OTU Level Research Articles

Unveiling the microbial diversity across the northern Ninety East Ridge in the Indian Ocean.

Prokaryotes play a crucial role in marine ecosystem health and drive biogeochemical processes. The northern Ninety East Ridge (NER) of the Indian Ocean, a pivotal yet understudied area for these cycles, has been the focus of our study. We employed high-throughput 16S rRNA gene sequencing to analyze 35 water samples from five stations along the ridge, categorized into three depth- and dissolved oxygen-level-based groups. Our approach uncovered a clear stratification of microbial communities, with key bioindicators such as Prochlorococcus MIT9313, Sva0996 marine group, and Candidatus Actinomarina in the upper layer; Ketobacter, Pseudophaeobacter, Nitrospina, and SAR324 clade in the middle layer; and Methylobacterium-Methylorubrum, Sphingomonas, Sphingobium, and Erythrobacter in the deep layer. Methylobacterium-Methylorubrum emerged as the most abundant bacterial genus, while Nitrosopumilaceae predominated among archaeal communities. The spatial and depth-wise distribution patterns revealed that Ketobacter was unique to the northern NER, whereas Methylobacterium-Methylorubrum, UBA10353, SAR324 clade, SAR406, Sva0996_marine_group, Candidatus Actinomarina were ubiquitous across various marine regions, exhibiting niche differentiation at the OTU level. Environmental factors, especially dissolved oxygen (DO), silicate, nitrate, and salinity, significantly influence community structure. These findings not only reveal the novelty and adaptability of the microbial ecosystem in the northern NER but also contribute to the broader understanding of marine microbial diversity and its response to environmental heterogeneity.

Host specificity and cophylogeny in the “animal-gut bacteria-phage” tripartite system

Cophylogeny has been identified between gut bacteria and their animal host and is highly relevant to host health, but little research has extended to gut bacteriophages. Here we use bee model to investigate host specificity and cophylogeny in the “animal-gut bacteria-phage” tripartite system. Through metagenomic sequencing upon different bee species, the gut phageome revealed a more variable composition than the gut bacteriome. Nevertheless, the bacteriome and the phageome showed a significant association of their dissimilarity matrices, indicating a reciprocal interaction between the two kinds of communities. Most of the gut phages were host generalist at the viral cluster level but host specialist at the viral OTU level. While the dominant gut bacteria Gilliamella and Snodgrassella exhibited matched phylogeny with bee hosts, most of their phages showed a diminished level of cophylogeny. The evolutionary rates of the bee, the gut bacteria and the gut phages showed a remarkably increasing trend, including synonymous and non-synonymous substitution and gene content variation. For all of the three codiversified tripartite members, however, their genes under positive selection and genes involving gain/loss during evolution simultaneously enriched the functions into metabolism of nutrients, therefore highlighting the tripartite coevolution that results in an enhanced ecological fitness for the whole holobiont.

Gut microbiome and antibiotic resistance genes in plateau model animal (Ochotona curzoniae) exhibit a relative stability under cold stress

Antibiotic resistance genes (ARGs) carried by gut pathogens may pose a threat to the host and ecological environment. However, few studies focus on the effects of cold stress on intestinal bacteria and ARGs in plateau animals. Here, we used 16S rRNA gene sequencing and gene chip technique to explore the difference of gut microbes and ARGs in plateau pika under 4 °C and 25 °C. The results showed that tetracycline and aminoglycoside resistance genes were the dominant ARGs in pika intestine. Seven kinds of high-risk ARGs (aadA-01, aadA-02, ermB, floR, mphA-01, mphA-02, tetM-02) existed in pika’s intestine, and cold had no significant effect on the composition and structure of pika’s intestinal ARGs. The dominant phyla in pika intestine were Bacteroidetes and Firmicutes. Cold influenced 0.47 % of pika intestinal bacteria in OTU level, while most other bacteria had no significant change. The diversity and community assembly of intestinal bacteria in pika remained relatively stable under cold conditions, while low temperature decreased gut microbial network complexity. In addition, low temperature led to the enrichment of glycine biosynthesis and metabolism-related pathways. Moreover, the correlation analysis showed that eight opportunistic pathogens (such as Clostridium, Staphylococcus, Streptococcus, etc.) detected in pika intestine might be potential hosts of ARGs.

Effectiveness of a novel compound microbial agent for water quality and the gut microbiota of Micropterus salmoides

The cultivation of largemouth bass (Micropterus salmoides), a species of significant economic value in aquaculture, has experienced notable growth recently. However, the deterioration of water quality seriously affects the metabolic responses of M. salmoides. While compound microbial agent (CMA) is widely utilized for ecological rehabilitation and water filtration, its application in M. salmoides has not been reported. Here, based on physio-biochemical tests and 16S rRNA sequencing, we investigated the effects of CMA (yeast, Bacillus subtilis, and lactic acid bacteria) on the water quality within the recirculating aquaculture system, along with physiological indices and gut microbiota of M. salmoides. Compared to the control and single microbial agent (yeast), CMA treatment improved the water quality by improving the dissolved oxygen and delaying the increase of pH, total nitrogen, total phosphorus, ammonia nitrogen, and nitrite. The 16s rRNA gene sequencing revealed that the water treated with CMA exhibited elevated levels of chao1, Shannon, Pd, and a larger population of dominant bacterial. Besides, higher values of ACE, chao1, Shannon, and OTU level, and lower Simpson index were found in CMA treated M. salmoides samples, suggesting that CMA treatment enhanced the species richness and diversity of gut microbiota of M. salmoides. Furthermore, CMA treatment hindered the generation and proliferation of harmful bacteria, such as the Mycoplasma mobile 163K species and the Erysipelotrichaceae family, which was associated with enhanced antioxidant enzymatic activity and decreased MDA level in both the serum and liver. These findings shed light on the essential roles of CMA in M. salmoides culturing and introduce an innovative approach to enhance the aquatic environment.

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts.

Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48-100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4+, and Cl- played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.

Diazotrophic community in the sediments of Poyang Lake in response to water level fluctuations.

Water level fluctuations (WLFs) are typical characteristic of floodplain lakes and dominant forces regulating the structure and function of lacustrine ecosystems. The sediment diazotrophs play important roles in contributing bioavailable nitrogen to the aquatic environment. However, the relationship between the diazotrophic community and WLFs in floodplain lakes is unknown. In this paper, we carried out a comprehensive investigation on the alpha diversity, abundance, composition and co-occurrence network of the sediment diazotrophs during different water level phases in Poyang Lake. There were no regular variation patterns in the alpha diversity and abundance of the sediment diazotrophs with the water level phase transitions. The relative abundance of some diazotrophic phyla (including Alphaproteobacteria, Deltaproteobacteri, Euryarchaeota, and Firmicutes) and genera (including Geobacter, Deferrisoma, Desulfuromonas, Rivicola, Paraburkholderia, Methylophilus, Methanothrix, Methanobacterium, and Clostridium) was found to change with the water level phase transitions. The results of ANOSIM, PerMANOVA, and DCA at the OTU level showed that the diazotrophic community structure in the low water level phase was significantly different from that in the two high water level phases, while there was no significant difference between the two high water level phases. These results indicated that the diazotrophic community was affected by the declining water level in terms of the composition, while the rising water level contributed to the recoveries of the diazotrophic community. The diazotrophs co-occurrence network was disrupted by the declining water level, but it was strengthened by the rising water level. Moreover, redundancy analysis showed that the variation of the diazotrophic community composition was mostly related to sediment total nitrogen (TN) and total phosphorous (TP). Interestingly, the levels of sediment TN and TP were also found to vary with the water level phase transitions. Therefore, it might be speculated that the WLFs may influence the sediment TN and TP, and in turn influence the diazotrophic community composition. These data can contribute to broadening our understanding of the ecological impacts of WLFs and the nitrogen fixation process in floodplain lakes.

Microbial community, pathogenic bacteria and high-risk anti-biotic resistance genes at two tropical coastal beaches adjacent to villages in Hainan, China.

The aim of the study was to explore the correlation between characteristics of microbial community, pathogenic bacteria and high-risk antibiotic-resistant genes, between coastal beaches and a multi-warm-blooded host, as well as to determine potential species biomarkers for faecal source contamination on tropical coastal beaches in China. The 'One-Health' approach was used in a microbiological study of beaches and warm-blooded hosts. The microbial.community was analyzed using 16S rRNA gene amplicons and shotgun metagenomics on Illumina NovaSeq. The Chao, Simpson, Shannon, and ACE indices of non-salt beach were greater than those of salt beaches at the genus and OTU levels (P < 0.001). Bacteroidota, Halanaerobiaeota, Cyanobacteria, and Firmicutes were abundant on salt beaches (P<0.01). Human-sourced microorganisms were more abundant on salt beaches, which accounted for 0.57%. Faecalibacterium prausnitzii and Eubacterium hallii were considered as reliable indicators for the contamination of human faeces. High-risk carbapenem-resistant Klebsiella pneumoniae and the genotypes KPC-14 and KPC-24 were observed on salt beaches. Tet(X3)/tet(X4) genes and four types of MCR genes co-occurred on beaches and humans; MCR9.1 accounted for the majority. Tet(X4) found among Cyanobacteria. Although rarely reported at Chinese beaches, pathogens, such as Vibrio vulnificus, Legionella pneumophila, and Helicobacter pylori, were observed. The low microbial community diversity, however, did not indicate a reduced risk. The transfer of high-risk ARGs to extreme coastal environments should be given sufficient attention.

Microbial community structure and its driving mechanisms in the Hangbu estuary of Chaohu Lake under different sedimentary areas

Estuaries are known for their high ecological diversity and biological productivity. Sediment microorganisms, as crucial components of estuarine ecosystems, play a pivotal role in reflecting the intricate and dynamic ecological niches. However, our research on microbial community characteristics in estuarine ecosystems under different sedimentary types remains limited. In this study, we collected a total of 27 samples from three sampling sites at Hangbu estuary in Chaohu Lake, and three sedimentary areas were classified based on the overlying water flow conditions and sediment particle properties to elucidate their microbial community structure, environmental drivers, assembly processes, and co-occurrence network characteristics. Our results showed significant differences in microbial community composition and diversity among three sedimentary areas. Redundancy analysis indicated that the differences in microbial community composition at the OTU level among the three sedimentary areas were mainly determined by nitrate-nitrogen, temperature, and water content. Phylogenetic bin-based null model analysis revealed that temperature was a key factor influencing deterministic processes among the three sedimentary areas, while stochastic processes predominantly governed the assembly of microbial communities. In addition, co-occurrence network analysis demonstrated that the network in the hydraulically driven sedimentary area of the lake, consisting mainly of medium and fine silt, had the highest complexity, stability, and cohesion, but was missing potential keystone taxa. The remaining two sedimentary areas had 5 and 8 potential keystone taxa, respectively. Overall, our study proposes the delineation of sedimentary types and comprehensively elucidates the microbial community characteristics under different sedimentary areas, providing a new perspective for studying sediment microbial community structure and helping future scholars systematically study ecological dynamics in estuaries.

Interkingdom multi-omics analysis reveals the effects of nitrogen application on growth and rhizosphere microbial community of Tartary buckwheat.

Tartary buckwheat (Fagopyrum tataricum Gaertn.) is an important pseudocereal crop with excellent edible, nutritional and medicinal values. However, the yield of Tartary buckwheat (TB) is very low due to old-fashioned cultivation techniques, particularly unreasonable application of nitrogen fertilizer. To improve the understanding on the theories of nitrogen use in TB, the effects of nitrogen application on growth, as well as chemical properties and microbial community of rhizosphere soil were investigated in this study. Nitrogen application could promote the plant height, stem diameter, nitrogen accumulation and yield of TB. The relative abundance and diversity of bacteria and fungi in the rhizosphere soil of TB were improved by nitrogen fertilizer. Nitrogen application increased the abundance of beneficial bacteria such as Lysobacter and Sphingomonas in rhizosphere soil, and decreased the abundance of pathogenic fungi such as Fusarium and Plectosphaerella. The results indicated that nitrogen application changed the distribution of microbial communities in TB rhizosphere soil. Furthermore, the specific enriched or depleted microorganisms in the rhizosphere soil of four TB varieties were analyzed at OTU level. 87 specific nitrogen-responsive genes with sequence variation were identified in four varieties by integrating genomic re-sequencing and transcriptome analysis, and these genes may involve in the recruitment of specific rhizosphere microorganisms in different TB varieties. This study provided new insights into the effects of nitrogen application on TB growth and rhizosphere microbial community, and improved the understanding on the mechanisms of TB root-microbe interactions.

Does PM1 exposure during pregnancy impact the gut microbiota of mothers and neonates?

BackgroundAmbient air pollutant exposure can change the composition of gut microbiota at 6-months of age, but there is no epidemiological evidence on the impacts of exposure to particulate matter with an aerodynamic diameter ≤1 μm (PM1) during pregnancy on gut microbiota in mothers and neonates. We aimed to determine if gestational PM1 exposure is associated with the gut microbiota of mothers and neonates. MethodsLeveraging a mother-infant cohort from the central region of China, we estimated the exposure concentrations of PM1 during pregnancy based on residential address records. The gut microbiota of mothers and neonates was analyzed using 16 S rRNA V3–V4 gene sequences. Functional pathway analyses of 16 S rRNA V3–V4 bacterial communities were conducted using Tax4fun. The impact of PM1 exposure on α-diversity, composition, and function of gut microbiota in mothers and neonates was evaluated using multiple linear regression, controlling for nitrogen dioxide (NO2) and ozone (O3). Permutation multivariate analysis of variance (PERMANOVA) was used to analyze the interpretation degree of PM1 on the sample differences at the OTU level using the Bray-Curtis distance algorithm. ResultsGestational PM1 exposure was positively associated with the α-diversity of gut microbiota in neonates and explained 14.8% (adj. P = 0.026) of the differences in community composition among neonatal samples. In contrast, gestational PM1 exposure had no impact on the α- and β-diversity of gut microbiota in mothers. Gestational PM1 exposure was positively associated with phylum Actinobacteria of gut microbiota in mothers, and genera Clostridium_sensu_stricto_1, Streptococcus, Faecalibacterium of gut microbiota in neonates. At Kyoto Encyclopedia of Genes and Genomes pathway level 3, the functional analysis results showed that gestational PM1 exposure significantly down-regulated Nitrogen metabolism in mothers, as well as Two-component system and Pyruvate metabolism in neonates. While Purine metabolism, Aminoacyl-tRNA biosynthesis, Pyrimidine metabolism, and Ribosome in neonates were significantly up-regulated. ConclusionsOur study provides the first evidence that exposure to PM1 has a significant impact on the gut microbiota of mothers and neonates, especially on the diversity, composition, and function of neonatal meconium microbiota, which may have important significance for maternal health management in the future.

Effect of eucalyptus saponin and sophorolipid amendment on soil and sediment microbial communities and seed germination: potential application for PAH bioremediation

PurposeThe potential toxic effects due to the application of sophorolipid and the novel saponin biosurfactant extracted from the leaves of Eucalyptus camaldulensis for the purpose of bioremediating PAH-contaminated soils and sediments were studied.MethodsThe phytotoxic effects of sophorolipid and eucalyptus saponin were determined based on the seed germination assays carried out using the seeds of Lactuca sativa L and compared with commonly used rhamnolipid and Tween 20 surfactants. Further, biosurfactant-induced changes in soil/sediment bacterial structure and diversity were investigated by conducting Miseq amplicon sequencing of the bacterial genes.ResultsGermination indices (GI) demonstrated the non-phytotoxic effects (GI > 80%) of saponin and sophorolipid biosurfactants (100–500 mg/L), while rhamnolipid demonstrated greater phytotoxicity than Tween 20 at high concentrations (500 mg/L). Saponin-amended soil resulted in greater bacterial diversity and richness compared to controls, while sophorolipid produced the opposite effect. These significant variations were not observed in sediment samples. Incubation of biosurfactants for 20 and 40 days did not result in significant changes in bacterial diversity and structure in any of the samples. Increased abundance of some of the PAH-degrading bacteria was noted at OTU level, in the presence of saponin and sophorolipid. Saponin had less impact on native soil/sediment bacteria relative to sophorolipid based on the prevalence of the significantly shifted OTUs.ConclusionAs saponin and sophorolipid were shown to have no adverse impacts on the microbiome, and non-phytotoxic effects, their sustainable applications to remediate PAH-contaminated soils and sediments can be recommended.

Impact of environmental factors on diversity of fungi in sediments from the Shenzhen River Estuary

In this study, to explore the relationship between environmental factors and fungal diversity in the Shenzhen River ecosystem, multiple methods including chemical analysis, culture isolation, qPCR analysis of fungal ITS region and ITS-based Illumina next-generation-sequencing were integrated. A total of 115 isolates were finally isolated and could be classified into 23 genera. Top three abundant genera isolated were Meyerozyma (18 strains), Aspergillus (17 strains) and Penicillium (14 strains). Based on the Illumina sequencing approach, 829 OTUs were affiliated to seven phyla, 17 known classes, and 162 genera, indicating the Shenzhen estuary sediments are rich in fungal diversity. The major fungal genera were Meyerozyma, Trichoderma and Talaromyces. Environmental factors showed a gradient change in Shenzhen estuary, and fungal abundance was only significantly correlated with NH4+. Shannon index was significantly correlated with pH and IC (P < 0.05). Principal coordinate analysis based on OTU level grouped into three clusters among sampling sites along with the IC and pH gradient. Functional guilds analysis suggests most of the fungi in this studying area were almost all saprotrophs, suggesting a large number of saprophytic fungi may play a significant role in the organic matter decomposition and nutrient cycling process. In summary, this study will deepen our understanding of fungi community in Shenzhen River ecosystem and their distribution and potential function shaped by environmental factors.

P380 Changes in faecal microbiome and metabolome are more pronounced in Crohn’s disease patients who adhered to the CD-TREAT diet and responded by calprotectin.

Abstract Background Treatment with the CD-TREAT solid food diet improves disease activity indices, faecal calprotectin (FCAL) levels and quality of life in adults and children with active Crohn’s disease (CD); particularly in patients who adhere to the diet. Here we describe changes in faecal microbiome parameters during therapy with CD-TREAT and explore these changes against adherence. Methods Children and adult patients with active CD completed an 8-week treatment with CD-TREAT. The levels of FCAL, pH, total sulphide (colorimetry), short chain fatty acids (SCFA), branched chain fatty acids (BCFA) (gas chromatography), total bacterial load (qPCR for total 16S rRNA gene copy number/g) were measured in baseline faecal samples and at four and eight weeks of CD-TREAT. Liquid chromatography mass spectrometry (LC-MS) faecal metabolomics and 16s rRNA sequencing of the faecal microbiome were performed at the same timepoints. Since CD-TREAT is gluten-free, detection of the gluten immunogenic peptide (GIP) in faeces was used as an objective biomarker of treatment adherence. Data are presented as median (IQR). Results Forty patients [17 children, age: 14.0 (11.3-15.1) years; 23 adults, age: 33.9 (27.8-45.9) years] participated. Eighteen (45%) patients had detectable GIP in at least one of the two follow-up timepoints, suggesting incomplete adherence; the remaining 22 (55%) patients had undetectable GIP throughout the treatment course. Baseline FCAL levels decreased significantly in the group of patients with undetectable GIP [mg/kg, baseline: 1,190 (3,611-129); 8 weeks: 534 (92-1,230), p&amp;lt;0.05] but not in patients with detectable GIP [mg/kg, baseline: 599 (328-1,857); 8 weeks: 702 (278-1,496)]. During CD-TREAT, the concentration of faecal acetate, propionate, butyrate, total sulphide, total microbial load and faecal pH significantly changed in those with undetectable GIP but were less pronounced where GIP was detectable (Figure 1). Shannon diversity and richness significantly increased at both genus and OTU level, the abundance of several taxa changed, and LC-MS faecal metabolome shifted during CD-TREAT, but only in those with undetectable GIP (Figures 2 &amp; 3). Conclusion We have identified that full adherence with CD-TREAT only occurs in ~55% of recipients, however a significant reduction in calprotectin is seen in those who adhere, and this is associated with microbial and metabolic changes which parallel those seen in successful exclusive enteral nutrition.

Differential responses of soil bacterial communities to elevated CO2 between strongly CO2-responsive and weakly CO2-responsive rice cultivars

Effects of elevated CO2 (eCO2) on paddy soil microbial communities remain unclear, particularly when different rice cultivars exposed to eCO2. We thus compared responses of soil bacterial communities to ambient CO2 (aCO2) and eCO2 (aCO2 + 200 μmol CO2 mol−1) between two weakly CO2-responsive (Wuyunjing27, W27; Huaidao5, H5) and two strongly CO2-responsive rice cultivars (Yongyou1540, Y1540; LongIIyou1988, L1988) throughout six growth stages (early tillering, late tillering, jointing, heading, grain filling and ripening) in a paddy field in Jiangdu, China in 2018. No significant changes in soil bacterial diversities were observed between eCO2 and aCO2 or between cultivars for any single growth stage at the OTU level, but α diversity significantly changed at the phylum level except for the ripening stage. For a single cultivar, particularly two strongly CO2-responsive cultivars, over their whole growth stage, eCO2 enhanced differences in bacterial β diversity at both OTU and phylum levels under H5, Y1540 and L1988. Soil bacterial community complexity at the phylum level under eCO2 was weakened under W27, H5 and Y1540, but enhanced under L1988. eCO2-induced changes in soil DOC under these four cultivars had significantly positive impact on bacterial abundances. However, structural equation modeling illustrated that changes in soil DOC induced by eCO2 significantly decreased soil bacterial community richness. eCO2 did not significantly affect relationships between soil bacterial community diversities and rice yields, but displayed significantly negative correlations between strongly CO2-responsive rice cultivars' yields and relative abundances of Proteobacteria at the ripening stage. Dynamics that how soil microbial communities can differentiate their eCO2 responses between strongly- and weakly-responsive rice cultivars will provide a new insight into promoting rice productivity and soil health.

Assessment of the impact of intravenous antibiotics treatment on gut microbiota in patients: Clinical data from pre-and post-cardiac surgery.

Surgical site infection is a common complication after surgery. Periprocedural antibiotics are necessary to prescribe for preventing or treating infections. The present study aimed to explore the effect of intravenous antibiotics on gut microbiota and menaquinone biosynthesis in patients, especially in elderly patients undergoing cardiac surgery. A total of 388 fecal samples were collected from 154 cardiac surgery patients. The V3-V4 hypervariable region of the bacterial 16S rRNA gene was amplified and sequenced on a MiSeq PE300. The gut microbiota diversity of samples was analyzed in terms of α- and β-diversity at the OTU level. The different groups were classified according to antibiotics in combinations and single antibiotics. PICRUSt2 was used for preliminary prediction of the gut microbiota function for menaquinone biosynthesis. The intravenously administered antibiotics which are excreted via bile represents the main antibiotics that could disturb the gut microbiota's composition in cardiac surgery patients, especially for elderly patients. The effect of antibiotics on gut microbiota is produced after antibiotics treatments over one week. The recovery of gut microbiota to the state of pre-antibiotics may require over two weeks of antibiotics withdrawal. Sex factor doesn't represent as an influencer in gut microbiota composition. Long-term use of cefoperazone-sulbactam may affect coagulation function. The composition of the gut microbiota had a significant change post-intravenous antibiotics treatment in cardiac surgery patients. The richness and diversity of gut microbiota are increased in elderly patients.

Integrating data from spontaneous and induced trans-10 shift of ruminal biohydrogenation reveals discriminant bacterial community changes at the OTU level.

Microbial digestion is of key importance for ruminants, and disturbances can affect efficiency and quality of products for human consumers. Ruminal biohydrogenation of dietary unsaturated fatty acids leads to a wide variety of specific fatty acids. Some dietary conditions can affect the pathways of this transformation, leading to trans-10 fatty acids rather than the more usual trans-11 fatty acids, this change resulting in milk fat depression in dairy cows. We combined data from an induced and spontaneous trans-10 shift of ruminal biohydrogenation, providing new insight on bacterial changes at different taxonomic levels. A trans-10 shift was induced using dietary addition of concentrate and/or unsaturated fat, and the spontaneous milk fat depression was observed in a commercial dairy herd. Most changes of microbial community related to bacteria that are not known to be involved in the biohydrogenation process, suggesting that the trans-10 shift may represent the biochemical marker of a wide change of bacterial community. At OTU level, sparse discriminant analysis revealed strong associations between this change of biohydrogenation pathway and some taxa, especially three taxa belonging to [Eubacterium] coprostanoligenes group, Muribaculaceae and Lachnospiraceae NK3A20 group, that could both be microbial markers of this disturbance and candidates for studies relative to their ability to produce trans-10 fatty acids.

Study on community structure and nitrogen metabolism mechanism in A2O process under different hydraulic retention time conditions at high altitude region

&lt;p&gt;The unique high-altitude environmental factors in the Linzhi region of Tibet have not been fully investigated in terms of their impact on the microbial mechanisms of water ecology, for which we explored the response of activated sludge microorganisms to different hydraulic retention times (HRT) based on 16S rRNA gene sequencing and PICRUST2 functional prediction. The results showed that different HRT had significant effects on Phylum, Class, Genus, Species and OTU levels, as well as on diversity, richness and evenness (P &amp;lt; 0.05). The relative abundance of Bacteroidetes, Chloroflexi, Firmicutes and AAP99 in the dominant bacterial phylum and genus was significantly influenced by different HRT. In addition, we identified the denitrification reaction as the major pathway in nitrogen metabolism in this study, as well as most of the significantly enriched genera were denitrifying genera as determined by LEfSe analysis. The overall low relative abundance of the nitrifying bacteria genera AOB and NOB may also be an important reason for the poor nitrogen removal. The effect of HRT on the expression of genes of the five functional modules of nitrogen metabolism was inconsistent. In conclusion, the above studies further complement the studies on the effects of plateau-specific environments on the microbial mechanisms of water ecology under different HRT conditions.&lt;/p&gt;&#x0D;

Association of Gut Microbiota Composition in Pregnant Women Colonized with Group B Streptococcus with Maternal Blood Routine and Neonatal Blood-Gas Analysis.

Group B Streptococcus (GBS) colonizes the vaginal and rectal mucosa in a substantial proportion of healthy women, and GBS is a risk factor for GBS-associated adverse birth outcomes, such as bacterial infection, in neonates. Whether changes in the gut microbiota of GBS-infected pregnant women are associated with maternal complete blood cell count (CBC) and neonatal blood-gas analysis is unknown. To explore the relationship between the intestinal microecological composition of pregnant women and maternal blood routine and neonatal blood-gas analysis, we collected intestinal microecology samples of 26 pregnant women in clinic. They were divided into a positive group(GBS positive,GBS +) and a negative group (GBS negative, GBS-), with 12 in the positive group and 14 in the negative group. 16S rRNA gene sequencing was used to examine the gut microbiota profile from a fecal sample of pregnant women. CBC was carried out in enrolled pregnant women and umbilical arterial blood-gas analysis (UABGA)was conducted for analysis of intestinal microbiota composition, maternal blood routine and neonatal blood gas. Our results showed significant differences in the total number of organisms and microbial diversity of intestinal microbiota between healthy pregnant women and GBS-positive pregnant women. Particularly, abundances of Lentisphaerae, Chlorobi, Parcubacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria, Fusobacteria and Fibrobacteres were only detected in participants with GBS colonization. Blood-gas analysis revealed that neonates born to mothers with GBS colonization had significantly higher fractions of carboxyhemoglobin (FCOHb) and lower methemoglobin (FMetHb), and abundances of OTU80, OTU122, OTU518 and OTU375 were associated with blood-gas indicators, such as carboxyhemoglobin, methemoglobin, PCO2, PH and ABE. Interestingly, there were significant correlations between OTU levels and inflammatory indexes in pregnant women with GBS infection. Together, this study revealed for the first time that altered gut microbiota compositions are related to the inflammatory state in GBS-positive pregnant women and neonatal blood-gas indicators. GBS colonization may lead to significant changes in the gut microbiome, which might be involved in the pathogenesis of the maternal inflammatory state and neonatal blood gas abnormalities.

Regional microbiome differentiation of the invasive Sargassum muticum (Fucales, Phaeophyceae) follows the generalist host hypothesis across the North East Atlantic

ABSTRACT Over 90% of introduced marine species are seaweeds. Seaweeds rely on their microbiome for host settlement, nutrition, development and health. As such, it is likely that microbiomes are involved in seaweed invasions. Sargassum muticum, indigenous to Southeast Asia, inhabits the North-east Atlantic from Norway to Morocco. This is the only known successful case of a non-clonal marine invader with almost no genetic variation over its large NE Atlantic introduced range. This makes it a very interesting model to study an invasive seaweeds microbiome, as it practically uncouples host genetic variation from microbiome variation. Associated bacteria potentially contribute to the plasticity and acclimation of S. muticum leading to its success over the last 50 years. Dispersing host organisms can either bring their acquired microbes along or obtain new ones locally, following the mutualist and generalist host hypothesis, respectively. We used partial 16S rRNA gene amplicon sequencing to characterize the total and core microbiome across S. muticum structures/tissues from five NE Atlantic regions, from Norway to Morocco, covering over 30° of latitude. In contrast to host genotypes, highly diverse, regional, total and core microbiomes, with differentiation levels depending on tissue, bacterial community structure were detected. Atlantic S. muticum follows the generalist host hypothesis, possibly recruiting a new microbiome in each new region. This host promiscuity may promote the invasiveness of S. muticum. Diversity was lower in the young/annual tissues compared with the older tissues for the total bacterial community, suggesting that these are mostly transitory bacteria accumulating over time in the older parts. The total core microbiome included 10 OTUs, representing dominant community members commonly found in other seaweeds’ cores. The core Granulosicoccus OTU followed a clear regional pattern where northern and southern regions clustered differentially, suggesting a regional signature even at an OTU level. HIGHLIGHTS North-east (NE) Atlantic Sargassum muticum microbiome differentiation does not match host genetic background. NE Atlantic S. muticum shows a geographic region and tissue-specific total and core bacterial community matching bestthe generalist host hypothesis. Core OTU – the bacterium Granulosicoccus – shows a strong regional specialization.

Sodium Butyrate Attenuated Diabetes-Induced Intestinal Inflammation by Modulating Gut Microbiota.

Background Diabetes mellitus (DM) continues to be one of the world's most costly and complex metabolic disorders. Accumulating evidence has shown that intestinal dysbiosis and associated inflammation can facilitate the onset and progression of DM. In this work, our goal was to investigate how sodium butyrate (SB) controls the gut microbiota to reduce the intestinal inflammation brought on by diabetes. Methods Male KK-Ay mice were randomized into two groups: the DM model group (intragastric administration of 0.9% normal saline) and the SB treatment group (intragastric administration of 1,000 mg/kg/d SB). The C57BL/6J mice were used as the control group (intragastric administration of 0.9% normal saline). These mice were administered via gavage for 8 weeks. Results The results revealed that SB-treated mice significantly reduced fasting blood glucose (FBG), body weight, 24 h food and water intake, and improved islet histopathology in DM model mice. SB reduced TNF-α, IL-1β, and iNOS, whereas it enhanced the expression of the anti-inflammatory Arg-1 marker on intestinal macrophages and the secretion of anti-inflammatory IL-10. Specifically, SB was linked to a marked drop in the expression of the Th17 marker RORγt and a substantial increase in the expression of the Treg marker Foxp3. SB treatment was associated with significant reductions in the levels of Th17-derived cytokines such as IL-17 and IL-6, whereas anti-inflammatory Treg-derived cytokines such as TGF-β were increased. Additionally, the analysis results from 16S rDNA sequencing suggested that SB significantly reversed the variations in intestinal flora distribution and decreased the relative abundance of Weissella confusa and Anaerotruncus colihominis DSM 17241 at the species level as well as Leuconostocaceae, Streptococcaceae, and Christensenellaceae at the family, genus, and species levels. These distinct florae may serve as a diagnostic biomarker for DM-induced intestinal inflammation. In addition, the heat map of phylum and OTU level revealed a close relationship between DM-induced intestinal inflammation and intestinal microbiota. Conclusions The present study suggested that SB may reduce DM-induced intestinal inflammation by regulating the gut microbiota.