA Crenarchaeota and Thermoplasmata sequences retrieved from 22 anaerobic digesters were analysed. 4.8 and 0.53 % of archaeal sequences were simultaneously affiliated to these lineages. A core of 2 operational taxonomic units (OTUs) representing 0.6 to -33.6 % of all archaeal sequences were defined for the Crenarchaeotes and identified to already known but not yet cultivable organisms in almost half of the digesters sampled. For the Thermoplasmata, apparently less abundant with 0.7 to -4.7 % of the archaeal sequences, 3 OTUs were identified. We showed here that Crenarchaeotes coexist with methanogens and are particularly abundant when Arch I lineage (also called WSA2 by Hugenholtz) is dominant in digesters. Moreover, Thermoplasmata were detected when Crenarchaeota were present. Interactions between methanogens, Crenarchaeotea and Thermoplamata were thus discussed.

Biomass yield efficiency of the marine anammox bacterium, "Candidatus Scalindua sp.," is affected by salinity

The growth rate and biomass yield efficiency of anaerobic ammonium oxidation (anammox) bacteria are markedly lower than those of most other autotrophic bacteria. Among the anammox bacterial genera, the growth rate and biomass yield of the marine anammox bacterium "Candidatus Scalindua sp." is still lower than those of other anammox bacteria enriched from freshwater environments. The activity and growth of marine anammox bacteria are generally considered to be affected by the presence of salinity and organic compounds. Therefore, in the present study, the effects of salinity and volatile fatty acids (VFAs) on the anammox activity, inorganic carbon uptake, and biomass yield efficiency of "Ca. Scalindua sp." enriched from the marine sediments of Hiroshima Bay, Japan, were investigated in batch experiments. Differences in VFA concentrations (0-10 mM) were observed under varying salinities (0.5%-4%). Anammox activity was high at 0.5%-3.5% salinity, but was 30% lower at 4% salinity. In addition, carbon uptake was higher at 1.5%-3.5% salinity. The results of the present study clearly demonstrated that the biomass yield efficiency of the marine anammox bacterium "Ca. Scalindua sp." was significantly affected by salinity. On the other hand, the presence of VFAs up to 10 mM did not affect anammox activity, carbon uptake, or biomass yield efficiency.

Bias in Whole Genome Amplification: Causes and Considerations

Whole genome amplification (WGA) is a widely used molecular technique that is becoming increasingly necessary in genetic research on a range of sample types including individual cells, fossilized remains and entire ecosystems. Multiple methods of WGA have been developed, each with specific strengths and weaknesses, but with a common defect in that each method distorts the initial template DNA during the course of amplification. The type, extent, and circumstance of the bias vary with the WGA method and particulars of the template DNA. In this review, we endeavor to discuss the types of bias introduced, the susceptibility of common WGA techniques to these bias types, and the interdependence between bias and characteristics of the template DNA. Finally, we attempt to illustrate some of the criteria specific to the analytical platform and research application that should be considered to enable combination of the appropriate WGA method, template DNA, sequencing platform, and intended use for optimal results.

Nitrogen removal using an anammox membrane bioreactor at low temperature

Membrane bioreactors (MBRs) have the ability to completely retain biomass and are thus suitable for slowly growing anammox bacteria. In the present study, an anammox MBR was operated to investigate whether the anammox activity would remain stable at low temperature, without anammox biomass washout. The maximum nitrogen removal rates were 6.7 and 1.1 g-N L⁻¹ day⁻¹ at 35 °C and 15 °C, respectively. Fluorescence in situ hybridization and 16S rRNA-based phylogenetic analysis revealed no change in the predominant anammox species with temperature because of the complete retention of anammox biomass in the MBR. These results indicate that the predominant anammox bacteria in the MBR cannot adapt to a low temperature during short-term operation. Conversely, anammox activity recovered rapidly after restoring the temperature from the lower value to the optimal temperature (35 °C). The rapid recovery of anammox activity is a distinct advantage of using an MBR anammox reactor.

Partial nitritation and o-cresol removal with aerobic granular biomass in a continuous airlift reactor

Several chemical industries produce wastewaters containing both, ammonium and phenolic compounds. As an alternative to treat this kind of complex industrial wastewaters, this study presents the simultaneous partial nitritation and o-cresol biodegradation in a continuous airlift reactor using aerobic granular biomass. An aerobic granular sludge was developed in the airlift reactor for treating a high-strength ammonium wastewater containing 950 ± 25 mg N-NH4(+) L(-1). Then, the airlift reactor was bioaugmented with a p-nitrophenol-degrading activated sludge and o-cresol was added progressively to the ammonium feed to achieve 100 mg L(-1). The results showed that stable partial nitritation and full biodegradation of o-cresol were simultaneously maintained obtaining a suitable effluent for a subsequent anammox reactor. Moreover, two o-cresol shock-load events with concentrations of 300 and 1000 mg L(-1) were applied to assess the capabilities of the system. Despite these shock load events, the partial nitritation process was kept stable and o-cresol was totally biodegraded. Fluorescence in situ hybridization technique was used to identify the heterotrophic bacteria related to o-cresol biodegradation and the ammonia oxidising bacteria along the granules.

Biological properties of carotenoids extracted from Halobacterium halobium isolated from a Tunisian solar saltern

Background

Bioactive molecules have received increasing attention due to their nutraceutical attributes and anticancer, antioxidant, antiproliferative and apoptosis-inducing properties. This study aimed to investigate the biological properties of carotenoids extracted from Archaea.

Methods

Halophilic Archaea strains were isolated from the brine of a local crystallizer pond (TS7) of a solar saltern at Sfax, Tunisia. The most carotenoid-producing strain (M8) was investigated on heptoma cell line (HepG2), and its viability was assessed by the MTT-test. The cells were incubated with different sub-lethal extract rates, with carotenoid concentrations ranging from 0.2 to 1.5 μM. Antioxidant activity was evaluated through exposing the cells to sub-lethal extract concentrations for 24 hours and then to oxidative stress induced by 60 μM arachidonic acid and 50 μM H₂O₂.

Results

Compared to non-treated cells, bacterial carotenoid extracts inhibited HepG2 cell viability (50%). A time and dose effect was observed, with cell viability undergoing a significant (P < 0.05) decrease with extract concentration. After exposure to oxidative stress, control cells underwent a significant (P < 0.05) decrease in viability as compared to the non-treated cells.

Conclusions

The bacterial extracts under investigation were noted to exhibit the strongest free radical scavenging activity with high carotenoid concentrations. The carotenoid extract also showed significant antiproliferative activity against HepG2 human cancer cell lines.

New insights on the genetic diversity of the honeybee parasiteNosema ceranaebased onmultilocussequence analysis

The microsporidian parasiteNosema ceranaeis a common pathogen of the Western honeybee (Apis mellifera) whose variable virulence could be related to its genetic polymorphism and/or its polyphenism responding to environmental cues. Since the genotyping ofN. ceranaebased on unique marker sequences had been unsuccessful, we tested whether amultilocusapproach, assessing the diversity of ten genetic markers – encoding nine proteins and the small ribosomal RNA subunit – allowed the discrimination betweenN. ceranaevariants isolated from singleA. melliferaindividuals in four distant locations. High nucleotide diversity and allele content were observed for all genes. Most importantly, the diversity was mainly present within parasite populations isolated from single honeybee individuals. In contrast the absence of isolate differentiation precluded anytaxadiscrimination, even through amultilocusapproach, but suggested that similar populations of parasites seem to infect honeybees in distant locations. As statistical evolutionary analyses showed that the allele frequency is under selective pressure, we discuss the origin and consequences ofN. ceranaeheterozygosity in a single host and lack of population divergence in the context of the parasite natural and evolutionary history.

A comparative study of microbial diversity and community structure in marine sediments using poly(A) tailing and reverse transcription-PCR

To obtain a better understanding of metabolically active microbial communities, we tested a molecular ecological approach using poly(A) tailing of environmental 16S rRNA, followed by full-length complementary DNA (cDNA) synthesis and sequencing to eliminate potential biases caused by mismatching of polymerase chain reaction (PCR) primer sequences. The RNA pool tested was extracted from marine sediments of the Yonaguni Knoll IV hydrothermal field in the southern Okinawa Trough. The sequences obtained using the poly(A) tailing method were compared statistically and phylogenetically with those obtained using conventional reverse transcription-PCR (RT-PCR) with published domain-specific primers. Both methods indicated that Deltaproteobacteria are predominant in sediment (>85% of the total sequence read). The poly(A) tailing method indicated that Desulfobacterales were the predominant Deltaproteobacteria, while most of the sequences in libraries constructed using RT-PCR were derived from Desulfuromonadales. This discrepancy may have been due to low coverage of Desulfobacterales by the primers used. A comparison of library diversity indices indicated that the poly(A) tailing method retrieves more phylogenetically diverse sequences from the environment. The four archaeal 16S rRNA sequences that were obtained using the poly(A) tailing method formed deeply branching lineages that were related to Candidatus "Parvarchaeum" and the ancient archaeal group. These results clearly demonstrate that poly(A) tailing followed by cDNA sequencing is a powerful and less biased molecular ecological approach for the study of metabolically active microbial communities.

Activated zeolite--suitable carriers for microorganisms in anaerobic digestion processes?

Plant cell wall structures represent a barrier in the biodegradation process to produce biogas for combustion and energy production. Consequently, approaches concerning a more efficient de-polymerisation of cellulose and hemicellulose to monomeric sugars are required. Here, we show that natural activated zeolites (i.e. trace metal activated zeolites) represent eminently suitable mineral microhabitats and potential carriers for immobilisation of microorganisms responsible for anaerobic hydrolysis of biopolymers stabilising related bacterial and methanogenic communities. A strategy for comprehensive analysis of immobilised anaerobic populations was developed that includes the visualisation of biofilm formation via scanning electron microscopy and confocal laser scanning microscopy, community and fingerprint analysis as well as enzyme activity and identification analyses. Using SDS polyacrylamide gel electrophoresis, hydrolytical active protein bands were traced by congo red staining. Liquid chromatography/mass spectroscopy revealed cellulolytical endo- and exoglucanase (exocellobiohydrolase) as well as hemicellulolytical xylanase/mannase after proteolytic digestion. Relations to hydrolytic/fermentative zeolite colonisers were obtained by using single-strand conformation polymorphism analysis (SSCP) based on amplification of bacterial and archaeal 16S rRNA fragments. Thereby, dominant colonisers were affiliated to the genera Clostridium, Pseudomonas and Methanoculleus. The specific immobilisation on natural zeolites with functional microbes already colonising naturally during the fermentation offers a strategy to systematically supply the biogas formation process responsive to population dynamics and process requirements.

Green tea powder and Lactobacillus plantarum affect gut microbiota, lipid metabolism and inflammation in high-fat fed C57BL/6J mice

Background

Type 2 diabetes is associated with obesity, ectopic lipid accumulation and low-grade inflammation. A dysfunctional gut microbiota has been suggested to participate in the pathogenesis of the disease. Green tea is rich in polyphenols and has previously been shown to exert beneficial metabolic effects. Lactobacillus plantarum has the ability to metabolize phenolic acids. The health promoting effect of whole green tea powder as a prebiotic compound has not been thoroughly investigated previously.

Methods

C57BL/6J mice were fed a high-fat diet with or without a supplement of 4% green tea powder (GT), and offered drinking water supplemented with Lactobacillus plantarum DSM 15313 (Lp) or the combination of both (Lp + GT) for 22 weeks. Parameters related to obesity, glucose tolerance, lipid metabolism, hepatic steatosis and inflammation were examined. Small intestinal tissue and caecal content were collected for bacterial analysis.

Results

Mice in the Lp + GT group had significantly more Lactobacillus and higher diversity of bacteria in the intestine compared to both mice in the control and the GT group. Green tea strongly reduced the body fat content and hepatic triacylglycerol and cholesterol accumulation. The reduction was negatively correlated to the amount of Akkermansia and/or the total amount of bacteria in the small intestine. Markers of inflammation were reduced in the Lp + GT group compared to control. PLS analysis of correlations between the microbiota and the metabolic variables of the individual mice showed that relatively few components of the microbiota had high impact on the correlation model.

Conclusions

Green tea powder in combination with a single strain of Lactobacillus plantarum was able to promote growth of Lactobacillus in the intestine and to attenuate high fat diet-induced inflammation. In addition, a component of the microbiota, Akkermansia, correlated negatively with several metabolic parameters known to be risk factors for the development of type 2 diabetes.

Anaerobic treatment of municipal wastewater at ambient temperature: Analysis of archaeal community structure and recovery of dissolved methane

Anaerobic treatment is an attractive option for the biological treatment of municipal wastewater. In this study, municipal wastewater was anaerobically treated with a bench-scale upflow anaerobic sludge blanket (UASB) reactor at temperatures from 6 to 31 °C for 18 months to investigate total chemical oxygen demand (COD) removal efficiency, archaeal community structure, and dissolved methane (D-CH(4)) recovery efficiency. The COD removal efficiency was more than 50% in summer and below 40% in winter with no evolution of biogas. Analysis of the archaeal community structures of the granular sludge from the UASB using 16S rRNA gene-cloning indicated that after microorganisms had adapted to low temperatures, the archaeal community had a lower diversity and the relative abundance of acetoclastic methanogens decreased together with an increase in hydrogenotrophic methanogens. D-CH(4), which was detected in the UASB effluent throughout the operation, could be collected with a degassing membrane. The ratio of the collection to recovery rates was 60% in summer and 100% in winter. For anaerobic treatment of municipal wastewater at lower temperatures, hydrogenotrophic methanogens play an important role in COD removal and D-CH(4) can be collected to reduce greenhouse gas emissions and avoid wastage of energy resources.

Vertical distributions of sulfate-reducing bacteria and methane-producing archaea quantified by oligonucleotide probe hybridization in the profundal sediment of a mesotrophic lake

Abstract Vertical distributions of sulfate-reducing bacteria and methane-producing archaea were investigated in the profundal sediment of a freshwater lake using membrane-immobilized small subunit rRNA hybridization with group- and genus-specific oligonucleotide probes. The annual average of the relative abundance of small subunit rRNA hybridized with all probes for sulfate-reducing bacteria to total small subunit rRNA was 2.3% at 0-2 cm and increased with depth up to 22.9% at 8-14 cm where sulfate concentration was less than 10 nmol ml(-1) in interstitial water, suggesting that these bacteria may survive on alternative metabolisms. The signal of probe Dsv687 (the family Desulfovibrionaceae and some Geobacteraceae) was the main factor in this increase. The relative abundance of methane-producing archaea to total small subunit rRNA was highest (7.8%) at 8-14 cm, dominated by the order Methanosarcinales. The metabolic rates measured in the sediments demonstrated that the peaks of sulfate reduction and methane production were separated vertically, and were not linked to their small subunit rRNA distributions. Our data indicate that sulfate-reducing bacteria can coexist with methane-producing archaea from 0 to 20 cm in the freshwater lake sediment.

Microbial distribution and abundance in the digestive system of five shipworm species (Bivalvia: Teredinidae)

Marine bivalves of the family Teredinidae (shipworms) are voracious consumers of wood in marine environments. In several shipworm species, dense communities of intracellular bacterial endosymbionts have been observed within specialized cells (bacteriocytes) of the gills (ctenidia). These bacteria are proposed to contribute to digestion of wood by the host. While the microbes of shipworm gills have been studied extensively in several species, the abundance and distribution of microbes in the digestive system have not been adequately addressed. Here we use Fluorescence In-Situ Hybridization (FISH) and laser scanning confocal microscopy with 16S rRNA directed oligonucleotide probes targeting all domains, domains Bacteria and Archaea, and other taxonomic groups to examine the digestive microbiota of 17 specimens from 5 shipworm species (Bankia setacea, Lyrodus pedicellatus, Lyrodus massa, Lyrodus sp. and Teredo aff. triangularis). These data reveal that the caecum, a large sac-like appendage of the stomach that typically contains large quantities of wood particles and is considered the primary site of wood digestion, harbors only very sparse microbial populations. However, a significant number of bacterial cells were observed in fecal pellets within the intestines. These results suggest that due to low abundance, bacteria in the caecum may contribute little to lignocellulose degradation. In contrast, the comparatively high population density of bacteria in the intestine suggests a possible role for intestinal bacteria in the degradation of lignocellulose.