Bacterial Contribution Research Articles

Assessment of bacterial contributions to the biochemical changes of chill-stored blunt snout bream (Megalobrama amblycephala) fillets: Protein degradation and volatile organic compounds accumulation

In this study, we evaluated the contributions of three bacteria (Pseudomonas versuta, Shewanella putrefaciens, and Aeromonas sobria) to the proteolysis, biogenic amines formation, volatile organic compounds accumulation, lipid oxidation, nucleotide catabolism, discoloration, and water migration of bream flesh during chilled storage. The results showed that P. versuta exhibited hydrolyzing activity against sarcoplasmic proteins, and all three strains could degrade myofibrillar proteins, specifically actin. The highest producer of putrescine was S. putrefaciens, which reached a maximum level 5.05 mg/kg after 14 days. Compared with the A. sobria group, hypoxanthine riboside degraded faster in samples inoculated with P. versuta or S. putrefaciens, A. sobria, P. versuta, and S. putrefaciens were responsible for the production of alcohol and aldehydes, whereas only S. putrefaciens produced thiophene and partial esters. Fish flesh inoculated with P. versuta, S. putrefaciens, and A. sobria presented slight green, yellow, and pink discoloration, respectively.

Total lactic acid bacteria, phenolic compounds and antioxidant activities of pineapple waste and Indigofera zollingeriana leaves by liquid fermentation

This study aims to determine the best combination of pineapple waste liquid fermentation and Indigofera zollingeriana leaves, which produces the highest amount of lactic acid bacteria, the highest vitamin C content, and total phenols, and the best antioxidant from the combination of the fermentation results. The resulting fermentation product will be used as a natural feed additive in poultry rations. This research was conducted with an experimental method using a Completely Randomized Design (CRD), which consisted of five preparations and four replications. The treatments were combination of pineapple waste and Indigofera zollingeriana leaves: P1 (100% pineapple waste), P2 (98% pineapple waste and 2% Indigofera zollingeriana leaves), P3 (96% pineapple waste and 4% Indigofera zollingeriana leaves), P4 (94% pineapple waste and 6% Indigofera zollingeriana leaves) and P5 (92% pineapple waste and 8% Indigofera zollingeriana leaves). Substrate from each combination of pineapple waste and leaves of Indigofera zollingeriana was fermented with the contribution of 10% of lactic acid bacteria obtained from commercial yogurt and incubated for 72 hours. The parameters in this study consisted of total lactic acid (Lactobacillus bulgarius), the concentration of vitamin C, total phenols, and antioxidant activity. The results showed that the combination of pineapple waste and Indigofera zollingeriana leaves proved significantly (P <0.05) to total lactic acid bacteria (Lactobacillus bulgarius), vitamin C concentration, total phenols and antioxidant activity of the fermented liquid (supernatant) products. In conclusion, the combination of 92% pineapple waste and 8% leaves of Indigofera zollingeriana had the highest total bacterial contribution, produced the highest vitamin C and phenolic compounds, and increased antioxidants.

Relationship between bacterial compartment and particulate organic matter (POM) in coastal systems: An assessment using fatty acids and stable isotopes

Particulate organic matter (POM) in coastal systems is a mixture of different organic matter (OM) sources originating from land and sea. Among sources, bacterial biomass plays a large role in OM processing and carbon recycling in the ocean and is often neglected as a source in common approaches. The present study proposes to use elemental and isotopic ratio of carbon and nitrogen (C:N, δ13C, δ15N) and fatty acids to investigate the relationship between bacteria and surface water POM composition of three systems with different characteristics (two marine and one estuarine) over an annual cycle. Overall, our results highlight a positive relationship between bacterial contribution and continental degraded or undergoing degradation POM for all the studied systems and an inverse relationship with pelagic primary producers. At multisystem scale, high bacterial contribution is linked to high proportion of refractory terrestrial material characterizing estuarine stations whereas in marine systems, the occurrence of bacteria is mainly linked to river POM. Over the annual cycle, bacterial markers are more abundant during the winter period characterized by larger river and/or benthic POM contribution. This seasonal pattern is mainly driven by changes in river flows and resuspension. This study highlights the importance of bacterial compartment as a component of coastal and estuarine POM. Even though these results remains semi-quantitative, similar studies in other types of systems can help to understand microbial role in OM dynamic and to better estimate bacterial source in carbon budgets and food web studies.

Origin and Evolution of Polycyclic Triterpene Synthesis.

Polycyclic triterpenes are members of the terpene family produced by the cyclization of squalene. The most representative polycyclic triterpenes are hopanoids and sterols, the former are mostly found in bacteria, whereas the latter are largely limited to eukaryotes, albeit with a growing number of bacterial exceptions. Given their important role and omnipresence in most eukaryotes, contrasting with their scant representation in bacteria, sterol biosynthesis was long thought to be a eukaryotic innovation. Thus, their presence in some bacteria was deemed to be the result of lateral gene transfer from eukaryotes. Elucidating the origin and evolution of the polycyclic triterpene synthetic pathways is important to understand the role of these compounds in eukaryogenesis and their geobiological value as biomarkers in fossil records. Here, we have revisited the phylogenies of the main enzymes involved in triterpene synthesis, performing gene neighborhood analysis and phylogenetic profiling. Squalene can be biosynthesized by two different pathways containing the HpnCDE or Sqs proteins. Our results suggest that the HpnCDE enzymes are derived from carotenoid biosynthesis ones and that they assembled in an ancestral squalene pathway in bacteria, while remaining metabolically versatile. Conversely, the Sqs enzyme is prone to be involved in lateral gene transfer, and its emergence is possibly related to the specialization of squalene biosynthesis. The biosynthesis of hopanoids seems to be ancestral in the Bacteria domain. Moreover, no triterpene cyclases are found in Archaea, invoking a potential scenario in which eukaryotic genes for sterol biosynthesis assembled from ancestral bacterial contributions in early eukaryotic lineages.

Bacterial contribution to genesis of the novel germ line determinant oskar.

New cellular functions and developmental processes can evolve by modifying existing genes or creating novel genes. Novel genes can arise not only via duplication or mutation but also by acquiring foreign DNA, also called horizontal gene transfer (HGT). Here we show that HGT likely contributed to the creation of a novel gene indispensable for reproduction in some insects. Long considered a novel gene with unknown origin, oskar has evolved to fulfil a crucial role in insect germ cell formation. Our analysis of over 100 insect Oskar sequences suggests that oskar arose de novo via fusion of eukaryotic and prokaryotic sequences. This work shows that highly unusual gene origin processes can give rise to novel genes that may facilitate evolution of novel developmental mechanisms.

The use of amino sugars for assessing seasonal dynamics of particulate organic matter in the Yangtze River estuary

The particulate amino sugars (PAS), organic carbon (POC) and nitrogen (PN), the chlorophyll a (Chl-a), and the heterotrophic bacterial cell count (HBC) in the Yangtze River Estuary (YRE) were determined to study the biological source, bioavailability and bacterial contribution of particulate organic matter (POM) under the influence of algal bloom during the spring and autumn of 2017. The contents of PAS were 2.6–69.6 nmol/(mg dw) and made up 5.29 ± 2.55% of POC and 5.39 ± 2.77% of PN. The strong positive correlations between Chl-a and POC, PN and PAS and their similar distributions indicated that phytoplankton was a major source of POM and PAS in the YRE. When algal blooms occurred, the high ratios of glucosamine to galactosamine (GlcN/GalN) (~10.9) and the high carbon and nitrogen normalized yields of PAS (%PAS-POC and %PAS-PN, respectively) clearly indicated the planktonic (especially zooplankton) source of POM, although the high muramic acid (Mur) contents implying high contents of fresh bacterial organic matter (OM) were also found. Additionally, the high proportion of fresh plankton- and bacterial-derived OM indicated that the POM was more labile when algal bloom occurred. In contrast, when the primary production was low, the lower %PAS-POC and GlcN/GalN ratios (< 3) in the POM demonstrated the decreased contribution of planktonic OM and the relatively elevated contribution of bacterial OM. In addition, the higher %PAS-PN and the lower DO concentrations in seawater indicated that the POM experienced some degree of degradation but was still at an early stage in the nearshore site in autumn. In spring, the Changjiang diluted water (CDW) carried considerable plankton-derived POM into the estuary and influenced the distribution of POM. In autumn, the terrestrial OM might become more bacterial-derived and had less influence on the bulk POM of the estuary. The bacterial OM estimated by the Mur accounted for an average of 10.8 ± 3.7% and 40.5 ± 19.1% of the POC in spring and autumn, respectively, which was approximately two times higher than the results based on the heterotrophic bacterial cell count (HBC), indicating that most of the bacterial OM in the POM was detritus. In summary, the content, source and bioavailability of POM were significantly affected by algal bloom and the CDW, and the amino sugars represent a reliable tool to indicate the source and bioavailability of POM.

Depth-specific distribution and significance of nitrite-dependent anaerobic methane oxidation process in tidal flow constructed wetlands used for treating river water.

Tidal flow constructed wetlands (TF CWs) have been considered an effective approach to treat contaminated river water, as well as a significant role in global matter cycles, especially for carbon and nitrogen. Notably, it has been thought that methane oxidation was completely catalyzed by the aerobic process, ignoring the anaerobic methane oxidation, such as the nitrite-dependent anaerobic methane oxidation (n-damo) process. In our current work, therefore, we used molecular and stable isotopes to investigate the biodiversity, quantity and potential rate of n-damo bacteria in the TF CWs located in the Xisha Wetland Park in the Yangtze River estuary, China. The results revealed that n-damo process was active in the collected soil cores, with a decreasing trend along water depths and rates ranging from 8.48 to 23.45nmol CO2 g-1 dry soil d-1. The n-damo bacterial contributions to CH4 oxidation and N2 production in TF CWs reached 9.49-26.26% and 20.73-47.11%, respectively, suggesting that n-damo bacteria was an important nitrogen and methane sink in the TF CWs, but had been previously overlooked. The copy numbers of total bacterial 16S rRNA and pmoA genes were 1.84-11.21×109 and 0.59-2.72×106 copies g-1 ds, respectively, as the higher abundance was found in the soil at lower water levels during tidal submergence. Diverse n-damo bacterial 16S rRNA gene sequences belonged to group B, C and D were measured, and it was found that group B and C were the most frequently measured n-damo clusters in the TF CWs. In addition, nitrite was the key factor regulating the n-damo bacterial distribution in the TF CWs. This study would broaden our horizons and help us better understand the nitrogen and methane cycles in tidal ecosystems.

The geochemical characteristics of the Fengcheng Formation source rocks from the Halaalate area, Junggar Basin, China

Abstracts The organic-rich sediments of the Fengcheng Formation in the Halaalate area, Junggar Basin, China are important source rocks and significant tight oil exploration targets. However, their geochemical characteristics have not been well documented. The hydrocarbon generation potential, genetic type of kerogen, organic matter (OM) sources, depositional conditions, and thermal maturity have been investigated based on a sample set of 11 mudstones. These source rock samples represent good to very good hydrocarbon generation potential, and primarily contain type I to II kerogen. The major organic input sources to the Fengcheng Formation from algae and bacteria were identified using stable carbon isotopes and biomarkers. Limited higher plant input can be inferred from trace amount of terrigenous OM biomarkers and minor contents of vitrinites and inertinites. The Fengcheng sediments were deposited under hypersaline and anoxic environments. Paleoclimate was arid during the deposition of the Fengcheng Formation. The presence of evaporites, mineral-bituminous groundmasses (MBG), alginites and microbial mats also supports these conclusions about depositional environments and biological source. The OM enrichment in the studied samples are attributed to the reducing environments, the booming of algae and the important bacterial contribution. Vitrinite reflectance and Tmax suggest a low thermal maturity of the studied Fengcheng sediments, in agreement with maturity-related hopane and sterane ratios and detection of hop-17(21)-enes. In a consideration of the quantity, quality and maturity of OM and their large thickness, the Fengcheng sediments have a good petroleum exploration potential.

Impact of nitrogen compounds on fungal and bacterial contributions to codenitrification in a pasture soil

Ruminant urine patches on grazed grassland are a significant source of agricultural nitrous oxide (N2O) emissions. Of the many biotic and abiotic N2O production mechanisms initiated following urine-urea deposition, codenitrification resulting in the formation of hybrid N2O, is one of the least understood. Codenitrification forms hybrid N2O via biotic N-nitrosation, co-metabolising organic and inorganic N compounds (N substrates) to produce N2O. The objective of this study was to assess the relative significance of different N substrates on codenitrification and to determine the contributions of fungi and bacteria to codenitrification. 15N-labelled ammonium, hydroxylamine (NH2OH) and two amino acids (phenylalanine or glycine) were applied, separately, to sieved soil mesocosms eight days after a simulated urine event, in the absence or presence of bacterial and fungal inhibitors. Soil chemical variables and N2O fluxes were monitored and the codenitrified N2O fluxes determined. Fungal inhibition decreased N2O fluxes by ca. 40% for both amino acid treatments, while bacterial inhibition only decreased the N2O flux of the glycine treatment, by 14%. Hydroxylamine (NH2OH) generated the highest N2O fluxes which declined with either fungal or bacterial inhibition alone, while combined inhibition resulted in a 60% decrease in the N2O flux. All the N substrates examined participated to some extent in codenitrification. Trends for codenitrification under the NH2OH substrate treatment followed those of total N2O fluxes (85.7% of total N2O flux). Codenitrification fluxes under non-NH2OH substrate treatments (0.7–1.2% of total N2O flux) were two orders of magnitude lower, and significant decreases in these treatments only occurred with fungal inhibition in the amino acid substrate treatments. These results demonstrate that in situ studies are required to better understand the dynamics of codenitrification substrates in grazed pasture soils and the associated role that fungi have with respect to codenitrification.

The Microbiome and Prostate Cancer Risk.

There is an abundance of evidence that the human microbiome plays an important and nuanced role in controlling human metabolism, immunity, and cancer. Herein we aim to review the most current research looking at prostate cancer and its link with the gut and genitourinary microbiome. There is now a host of evidence for a unique genitourinary (GU) microbiome. The prostate microbiota, to include viral, bacterial, fungal, and parasitic contributions, as assessed from formalin-fixed tissue is described nicely in the study by Banerjee et al. Further hierarchical analysis by this group found a unique microbiome signature for higher Gleason score cancers and validation PCR studies noted a marked number of viral genomic insertions into host DNA. Shretha et al. also recently established unique GU microbiomes in patients with prostate cancer or benign prostate pathology based on urine samples. The gut microbiome likely also has an indirect but significant role in prostate cancer development and treatment. Liss et al. and Golombos et al. found significant associations between specific gut microbiota and prostate cancer. Interestingly, the balance of inflammatory and anti-inflammatory bacterial lipopolysaccharides, production of bile salts, and metabolism of dietary fiber to short chain fatty acids all likely play important roles in creating systemic pro- or anti-carcinogenic states. In terms of prostate cancer treatment effects, Sfanos et al. noted a unique microbial signature in patients undergoing oral androgen deprivation therapy (ADT) as compared with prostate cancer patients not on ADT. Patients undergoing ADT also had enrichment of bacterial metabolic pathways promoting androgen synthesis. Together, these studies have identified a unique GU microbiome and linked both the GU microbiome and unique gut microbial signatures with prostate cancer and prostate cancer treatments. Whether this information can be used in cancer prevention, treatment, or diagnosis are areas of ongoing and active research.

Composition of the mucosa-associated microbiota along the entire gastrointestinal tract of human individuals.

Background Homeostasis of the gastrointestinal tract depends on a healthy bacterial microbiota, with alterations in microbiota composition suggested to contribute to diseases. To unravel bacterial contribution to disease pathology, a thorough understanding of the microbiota of the complete gastrointestinal tract is essential. To date, most microbial analyses have either focused on faecal samples, or on the microbial constitution of one gastrointestinal location instead of different locations within one individual.ObjectiveWe aimed to analyse the mucosal microbiome along the entire gastrointestinal tract within the same individuals.MethodsMucosal biopsies were taken from nine different sites in 14 individuals undergoing antegrade and subsequent retrograde double-balloon enteroscopy. The bacterial composition was characterised using 16 S rRNA sequencing with Illumina Miseq.ResultsAt double-balloon enteroscopy, one individual had a caecal adenocarcinoma and one individual had Peutz-Jeghers polyps. The composition of the microbiota distinctively changed along the gastrointestinal tract with larger bacterial load, diversity and abundance of Firmicutes and Bacteroidetes in the lower gastrointestinal tract than the upper gastrointestinal tract, which was predominated by Proteobacteria and Firmicutes.ConclusionsWe show that gastrointestinal location is a larger determinant of mucosal microbial diversity than inter-person differences. These data provide a baseline for further studies investigating gastrointestinal microbiota-related disease.

Seasonal Mixing-Driven System in Estuarine-Coastal Zone Triggers an Ecological Shift in Bacterial Assemblages Involved in Phytoplankton-Derived DMSP Degradation.

The coastal zone has distinguishable but tightly connected ecosystems from rivers to the ocean and globally contributes to nutrient cycling including phytoplankton-derived organic matter. Particularly, bacterial contributions to phytoplankton-derived dimethylsulfoniopropionate (DMSP) degradation have been recently evaluated by using advanced sequencing technologies to understand their role in the marine microbial food web. Here, we surveyed the bacterial diversity and community composition under seasonal water mixing in the bay of Gwangyang (GW), a semi-enclosed estuary at the southern tip of the Korea Peninsula. We detected phylogenetic dissimilarities among season-specific habitats in GW and their specific bacterial taxa. Additionally, bacterial contribution to degradation of phytoplankton-derived DMSP from estuarine to coastal waters at euphotic depths in GW was investigated as the presence or absence of DMSP demethylation gene, encoded by dmdA. Among the operational taxonomic units (OTUs) in GW bacterial communities, the most dominant and ubiquitous OTU1 was affiliated with the SAR11 clade (SAR11-OTU). The population dynamics of SAR11-OTU in dmdA-detected GW waters suggest that water mass mixing plays a major role in shaping bacterial communities involved in phytoplankton-derived DMSP demethylation.

Direct and indirect impact of the bacterial strain Pseudomonas aeruginosa on the dissolution of synthetic Fe(III)- and Fe(II)-bearing basaltic glasses

This study investigates the direct and indirect bacterial contributions that influence the dissolution of basaltic glass. In this regard, three different types of glasses – with or without Fe, in the reduced Fe(II) or oxidized Fe(III) states – were prepared on the basis of a simplified basaltic glass composition. In order to prevent the direct contact between the glasses and the model siderophore-producing strain Pseudomonas aeruginosa, the glass samples were isolated in dialysis bags and immersed at 25 °C and pH 6.5 in bacterial cultures. Throughout the dissolution experiments, the following parameters were monitored: determination of bacterial growth, quantification of siderophore (i.e. pyoverdine) production, microscopic observation of the glass surface and determination of dissolution kinetics.Isolating the glass from the bacterial suspension only triggered the biosynthesis of siderophores in the Fe(III)-bearing glass dissolution experiments. Siderophores were produced in the presence of Fe(II)-bearing and Fe-free glass, independently on the experimental setup. The siderophore production appeared to be either continuous in the absence of Fe (glass-free control, Fe-free glass dissolution experiments) or stopped as soon as the bacteria entered their stationary phase when an Fe source was present (Fe(II) and Fe(III)-bearing glass dissolution experiments). The increase in the dissolution rates of each glass was correlated to the complex stability constants of the siderophore with the metallic cations in presence (KFe2+ < KAl3+ ≪ KFe3+). Among the three glasses, only the Fe(III)-bearing one seemed to be significantly impacted by the dialysis process: its dissolution rate was doubled by isolating the glass grains from the cells. These results particularly allow to separate the impact of such bacterial exudates from physical contact effects: they showed the efficiency of pyoverdine in increasing the dissolution of an Fe(III)-bearing glass and evidenced that a direct bacterial cell attachment to the surface of such a glass results in a more moderate enhancement of its dissolution process. This work is a new contribution regarding the high affinity of microorganisms for basaltic glasses as an Fe-source. It highlights the role of Fe(III) accessibility upon the bacterial cells as a key parameter regulating their activity and their efficiency in accelerating the dissolution.

Tracking of the activity of individual bacteria in temperate forest soils shows guild-specific responses to seasonality

Bacteria belong to the key players in the carbon cycling in forest soils and thus affect the global C balance. Our understanding of bacterial contribution to ecosystem processes relies on the analysis of whole communities. Here we combined strain isolation, genome sequencing and metatranscriptomics to analyse the activity of individual bacterial species in the topsoil of a temperate coniferous forest. Our results show that transcription profiles in litter and soil differ, indicating that bacterial activity is shaped by their habitat. Importantly, transcript pools also significant differ between summer when primary producers are active and winter. We show that Acidobacteria and Bacteroidetes with high metabolic capacity for polysaccharide decomposition in their genomes actively transcribe corresponding genes in situ. The rate of the transcription of ribosomal proteins, a proxy of growth, seasonally differs between these “decomposer” taxa and other “opportunistic” bacteria. While the former grow at similar rates in summer and winter, the latter grow much faster in summer when labile C, delivered by plant roots, is available. This paper demonstrates differences in activity of bacterial guilds as well as the importance of environmental drivers for the activity of individual bacteria.

Continuing Impacts of Selective Inhibition on Bacterial and Fungal Communities in an Agricultural Soil.

Selective inhibition (SI) has been routinely used to differentiate the contributions of bacteria and fungi to soil ecological processes. SI experiments typically measured rapid responses within hours since the addition of inhibitor, but the long-term effects of selective biocides on microbial community composition and function were largely unknown. In this study, a microcosm experiment was performed with an agricultural soil to explore the effectiveness of two bactericides (bronopol, streptomycin) and two fungicides (cycloheximide, captan), which were applied at two different concentrations (2 and 10mgg-1). The microcosms were incubated for 6weeks. A radiolabeled substrate, [1,2,3,4,4a,9a-14C] anthracene, was spiked to all microcosms, and the derived CO2 was monitored during the incubation. The abundance and composition of bacteria and fungi were assessed by qPCR and Miseq sequencing of ribosomal rRNA genes. It was demonstrated that only 2mgg-1 bronopol and cycloheximide significantly changed the bacteria to fungi ratio without apparent non-target inhibition on the abundances; however, community shifts were observed in all treatments after 6weeks incubation. The enrichment of specific taxa implicated a selection of resistant or adapted microbes by these biocides. Mineralization of anthracene was continuingly suppressed in all SI microcosms, which may result in biased estimate of bacterial and fungal contributions to pollutant degradation. These findings highlight the risks of long-term application of selective inhibition, and a preliminary assessment of biocide selection and concentration is highly recommended.

Effect of extruded linseed supplementation, grain source and pH on dietary and microbial fatty acid outflows in continuous cultures of rumen microorganisms

Using 6 continuous cultures of rumen microorganisms, we studied the effects of pH (low vs. high) and extruded linseed supplementation (10% of DM) in association with rapidly or slowly degraded starch sources (wheat vs. corn grains) 1) on fatty acid (FA) outflows and PUFA biohydrogenation (BH) processes 2) on FA microbial composition and its contribution to FA outflows, in two replicated periods of 10d (7d adaptation and 3d sampling). The control diet contained wheat. The buffer solutions infused in low or high pH cultures differed by the addition of 10 mL of 5 N H2SO4 or NaOH so as to allow fermentation medium pH fluctuations with diets and time after feeding. The fermentation pattern, daily amounts of hexoses fermented (HF), efficiency of microbial protein synthesis (EMPS), and specific production of gases (CH4 and H2) were measured. FA compositions were determined in total effluents and bacterial pools isolated from effluents. Lowering pH (from 6.46 to 6.16 measured just before feeding) increased the VFA concentration in the control diet whereas it decreased it in all linseed supplemented diets. Lowering pH tended to decrease CH4 specific production as well as acetate and propionate proportions and to increase butyrate and valerate proportions but did not alter HF and EMPS. Linseed but not grain source increased pH by 0.08 and did not modify fermentative parameters. Apparent BH of C18:3 9c,12c,15c and C18:2 9c,12c decreased at low pH but increased with linseed supplementation. Corn associated to linseed increased 18:3 9c,12c,15c BH compared to wheat. Consequently, C18:3 9c,12c,15c outflows increased at low pH and with linseed, and were higher with linseed-wheat diet than linseed-corn diet. For all treatments, the proportions of C18:0 (% of C18-FA outflows) remained low associated with high levels of BH intermediates (C18:2 11t, 15c and C18:1 11t) suggesting that BH did not proceed to completion. Lowering pH decreased C16:1 9c and C18:1 11c bacteria contents and tended to increase anteiso-FA. Linseed supplementation increased C18:0, C18:1 9c, C18:1 9t, C18:2 9c,12c bacteria contents without modifying the C18:3 9c,12c,15c and decreased their odd-FA content and anteiso-FA in tendency. Compared to wheat, corn decreased branched-FA bacteria content, as well as even-saturated FA. Lowering pH decreased the bacterial FA outflow whereas linseed increased it. Both decreased the bacterial FA contribution to total FA outflow. Results indicate that pH and diets modified PUFA BH while differing in their effect on odd- and branched-chain FA bacteria content and outflows.

Characterization of Host and Bacterial Contributions to Lung Barrier Dysfunction Following Co-infection with 2009 Pandemic Influenza and Methicillin Resistant Staphylococcus aureus.

Influenza viruses are a threat to global public health resulting in ~500,000 deaths each year. Despite an intensive vaccination program, influenza infections remain a recurrent, yet unsolved public health problem. Secondary bacterial infections frequently complicate influenza infections during seasonal outbreaks and pandemics, resulting in increased morbidity and mortality. Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), is frequently associated with these co-infections, including the 2009 influenza pandemic. Damage to alveolar epithelium is a major contributor to severe influenza-bacterial co-infections and can result in gas exchange abnormalities, fluid leakage, and respiratory insufficiency. These deleterious manifestations likely involve both pathogen- and host-mediated mechanisms. However, there is a paucity of information regarding the mechanisms (pathogen- and/or host-mediated) underlying influenza-bacterial co-infection pathogenesis. To address this, we characterized the contributions of viral-, bacterial-, and host-mediated factors to the altered structure and function of alveolar epithelial cells during co-infection with a focus on the 2009 pandemic influenza (pdm2009) and MRSA. Here, we characterized pdm2009 and MRSA replication kinetics, temporal host kinome responses, modulation of MRSA virulence factors, and disruption of alveolar barrier integrity in response to pdm2009-MRSA co-infection. Our results suggest that alveolar barrier disruption during co-infection is mediated primarily through host response dysregulation, resulting in loss of alveolar barrier integrity.

The shift of bacterial community composition magnifies over time in response to different sources of soybean residues

The transformation of plant residues by soil microorganisms contributes significantly to soil carbon (C) sequestration. Although the contribution of different soybean residue sources (leaf, stalk and root) to soil organic C have been quantified in the highly productive Mollisols, the temporal dynamics of microbial community composition during the transformation has not. This study examined the effect of the soybean residues and incubation time on the bacterial community in a Mollisol during 150 days of incubation. Compared to the non-residue control, the presence of soybean residues increased abundances of Bacteroidetes, Actinobacteria and Firmicutes, but decreased those of Proteobacteria and Acidobacteria 15 days after residue amendment. The bacterial community composition differed between the residue sources after 60 days of incubation with the abundance of Niastella increasing in the leaf (from 4.5% to 19.1%) and stalk (from 6.5% to 25.7%) but not root treatments. The abundance of Bacillus significantly decreased in the stalk (from 12.2% to 2.2%) and root (from 4.0% to 1.6%) but not leaf-residue treatments. The abundance of bacterial genera was significantly associated with soil chemical variables including soil C, N, and pH. Overall, chemical variables drove the temporal response of the bacterial community succession, which provides insight into bacterial contribution to C turnover in soils.

Determining bacterial and host contributions to the human salivary metabolome

ABSTRACTBackground: Salivary metabolomics is rapidly advancing.Aim and methods: To determine the extent to which salivary metabolites reflects host or microbial metabolic activity whole-mouth saliva (WMS), parotid saliva (PS) and plasma collected contemporaneously from healthy volunteers were analysed by 1H-NMR spectroscopy. Spectra underwent principal component analysis and k-means cluster analysis and metabolite quantification. WMS samples were cultured on both sucrose and peptide-enriched media. Correlation between metabolite concentration and bacterial load was assessed.Results: WMS contained abundant short-chain fatty acids (SCFAs), which were minimal in PS and plasma. WMS spectral exhibited greater inter-individual variation than those of PS or plasma (6.7 and 3.6 fold, respectively), likely reflecting diversity of microbial metabolomes. WMS bacterial load correlated strongly with SCFA levels. Additional WMS metabolites including amines, amino acids and organic acids were positively correlated with bacterial load. Lactate, urea and citrate appeared to enter WMS via PS and the circulation. Urea correlated inversely with WMS bacterial load.Conclusions: Oral microbiota contribute significantly to the WMS metabolome. Several WMS metabolites (lactate, urea and citrate) are derived from the host circulation. WMS may be particularly useful to aid diagnosis of conditions reflective of dysbiosis. WMS could also complement other gastrointestinal fluids in future metabolomic studies.

The responding and ecological contribution of biofilm-leaves of submerged macrophytes on phenanthrene dissipation in sediments

The bacterial communities and ecological contribution of biofilm-leaves of the Vallisneria natans (VN), Hydrilla verticillata (HV) and artificial plant (AP) settled in sediments with different polluted levels of phenanthrene were investigated by high-throughput sequencing in different growth periods. There was no significant difference among the detected Alpha diversity indices based on three classification, attached surface, spiking concentration and incubation time. While Beta diversity analysis assessed by PCoA on operational taxonomic units (OTU) indicated that bacterial community structures were significantly influenced in order of attached surface > incubation time > spiking concentration of phenanthrene in sediment. Moreover, the results of hierarchical dendrograms and heat maps at genus level were consistent with PCoA analysis. We speculated that the weak influence of phenanthrene spiking concentration in sediment might be related to lower concentration and smaller concentration gradient of phenanthrene in leaves. Meanwhile, difference analysis suggested that attached surface was inclined to influence the rare genera up to significant level than incubation time. In general, the results proved that phenanthrene concentrations, submerged macrophytes categories and incubation time did influence the bacterial community of biofilm-leaves. In turn, results also showed a non-negligible ecological contribution of biofilm-leaves in dissipating the phenanthrene in sediments (>13.2%–17.1%) in contrast with rhizosphere remediation (2.5%–3.2% for HV and 9.9%–10.6% for VN).