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In order to analyze the high-temperature Daqu bacterial taxa and their physicochemical properties in Linyi area, Shandong Province, Illumina MiSeq high-throughput sequencing technology and pure culture technology were used to analyze the bacterial taxa of high-temperature Daqu in Lanling wine, and then the physicochemical indexes were determined by conventional detection methods in this study. Finally, the correlation between bacterial taxa and physicochemical indexes in Daqu was explored. The results showed that the main genera of bacteria in Daqu were Kroppenstedtia, Thermoactinomyces, Saccharopolyspora, Staphylococcus, Rhodococcus, Weissella and Bacillus, et al. Bacillus subtilis, Bacillus licheniformis and Bacillus coagulans were cultureable dominant bacterial isolates. There was a large difference in saccharification, esterification, alcoholization and liquefaction between the 15 parts of high-temperature Daqu. Kroppenstedtia, Staphylococcus, Leucobacter, Rhodococcus and Weissella were significantly positively correlated with esterification, fermentation, alcoholization, esterification and liquefaction (P<0.05). Thus, there are a large number of core bacterial taxa in high-temperature Daqu in Lanling wine, and there is a significant correlation between various bacterial genera and physicochemical indexes, which further provides a reference for the improvement and enhancement of the quality of high-temperature Daqu in this area. [ABSTRACT FROM AUTHOR]

In order to analyze the high-temperature Daqu bacterial taxa and their physicochemical properties in Linyi area, Shandong Province, Illumina MiSeq high-throughput sequencing technology and pure culture technology were used to analyze the bacterial taxa of high-temperature Daqu in Lanling wine, and then the physicochemical indexes were determined by conventional detection methods in this study. Finally, the correlation between bacterial taxa and physicochemical indexes in Daqu was explored. The results showed that the main genera of bacteria in Daqu were Kroppenstedtia, Thermoactinomyces, Saccharopolyspora, Staphylococcus, Rhodococcus, Weissella and Bacillus, et al. Bacillus subtilis, Bacillus licheniformis and Bacillus coagulans were cultureable dominant bacterial isolates. There was a large difference in saccharification, esterification, alcoholization and liquefaction between the 15 parts of high-temperature Daqu. Kroppenstedtia, Staphylococcus, Leucobacter, Rhodococcus and Weissella were significantly positively correlated with esterification, fermentation, alcoholization, esterification and liquefaction (P

RNA molecules within ejaculated sperm can be characterized through whole-transcriptome sequencing, enabling the identification of pivotal transcripts that may influence reproductive success. However, the profiling of sperm transcriptomes through next-generation sequencing has several limitations impairing the identification of functional transcripts. In this study, we explored the nature of the RNA sequences present in the sperm transcriptome of two livestock species, cattle and horses, using RNA sequencing (RNA-seq) technology. Through processing of transcriptomic data derived from bovine and equine sperm cell preparations, low mapping rates to the reference genomes were observed, mainly attributed to the presence of ribosomal RNA and bacteria in sperm samples, which led to a reduced sequencing depth of RNAs of interest. To explore the presence of bacteria, we aligned the unmapped reads to a complete database of bacterial genomes and identified bacteria-associated transcripts which were characterized. This analysis examines the limitations associated with sperm transcriptome profiling by reporting the nature of the RNA sequences among which bacterial RNA was found. These findings can aid researchers in understanding spermatozoal RNA-seq data and pave the way for the identification of molecular markers of sperm performance.

This study appraises the progress in the understanding of the composition of the vaginal microflora with a focus on the microbiome during pregnancy. This knowledge is presented with the background of the global health contribution, along with the importance of these microbial communities to pregnancy. A brief review of current methods employed to investigate the structure of these microbial populations is included. Two types of studies, cross-sectional and longitudinal, have been used to characterise the vaginal microbiota; both types are reviewed since they provide information that serves to piece together a more complete picture of the vaginal microflora and its changes during pregnancy. The identity of microbes present in the vagina are examined in the context of health and disease, and, more specifically, in the setting of pregnancy outcomes. The protective role of lactobacilli in maintaining a healthy vaginal environment is evaluated, with analyses of the different roles of various Lactobacillus spp. Classifications of the vaginal microbiota into vagitypes in non-pregnant and pregnant women are discussed. The associations of specific taxa with three adverse pregnancy results, namely, miscarriage, stillbirth, and preterm birth, are examined in some detail. Longitudinal studies investigating changes in the bacterial community composition and taxa abundance demonstrate that this microbiota decreases in richness and diversity relative to those present in non-pregnant microbiomes. Notwithstanding the significant effort made to characterise the vagina bacterial microbiota, a large number of issues remain to be fully understood. [ABSTRACT FROM AUTHOR]

This study appraises the progress in the understanding of the composition of the vaginal microflora with a focus on the microbiome during pregnancy. This knowledge is presented with the background of the global health contribution, along with the importance of these microbial communities to pregnancy. A brief review of current methods employed to investigate the structure of these microbial populations is included. Two types of studies, cross-sectional and longitudinal, have been used to characterise the vaginal microbiota; both types are reviewed since they provide information that serves to piece together a more complete picture of the vaginal microflora and its changes during pregnancy. The identity of microbes present in the vagina are examined in the context of health and disease, and, more specifically, in the setting of pregnancy outcomes. The protective role of lactobacilli in maintaining a healthy vaginal environment is evaluated, with analyses of the different roles of various Lactobacillus spp. Classifications of the vaginal microbiota into vagitypes in non-pregnant and pregnant women are discussed. The associations of specific taxa with three adverse pregnancy results, namely, miscarriage, stillbirth, and preterm birth, are examined in some detail. Longitudinal studies investigating changes in the bacterial community composition and taxa abundance demonstrate that this microbiota decreases in richness and diversity relative to those present in non-pregnant microbiomes. Notwithstanding the significant effort made to characterise the vagina bacterial microbiota, a large number of issues remain to be fully understood.

In this study, the physicochemical characteristics and bacterial taxa of 11 fen-flavor Daqu samples from Changzhi, Shanxi Province were analyzed using a combination of physicochemical analysis and MiSeq high-throughput sequencing, and the correlation between them was revealed. The physicochemical analysis showed that the variation coefficients of amino acid nitrogen, liquefaction power and alcoholization power of different fen-flavor Daqu samples were greater than 15%, with the largest difference in liquefaction power and the smallest difference in ash. MiSeq high-throughput sequencing analysis found that the bacterial genera presented in all samples with an average relative content >1.0% were Aquabacterium, Pelomonas, Bacillus, Ralstonia, Sphingomonas, Burkholderia, Methylobacterium and Bradyrhizobium, and a large number of bacterial taxa were shared among the different samples. Correlation analysis revealed that Sphingomonas showed a significant positive correlation with protein content (P

The aim of this work was to achieve a better understanding of the bacterial pathogens associated with stillbirths that would serve to inform clinical interventions directed at reducing this adverse pregnancy outcome. A prospective observational study was conducted with the participation of 22 women from northern Peru, of whom 11 experienced fetal death in utero and 11 delivered preterm births. Swabs were taken from the vagina, placenta, amniotic fluid and axilla of the infant at birth by Caesarean section. The bacterial populations in the vagina and the amniotic space of each participant were determined by employing the amplicon sequencing of the V4 region of the 16S rRNA genes. The sequence data were analysed using bioinformatics tools. The work showed differences in the composition of the genital microbiomes of women who experienced preterm birth or fetal death in utero. There were no differences in the alpha diversity between the genital microbiotas of both groups of women, but there were more different taxa in the vagina and amniotic space of the preterm participants. Lactobacillus spp. was less abundant in the stillbirth cases. E. coli/Shigella, Staphylococcus, Gardnerella, Listeria and Bacteroides taxa were associated with the stillbirths. In each woman, there was a minimal concordance between the bacterial populations in the vagina and amniotic space. [ABSTRACT FROM AUTHOR]

This study was carried out to compare gut microbial community composition, diversity, and function with and without microbiota transplantation in a newly-hatched chick model. Two hundred and forty newly-hatched Arbor Acre male broilers were assigned randomly to either a microbiota transplantation group or a control group (n = 120; 6 replicates per group, and 20 broilers per replicate). Both groups were fed a basal diet that met all nutritional requirements, composed of corn, soybean meal, cottonseed meal, vitamins, and minerals. The microbiota transplantation group was inoculated with the microbiota from the ceca of healthy adult chicks on day 1 and 2, respectively, over a trial period of 42 d. For both groups, the numbers of total bacteria, Lactobacillus and Escherichia coli, operational taxonomic unit partitioning and classification, taxonomic composition, comparative microbiota, and key bacterial species were identified by a 16S rRNA sequencing analysis. The results showed that Aestuariispira, Christensenella, Fervidicella, Gracilibacter, Haloferula, Mycoplasma, Novispirillum, and Pantoea were more abundant (p < 0.05) in the microbiota transplantation group than those in the control group. This indicates that microbiota transplantation could directly influence the abundances of specific bacterial taxa in the ileum and cecum of broilers. These findings provide insight into the modulation of gut health for patients with abnormal bowel function, which should be of great interest to researchers in the area of gastroenterology, applied microbiology, and animal sciences. [ABSTRACT FROM AUTHOR]

The current study aimed to investigate the effect of periodontitis and long-term heavy metal (HM) exposure on the salivary microbiome. The patients were divided into four groups as Wu Wei control (WWC) group involved healthy individuals, Wu Wei periodontitis (WWP) patients having periodontitis, Jing Chang with metal pollution periodontally healthy individuals (JCP), and Kuang periodontitis (KP). The most abundant bacteria identified at the phylum level in the WWC group were Bacteroides, Firmicutes, and Fusobacteria. Firmicutes were observed in a significantly higher proportion in the KP group than in the WWC, WWP, and JCP. At the genus level, the WWC has major dominating bacterial genera (such as Leptotrichia, Neisseria, and Fusobacterium) which were similar to WWP and KP group. The significant difference (p < 0.05) was found in alpha diversity while in beta diversity, the significant (p = 0.005) results were found among the four groups. The correlation of oral microbiota revealed that HMs present in the soil (Cr, Ni, and Cu) are associated with the growth of Capnocytophaga, Selenomonas, Aggregatibacter, and Campylobacter. The bacterial functions in the KP group were higher in translation and nucleotide metabolism than in the WWP group. This demonstrated that long-term exposure to HMs can influence the salivary microbiota which can alter the functioning, and diversity of bacteria. [ABSTRACT FROM AUTHOR]

In this cross-sectional study, we hypothesized that a high dietary ratio of omega-6 (n-6) to omega-3 (n-3) fatty acids could be associated with an altered gut bacterial composition and with the disease severity in patients with nonalcoholic fatty liver disease (NAFLD). A total of 101 NAFLD patients were included in the study, of which 63 underwent a liver biopsy. All 101 patients completed a 14-day food and activity record. Ebispro 2016 professional software was used to calculate individual macronutrients and micronutrients consumed. Patients were grouped into 3 quantiles (Q) according to a low (Q1: <6.1, n = 34), moderate (Q2: 6.1-7.8, n = 33), or high (Q3: >7.8, n = 34) dietary n-6/n-3 ratio. Stool samples were analyzed using 16S rRNA gene sequencing. Spearman correlation coefficients and principal coordinate analysis were used to detect differences in the bacterial composition of the gut microbiota. The median dietary n-6/n-3 ratio of all patients was 6.7 (range, 3.1-14.9). No significant associations between the dietary n-6/n-3 ratio and the gut microbiota composition or disease severity were observed. However, the abundance of specific bacteria such as Catenibacterium or Lactobacillus ruminis were found to be positively correlated and the abundance of Clostridium were negatively correlated with dietary n-6 fatty acid intake. The results indicate that a high dietary n-6/n-3 ratio is probably not a highly relevant factor in the pathogenesis of human NAFLD. Further studies are needed to clarify the importance of interactions between gut bacterial taxa and n-6 fatty acids in the pathophysiology of NAFLD. Patients with nonalcoholic fatty liver disease consume a high proportion of dietary omega-6 polyunsaturated fatty acids (n-6 PUFAs). We did not detect significant associations between a high dietary n-6/n-3 PUFA ratio and histological disease severity or the gut microbiota composition. On the other hand, we could observe correlations between the dietary n-6 PUFA intake and the abundance of specific gut bacterial taxa. Only bacterial taxa with highly significant correlations are displayed (P <.01). [Display omitted] [ABSTRACT FROM AUTHOR]

RNA molecules within ejaculated sperm can be characterized through whole-transcriptome sequencing, enabling the identification of pivotal transcripts that may influence reproductive success. However, the profiling of sperm transcriptomes through next-generation sequencing has several limitations impairing the identification of functional transcripts. In this study, we explored the nature of the RNA sequences present in the sperm transcriptome of two livestock species, cattle and horses, using RNA sequencing (RNA-seq) technology. Through processing of transcriptomic data derived from bovine and equine sperm cell preparations, low mapping rates to the reference genomes were observed, mainly attributed to the presence of ribosomal RNA and bacteria in sperm samples, which led to a reduced sequencing depth of RNAs of interest. To explore the presence of bacteria, we aligned the unmapped reads to a complete database of bacterial genomes and identified bacteria-associated transcripts which were characterized. This analysis examines the limitations associated with sperm transcriptome profiling by reporting the nature of the RNA sequences among which bacterial RNA was found. These findings can aid researchers in understanding spermatozoal RNA-seq data and pave the way for the identification of molecular markers of sperm performance.

The aim of this work was to achieve a better understanding of the bacterial pathogens associated with stillbirths that would serve to inform clinical interventions directed at reducing this adverse pregnancy outcome. A prospective observational study was conducted with the participation of 22 women from northern Peru, of whom 11 experienced fetal death in utero and 11 delivered preterm births. Swabs were taken from the vagina, placenta, amniotic fluid and axilla of the infant at birth by Caesarean section. The bacterial populations in the vagina and the amniotic space of each participant were determined by employing the amplicon sequencing of the V4 region of the 16S rRNA genes. The sequence data were analysed using bioinformatics tools. The work showed differences in the composition of the genital microbiomes of women who experienced preterm birth or fetal death in utero. There were no differences in the alpha diversity between the genital microbiotas of both groups of women, but there were more different taxa in the vagina and amniotic space of the preterm participants. Lactobacillus spp. was less abundant in the stillbirth cases. E. coli/Shigella, Staphylococcus, Gardnerella, Listeria and Bacteroides taxa were associated with the stillbirths. In each woman, there was a minimal concordance between the bacterial populations in the vagina and amniotic space.

This study was carried out to compare gut microbial community composition, diversity, and function with and without microbiota transplantation in a newly-hatched chick model. Two hundred and forty newly-hatched Arbor Acre male broilers were assigned randomly to either a microbiota transplantation group or a control group (n = 120; 6 replicates per group, and 20 broilers per replicate). Both groups were fed a basal diet that met all nutritional requirements, composed of corn, soybean meal, cottonseed meal, vitamins, and minerals. The microbiota transplantation group was inoculated with the microbiota from the ceca of healthy adult chicks on day 1 and 2, respectively, over a trial period of 42 d. For both groups, the numbers of total bacteria, Lactobacillus and Escherichia coli, operational taxonomic unit partitioning and classification, taxonomic composition, comparative microbiota, and key bacterial species were identified by a 16S rRNA sequencing analysis. The results showed that Aestuariispira, Christensenella, Fervidicella, Gracilibacter, Haloferula, Mycoplasma, Novispirillum, and Pantoea were more abundant (p < 0.05) in the microbiota transplantation group than those in the control group. This indicates that microbiota transplantation could directly influence the abundances of specific bacterial taxa in the ileum and cecum of broilers. These findings provide insight into the modulation of gut health for patients with abnormal bowel function, which should be of great interest to researchers in the area of gastroenterology, applied microbiology, and animal sciences.

The intestinal microbiota play a vital role in the growth and health of the host. Probiotics could influence the homeostasis of intestinal microbiota, but the relationship between species and ecosystem stability is poorly understood. Here, four diets with different doses of Bacillus cereus (control, 0 cfu/kg; BL7, 107 cfu/kg; BL9, 109 cfu/kg; and BL11, 1011 cfu/kg) were designed to investigate the intestinal microbiota in Paramisgurnus dabryanus. The growth experiment demonstrated that the growth performance and the indices of Chao1, phylogenetic diversity, Simpson and Shannon improved significantly after loaches were fed a BL11 diet. The dominant composition of intestinal microbiota at phylum, class and genus levels did not change in loach after feeding different diets. Categories of bacterial taxa revealed that rare taxa and conditionally rare taxa were the dominant bacterial taxa in intestinal microbiota of loach. B. cereus supplemented with 1011 cfu/kg promoted the stability of the ecological network of intestinal microbiota by reinforcing the cooperation of interspecific interactions, promoting operational taxonomic units to shape larger submodules and increasing module hubs species and connectors species. Results of functional prediction revealed that a total of 5692 functions were shared among the four groups, which accounted for 91.7% of overall functions. To sum up, dietary supplementation with B. cereus had no significant influences on the composition and bacterial taxa of intestinal microbiota and the composition of bacterial functions. A dose of B. cereus appropriate to the diet could improve the growth performance and promote the homeostasis of intestinal microbiota in loach. [ABSTRACT FROM AUTHOR]

Succinic semialdehyde dehydrogenase deficiency (SSADHD) is an inherited inborn error of the γ-aminobutyric acid (GABA) metabolism pathway. It results from mutations in the ALDH5A1 gene leading to elevated GABA, γ-hydroxybutyric acid (GHB), succinic semialdehyde (SSA), decreased glutamine and alterations in several other metabolites. The phenotype includes developmental and cognitive delays, hypotonia, seizures, neuropsychiatric morbidity and other nervous system pathologies. The composition of the intestinal flora of patients with SSADHD has not been characterized, and dysbiosis of the gut microbiome may unveil novel treatment paradigms. We investigated the gut microbiome in SSADHD using 16S ribosomal DNA sequencing and unmasked evidence of dysbiosis in both aldh5a1 -deficient mice and patients with SSADHD. In the murine model, there was a reduction in α-diversity measurements, and there were 4 phyla, 3 classes, 5 orders, 9 families, and 15 genera that differed, with a total of 17 predicted metabolic pathways altered. In patients, there were changes in Fusobacterium, 3 classes, 4 orders, 11 families, and a predicted alteration in genes associated with the digestive system. We believe this is the first evaluation of microbiome structure in an IEM with a neurometabolic phenotype that is not treated dietarily. [ABSTRACT FROM AUTHOR]

Introduction and hypothesis: Growing literature details the critical importance of the microbiome in the modulation of human health and disease including both the gastrointestinal and genitourinary systems. Rectovaginal fistulae (RVF) are notoriously difficult to manage, many requiring multiple attempts at repair before correction is achieved. RVF involves two distinct microbiome communities whose characteristics and potential interplay have not been previously characterized and may influence surgical success. Methods: In this pilot study, rectal and vaginal samples were collected from 14 patients with RVF. Samples were collected preoperatively, immediately following surgery, 6–8 weeks postoperatively and at the time of any fistula recurrence. Amplification of the 16S rDNA V3-V5 gene region was done to identify microbiota. Data were summarized using both α-diversity to describe species richness and evenness and β-diversity to characterize the shared variation between communities. Differential abundance analysis was performed to identify microbial taxa associated with recurrence. Results: The rectal and vaginal microbiome in patients undergoing successful fistula repair was different than in those with recurrence (β-diversity, p = 0.005 and 0.018, respectively) and was characterized by higher species diversity (α-diversity, p = 0.07 and p = 0.006, respectively). Thirty-one taxa were enriched in patients undergoing successful repair to include Bacteroidetes, Alistipes and Rikenellaceae as well as Firmicutes, Subdoligranulum, Ruminococcaceae UCG-010 and NK4A214 group. Conclusions: Microbiome characteristics associated with fistula recurrence have been identified. The association of higher vaginal diversity with a favorable outcome has not been previously described. Expansion of this pilot project is needed to confirm findings. Taxa associated with successful repair could be targeted for subsequent therapeutic intervention. [ABSTRACT FROM AUTHOR]

Inborn errors of metabolism (IEMs) represent monogenic disorders in which specific enzyme deficiencies, or a group of enzyme deficiencies (e.g., peroxisomal biogenesis disorders) result in either toxic accumulation of metabolic intermediates or deficiency in the production of key end-products (e.g., low cholesterol in Smith-Lemli-Opitz syndrome (Gedam et al., 2012 [ 1 ]); low creatine in guanidinoacetic acid methyltransferase deficiency (Stromberger, 2003 [ 2 ])). Some IEMs can be effectively treated by dietary restrictions (e.g., phenylketonuria (PKU), maple syrup urine disease (MSUD)), and/or dietary intervention to remove offending compounds (e.g., acylcarnitine excretion with the oral intake of l -carnitine in the disorders of fatty acid oxidation). While the IEMs are predominantly monogenic disorders, their phenotypic presentation is complex and pleiotropic, impacting multiple physiological systems (hepatic and neurological function, renal and musculoskeletal impairment, cardiovascular and pulmonary activity, etc.). The metabolic dysfunction induced by the IEMs, as well as the dietary interventions used to treat them, are predicted to impact the gut microbiome in patients, and it is highly likely that microbiome dysbiosis leads to further exacerbation of the clinical phenotype. That said, only recently has the gut microbiome been considered as a potential pathomechanistic consideration in the IEMs. In this review, we overview the function of the gut-brain axis, the crosstalk between these compartments, and the expanding reports of dysbiosis in the IEMs recently reported. The potential use of pre- and probiotics to improve clinical outcomes in IEMs is also highlighted. [ABSTRACT FROM AUTHOR]

Purpose: To assess the effect of silver diamine fluoride (SDF) on microbial profiles present in plaque from root/cervical carious lesions, and its association with caries lesion arrest.Materials and Methods: Twenty patients with at least one soft cavitated root/cervical carious lesion were included. One lesion/patient was randomly selected and treated with 38% SDF. Supragingival plaque samples were harvested at preintervention and 1 month postintervention. Using an MiSeq platform, 16S rDNA sequencing of the V3-V4 regions was used to determine bacterial profiles. Clinical evaluation of lesion hardness was used to evaluate arrest. t tests, principal component analysis (PCA), multidimensional scaling (MDS), and generalized linear models (GLMs) tests were used for statistical comparisons.Results: From a total of 40 plaque samples, 468 probe targets were observed. Although 60% of lesions became hard postintervention, PCA and MDS tests showed no distinct pre- and postintervention groups. In addition, pre- and postintervention differences in diversity (Shannon index) of microbial profiles between patients with and without lesion arrest were not statistically different. A likelihood ratio test for pre- versus postintervention differences within patients, i.e., adjusting for differences between patients using negative binomial GLMs, showed 17 bacterial taxa with significant differences (FDR <0.05).Conclusion: Although 60% of lesions hardened after SDF treatment, this was not directly due to either overall statistically significant differences in microbial profiles or differences in microbial diversity. Nevertheless, there was a trend with some acid-producing species in that their relative abundance was reduced postintervention. The negative binomial GLMs showed 17 bacterial taxa that were significantly different after SDF treatment. [ABSTRACT FROM AUTHOR]

Abstract Soil microbial communities mediate soil feedbacks to climate; a thorough understanding of their response to increasing temperatures is therefore central to predict climate-induced changes in carbon (C) fluxes. However, it is unclear how microbial communities will change in structure and function in response to temperature change and to the availability of organic C which varies in complexity. Here we present results from a laboratory incubation study in which soil microbial communities were exposed to different temperatures and organic C complexity. Soil samples were collected from two land-use types differing in climatic and edaphic conditions and located in two regions in southwest Germany. Soils amended with cellobiose (CB), xylan, or coniferyl alcohol (CA, lignin precursor) were incubated at 5, 15 or 25 °C. We found that temperature predominantly controlled microbial respiration rates. Increasing temperature stimulated cumulative respiration rates but decreased total microbial biomass (total phospholipid fatty acids, PLFAs) in all substrate amendments. Temperature increase affected fungal biomass more adversely than bacterial biomass and the temperature response of fungal biomass (fungal PLFAs, ergosterol and ITS fragment) depended upon substrate quality. With the addition of CB, temperature response of fungal biomass did not differ from un-amended control soils, whereas addition of xylan and CA shifted the fungal temperature optima from 5 °C to 15 °C. These results provide first evidence that fungi which decompose complex C substrates (CA and xylan) may have different life strategies and temperature optima than fungal communities which decompose labile C substrate (CB). Gram-positive and gram-negative bacteria differed strongly in their capacity to decompose CB under different temperature regimes: gram-positive bacteria had highest PLFA abundance at 5 °C, while gram-negative bacteria were most abundant at 25 °C. Bacterial community composition, as measured by 16S rRNA gene abundance, and PLFAs showed opposite temperature and substrate decomposition trends. Using multivariate statistics, we found a general association of microbial life strategies and key members of the microbial community: oligotrophic Alphaproteobacteria and Acidobacteria were associated with complex substrates and copiotrophic Actinobacteria with labile substrates. Our study provides evidence that the response of C cycling to warming will be mediated by shifts in the structure and function of soil microbial communities. Highlights • Response of microbial abundance to temperature and substrate quality was measured. • Increased temperature reduced total microbial biomass. • Temperature response of fungi depended upon substrate quality. • Gram+ & gram-bacteria differed in temperature response in cellobiose amended soils. [ABSTRACT FROM AUTHOR]

The global demand for petroleum contributes to a significant increase in soil pollution with petroleum-based products that pose a severe risk not only to humans but also to plants and the soil microbiome. The increasing pollution of the natural environment urges the search for effective remediation methods. Considering the above, the objective of this study was to determine the usability of Dactylis glomerata for the degradation of hydrocarbons contained in diesel oil (DO), as well as the effects of both the plant tested and DO on the biochemical functionality and changes in the soil microbiome. The experiment was conducted in a greenhouse with non-polluted soil as well as soil polluted with DO and phytoremediated with Dactylis glomerata. Soil pollution with DO increased the numbers of microorganisms and soil enzymes and decreased the value of the ecophysiological diversity index of microorganisms. Besides, it contributed to changes in the bacterial structure at all taxonomic levels. DO was found to increase the abundance of Proteobacteria and to decrease that of Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes and Firmicutes. In the non-polluted soil, the core microbiome was represented by Kaistobacter and Rhodoplanes, whereas in the DO-polluted soil, it was represented by Parvibaculum and Rhodococcus. In soil sown with Dactylis glomerata, gasoline fraction (C6–C12) degradation was higher by 17%; mineral oil (C12–C35), by 9%; benzene, by 31%; anthracene, by 12%; chrysene, by 38%; benzo(a)anthracene, by 19%; benzo(a)pyrene, by 17%; benzo(b)fluoranthene, by 15%; and benzo(k)fluoranthene, by 18% than in non-sowed soil. To conclude, Dactylis glomerata proved useful in degrading DO hydrocarbons and, therefore, may be recommended for the phytoremediation of soils polluted with petroleum-based products. It has been shown that the microbiological, biochemical and chemical tests are fast and sensitive in the diagnosis of soil contamination with petroleum products, and a combination of all these tests gives a reliable assessment of the state of soils.

The microbial impact on waterlogged wooden cultural relics from Xiaobaijiao No. 1 shipwreck was investigated by means of a high-throughput sequencing technology, while the focus was on the composition of prokaryotic microorganisms in 10 wood samples collected from different parts of the shipwreck. A total of 28 501 different operational taxonomic units (OTUs) were obtained based on 97% sequence similarity. The _-diversity index is for the bacterial diversity, which was the highest and the lowest in the samples SS8 and SS5, respectively. Proteobacteria was the largest category of bacterial abundance (47.3%) followed by Bacteroidetes (10%). _-Proteobacteria was the first largest bacteria class with the maximum abundance (21.0%) followed by γ-Proteobacteria (16.9%). Other groups rich in the following species were found: Bacteroidales (13.3%), Thiotrichales (5.0%), Rhodobacterales (4.2%), Rhizobiales (4.0%), Chromatiales (3.5%), Oceanospirillales (3.3%), Flavobacteriales (2.9%) and Sphingomonadales (2.8%). At the level of the bacterial genus, Marinomonas was the most abundant one. Phylogenetic analysis revealed that there are some differences in the composition of bacterial communities from different wood samples. The species number of bacteria in the relics of this shipwreck was far more than that reported in those found in Europe, and in which species composition was similar to the benthic bacteria in the corresponding sea area. The coexistence of anaerobic and aerobic bacteria is remarkable. [ABSTRACT FROM AUTHOR]

The spread of antimicrobial resistance in environment is promoted at least in part by the inappropriate use of antibiotics in animals and humans. The present study was designed to investigate the impact of different concentrations of ciprofloxacin in soil containing manure on the development of plasmid-mediated quinolone resistance (PMQR) - encoding genes and the abundance of soil bacterial communities. For these studies, high-throughput next-generation sequencing of 16S rRNA, real-time PCR and standard microbiologic culture methods were utilized. We demonstrated that the dissipate rate of relative abundances of some of PMQR-encoding genes, such as qnrS, oqxA and aac(6’)-Ib-cr, were significantly lower with ciprofloxacin 0.04 and 0.4 mg/kg exposure as compared to no-ciprofloxacin control and ciprofloxacin 4 mg/kg exposure during two month. Also, the number of ciprofloxacin resistant bacteria was significantly greater in ciprofloxacin 0.04 and 0.4 mg/kg exposure as compared with no-ciprofloxacin control and the ciprofloxacin 4 mg/kg exposure. In addition, lower ciprofloxacin concentration provided a selective advantage for the populations of Xanthomonadales and Bacillales in orders while Agrobacterium, Bacillus, Enterococcus and Burkholderia in genera. These findings suggest that lower concentration of ciprofloxacin resulted in a slower rate of PMQR- encoding genes dissipation and selected development of ciprofloxacin-resistant bacteria in soil amended with manure.

Links between the microbial community structure and soil functions are unclear. The study of these relationships requires the development of highly specific experimental approaches. In this work, the soil microbial community structure and function relationship was evaluated in relation to heat stress in a soil microcosm incubated at 17 °C and 50 °C. We selected a luvisol that included two land uses. Samples were taken from the soil of a long-term (>10 year) arable cropping plot (CC) and a permanent grassland (PG) (>25 years). The soil functions were evaluated by measuring the enzyme activities, including cellulase, N -acetyl-glucosaminidase, β-glucosidase, xylanase and dehydrogenase. The total microbial biomass was assayed by the quantification of the total DNA extracted from the microcosm soils. The abundance of total bacterial and fungal communities and different bacterial taxa were measured by qPCR rRNA genes. For both soil types, heat stress induced changes in the microbial community structure and soil functions. In most cases, the results yielded effects following heat treatment. All of the enzymes were inhibited except xylanase. Heat stress significantly reduced the total microbial biomass and fungal abundance in the soils. The abundance of the total bacterial community was not affected by heat stress. In the two soils, the dominant taxa were Actinobacteria (13–40%) and Bacteroidetes (14–32%), while Planctomycetes and Gammaproteobacteria exhibited lower abundance (0–3%). Changes in the microbial community structure and changes in the functions were correlated; the correlation was positive in the PG soil and negative in the CC soil. The changes in the CC soil structural and functional state were greater than of those observed in PG soil. Our initial hypothesis was confirmed, indeed, grassland soil is more resistant to drastic stress due to its highly abundant and highly diversified microbial community. These results represent a contribution to the understanding of soil microbial community structure and functions relationships. [ABSTRACT FROM AUTHOR]

Establishment of the microbiota of the gut has been shown to differ between infants delivered by Caesarian section (C-section) and those delivered vaginally. The aim of the present study was to compare the oral microbiota in infants delivered by these different routes. The oral biofilm was assayed by the Human Oral Microbe Identification Microarray (HOMIM) in healthy three-month-old infants, 38 infants born by C-section, and 25 infants delivered vaginally. Among over 300 bacterial taxa targeted by the HOMIM microarray, Slackia exigua was detected only in infants delivered by C-section. Further, significantly more bacterial taxa were detected in the infants delivered vaginally (79 species/species clusters) compared with infants delivered by C-section (54 species/species clusters). Multivariate modeling revealed a strong model that separated the microbiota of C-section and vaginally delivered infants into two distinct colonization patterns. In conclusion, our study indicated differences in the oral microbiota in infants due to mode of delivery, with vaginally delivered infants having a higher number of taxa detected by the HOMIM microarray. [ABSTRACT FROM PUBLISHER]

For many years, jellyfish were described as 'dead ends' in marine food webs, due to their high-water content and low nutritional value. However, it has been confirmed that silver pomfret (Pampus argenteus) has a particular preference for preying on jellyfish. In this study, we determined the effect of consuming jellyfish on the intestinal microbes of silver pomfret. Analysis of bacterial 16S rRNA gene amplicons showed that jellyfish had a dramatic impact on the composition of the gut microbiota. The content of Proteobacteria was reduced from 99% to 51%, while Firmicutes, Bacteroidetes and Actinobacteria increased, accounting for 35%, 9% and 2% of the total flora, respectively. At the genus level, the content of Photobacterium decreased sharply to <1% of the total flora. By contrast, Lactobacillus, Burkholderia and Sphingomonas increased to 12%, 9% and 7% of the total flora, respectively. After feeding jellyfish, the functions of intestinal microbes and the activity of digestive enzymes also changed, resulting in better digestion and absorption of jellyfish. The results provide insights into the specific bacterial taxa within the silver pomfret intestinal microbiome that are impacted by jellyfish. Silver pomfret can better digest and absorb jellyfish by adjusting the intestinal microbial composition. The findings provide a theoretical basis for the digestive mechanism by which silver pomfret consume jellyfish. [Display omitted] • Eating jellyfish has a dramatic impact on the gut microbiota of silver pomfret. • Proteobacteria decreased, but Firmicutes, Bacteroidetes and Actinobacteria increased. • Photobacterium decreased, but Lactobacillus, Burkholderia and Sphingomonas increased. • Intestinal microbe functions and digestive enzymes were also altered. [ABSTRACT FROM AUTHOR]

• Soil C chemistry and bacterial composition were studied in the paddy and upland soils. • The paddy soil and upland soil exhibited opposite shifts of OCH and alkyl C. • Nitrate-N and TN contents shape the bacterial community composition of the paddy soil. • SOC content affects the bacterial community composition of the upland soil. • Chemical nature of the paddy and upland soils associated with distinct bacterial taxa. The supposition that cropping system might affect fertilization-induced changes in chemical composition of soil organic carbon (SOC) and microbial community composition has mostly derived from field experiments in different sites, which may have been disturbed by different climate conditions and parent materials. Here, two adjacent long-term field experiments were used, which contained similar four fertilization regimes of NPK, 2NPK, NPKOM, and an unamended control (Control), while contrasting annual cropping system of rice–rice and maize–maize, to investigate how fertilization-induced changes in SOC chemistry differ in paddy soil from upland soil, and whether they correlate with different bacterial taxa. The bacterial community composition of the paddy soil was mainly determined by NO 3 –-N and total N, and that of the upland was mostly explained by SOC. The NPK, 2NPK, and NPKOM treatments from the paddy soil increased CCH 3 , decreased OCH, and reduced CH/CH 2 , while those from the upland soil decreased CH/CH 2 , increased OCH, and raised CH/CH 2 , respectively, indicating opposite shifts of OCH and alkyl C (i.e., CCH 3 and CH/CH 2) in each paired fertilizer treatment of the two soils. In the paddy soil, the CCH 3 from the NPK treatment showed no association with any bacterial taxa, the OCH from the 2NPK showed a negative association with NO 3 –-related species, and the CH/CH 2 from the NPKOM showed a negative association with Proteobacteria and Bacteroidetes. In the upland soil, the CH/CH 2 from the NPK negatively associated with Thermogemmatisporales and Acidobacteriaceae subgroup 1, the OCH from the 2NPK positively associated with Thermogemmatisporales, and the CH/CH 2 from the NPKOM positively associated with copiotrophic bacterial taxa. Our results provided direct evidence that cropping system mediated the shift direction of specific functional group under specific fertilization regimes, and implied that completely opposite shifts of OCH and alkyl C in each paired fertilizer treatment of the paddy soil and upland soil can likely be attributed to different fertilization-induced shifts in the microbial community composition resulting from soil N change in the paddy soil and soil C change in the upland soil. [ABSTRACT FROM AUTHOR]

This review summarises the evidence for a link between the porcine intestinal microbiota and growth and feed efficiency (FE), and suggests microbiota-targeted strategies to improve productivity. However, there are challenges in identifying reliable microbial predictors of host phenotype; environmental factors impact the microbe–host interplay, sequential differences along the intestine result in segment-specific FE- and growth-associated taxa/functionality, and it is often difficult to distinguish cause and effect. However, bacterial taxa involved in nutrient processing and energy harvest, and those with anti-inflammatory effects, are consistently linked with improved productivity. In particular, evidence is emerging for an association of Treponema and methanogens such as Methanobrevibacter in the small and large intestines and Lactobacillus in the large intestine with a leaner phenotype and/or improved FE. Bacterial carbohydrate and/or lipid metabolism pathways are also generally enriched in the large intestine of leaner pigs and/or those with better growth/FE. Possible microbial signalling routes linked to superior growth and FE include increased intestinal propionate production and reduced inflammatory response. In summary, the bacterial taxa and/or metabolic pathways identified here could be used as biomarkers for FE/growth in pigs, the taxa exploited as probiotics or the taxa/functionality manipulated via dietary/breeding strategies in order to improve productivity in pigs. [ABSTRACT FROM AUTHOR]

Background: the relationship between physical exercise and gut microbiota has opened new therapeutic frontiers for many inflammatory diseases. However, there is still a lot of uncertainty about how to administer exercise., Objectives: to review the literature to bridge this gap and examine the relationship between cardiorespiratory fitness (CRF) and microbiota., Design: systematic review., Setting and Participants: studies involving humans who undergoing exercise programmes of any lengths, intensities, and types were included. The research was carried out through PubMed, Scopus, and Web of Science., Main Outcome Measures: the primary outcome was change in gut microbiota composition (α and β-diversity), while the secondary outcome was the CRF level., Results: the 15 studies included (all with PEDro scale <=5) used aerobic training alone or combined with resistance exercises. In general, exercise has shown positive effects on the microbiota, influencing the faecal count of some bacterial phyla (in particular Bacteroidetes, Firmicutes, and Proteobacteria), with a weak tendency towards proportionality in relation to training duration and intensity. However, the evidence supporting the exercise effects on the gut microbiota and the relationship with CRF are of low quality., Conclusions: despite the weak evidence in favour of the effects of the practice of physical exercise on the intestinal microbiota, there are still many aspects that need to be explored. In particular, future studies shall have higher quality and methodological rigour, standardize the methods for outcome assessment, and determine type and thresholds of interventions intensity and duration.

The global demand for petroleum contributes to a significant increase in soil pollution with petroleum-based products that pose a severe risk not only to humans but also to plants and the soil microbiome. The increasing pollution of the natural environment urges the search for effective remediation methods. Considering the above, the objective of this study was to determine the usability of Dactylis glomerata for the degradation of hydrocarbons contained in diesel oil (DO), as well as the effects of both the plant tested and DO on the biochemical functionality and changes in the soil microbiome. The experiment was conducted in a greenhouse with non-polluted soil as well as soil polluted with DO and phytoremediated with Dactylis glomerata. Soil pollution with DO increased the numbers of microorganisms and soil enzymes and decreased the value of the ecophysiological diversity index of microorganisms. Besides, it contributed to changes in the bacterial structure at all taxonomic levels. DO was found to increase the abundance of Proteobacteria and to decrease that of Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes and Firmicutes. In the non-polluted soil, the core microbiome was represented by Kaistobacter and Rhodoplanes, whereas in the DO-polluted soil, it was represented by Parvibaculum and Rhodococcus. In soil sown with Dactylis glomerata, gasoline fraction (C6–C12) degradation was higher by 17%; mineral oil (C12–C35), by 9%; benzene, by 31%; anthracene, by 12%; chrysene, by 38%; benzo(a)anthracene, by 19%; benzo(a)pyrene, by 17%; benzo(b)fluoranthene, by 15%; and benzo(k)fluoranthene, by 18% than in non-sowed soil. To conclude, Dactylis glomerata proved useful in degrading DO hydrocarbons and, therefore, may be recommended for the phytoremediation of soils polluted with petroleum-based products. It has been shown that the microbiological, biochemical and chemical tests are fast and sensitive in the diagnosis of soil contamination with petroleum products, and a combination of all these tests gives a reliable assessment of the state of soils. [ABSTRACT FROM AUTHOR]

The use of next-generation sequencing and multiomic analysis reveals new insights on the identity of microbes in the lower airways blurring the lines between commensals and pathogens. Microbes are not found in isolation; rather they form complex metacommunities where microbe-host and microbe-microbe interactions play important roles on the host susceptibility to pathogens. In addition, the lower airway microbiota exert significant effects on host immune tone. Thus, this review highlights the roles that microbes in the respiratory tract play in the development of pneumonia., (Copyright © 2018 Elsevier Inc. All rights reserved.)

The spread of antimicrobial resistance in environment is promoted at least in part by the inappropriate use of antibiotics in animals and humans. The present study was designed to investigate the impact of different concentrations of ciprofloxacin in soil containing manure on the development of plasmid-mediated quinolone resistance (PMQR) - encoding genes and the abundance of soil bacterial communities. For these studies, high-throughput next-generation sequencing of 16S rRNA, real-time polymerase chain reaction and standard microbiologic culture methods were utilized. We demonstrated that the dissipate rate of relative abundances of some of PMQR-encoding genes, such as qnrS , oqxA and aac(6 ' )-Ib-cr , were significantly lower with ciprofloxacin 0.04 and 0.4 mg/kg exposure as compared to no-ciprofloxacin control and ciprofloxacin 4 mg/kg exposure during 2 month. Also, the number of ciprofloxacin resistant bacteria was significantly greater in ciprofloxacin 0.04 and 0.4 mg/kg exposure as compared with no-ciprofloxacin control and the ciprofloxacin 4 mg/kg exposure. In addition, lower ciprofloxacin concentration provided a selective advantage for the populations of Xanthomonadales and Bacillales in orders while Agrobacterium , Bacillus , Enterococcus , and Burkholderia in genera. These findings suggest that lower concentration of ciprofloxacin resulted in a slower rate of PMQR-encoding genes dissipation and selected development of ciprofloxacin-resistant bacteria in soil amended with manure.