Performance of Metagenomic Next-Generation Sequencing of Cell-Free DNA From Vitreous and Aqueous Humor for Diagnoses of Intraocular Infections.

BACKGROUND: Delayed diagnosis and improper therapy for intraocular infections usually result in poor prognosis. Due to limitations of conventional culture and polymerase chain reaction methods, most causative pathogens cannot be identified from vitreous humor (VH) or aqueous humor (AH) samples with limited volume. METHODS: Patients with suspected intraocular infections were enrolled from January 2019 to August 2021. Metagenomic next-generation sequencing (mNGS) was used to detected causative pathogens. RESULTS: This multicenter prospective study enrolled 488 patients, from whom VH (152) and AH (336) samples were respectively collected and analyzed using mNGS of cell-free DNA (cfDNA). Taking final comprehensive clinical diagnosis as the gold standard, there were 39 patients with indefinite final diagnoses, whereas 288 and 161 patients were diagnosed as definite infectious and noninfectious diseases, respectively. Based on clinical adjudication, the sensitivity (92.2%) and total coincidence rate (81.3%) of mNGS using VH samples were slightly higher than those of mNGS using AH samples (85.4% and 75.4%, respectively). CONCLUSIONS: Using mNGS of cfDNA, an era with clinical experience for more rapid, independent, and impartial diagnosis of bacterial and other intraocular infections can be expected.

Metatranscriptome of human lung microbial communities in a cohort of mechanically ventilated COVID-19 Omicron patients.

The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) infected a substantial proportion of Chinese population, and understanding the factors underlying the severity of the disease and fatality is valuable for future prevention and clinical treatment. We recruited 64 patients with invasive ventilation for COVID-19 and performed metatranscriptomic sequencing to profile host transcriptomic profiles, plus viral, bacterial, and fungal content, as well as virulence factors and examined their relationships to 28-day mortality were examined. In addition, the bronchoalveolar lavage fluid (BALF) samples from invasive ventilated hospital/community-acquired pneumonia patients (HAP/CAP) sampled in 2019 were included for comparison. Genomic analysis revealed that all Omicron strains belong to BA.5 and BF.7 sub-lineages, with no difference in 28-day mortality between them. Compared to HAP/CAP cohort, invasive ventilated COVID-19 patients have distinct host transcriptomic and microbial signatures in the lower respiratory tract; and in the COVID-19 non-survivors, we found significantly lower gene expressions in pathways related viral processes and positive regulation of protein localization to plasma membrane, higher abundance of opportunistic pathogens including bacterial Alloprevotella, Caulobacter, Escherichia-Shigella, Ralstonia and fungal Aspergillus sydowii and Penicillium rubens. Correlational analysis further revealed significant associations between host immune responses and microbial compositions, besides synergy within viral, bacterial, and fungal pathogens. Our study presents the relationships of lower respiratory tract microbiome and transcriptome in invasive ventilated COVID-19 patients, providing the basis for future clinical treatment and reduction of fatality.

High specificity of metagenomic next-generation sequencing using protected bronchial brushing sample in diagnosing pneumonia in children.

Background: Lower respiratory tract infections are the leading cause of morbidity and mortality in children worldwide. Timely and accurate pathogen detection is crucial for proper clinical diagnosis and therapeutic strategies. The low detection efficiency of conventional methods and low specificity using respiratory samples seriously hindered the accurate detection of pathogens. Methods: In this study, we retrospectively enrolled 1,032 children to evaluate the performance of metagenomics next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) sample and protected bronchial brushing (BB) sample in diagnosing pneumonia in children. In addition, conventional tests (CTs) were also performed. Results: The specificity of BB mNGS [67.3% (95% CI 58.6%-75.9%)] was significantly higher than that of BALF mNGS [38.5% (95% CI 12.0%-64.9%)]. The total coincidence rate of BB mNGS [77.6% (95% CI 74.8%-80.5%)] was slightly higher than that of BALF mNGS [76.5% (95% CI 68.8%-84.1%)] and CTs [38.5% (95% CI 35.2%-41.9%)]. During the epidemics of Mycoplasma pneumoniae, the detection rate of M. pneumoniae in the >6-year group (81.8%) was higher than that in the 3-6-year (78.9%) and <3-year groups (21.5%). The highest detection rates of bacteria, fungi, and viruses were found in the <3-year, >6-year, and 3-6-year groups, respectively. mNGS detection should be performed at the duration of 5-7 days after the start of continuous anti-microbial therapy or at the duration of 6-9 days from onset to mNGS test. Conclusions: This is the first report to evaluate the performance of BB mNGS in diagnosing pulmonary infections in children on a large scale. Based on our findings, extensive application of BB mNGS could be expected.

Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections.

Although the fast-growing metagenomic next-generation sequencing (mNGS) has been used in diagnosing infectious diseases, low detection rate of mNGS in detecting pathogens with low loads limits its extensive application. In this study, 130 patients with suspected pulmonary infections were enrolled, from whom bronchoalveolar lavage fluid (BALF) samples were collected. The conventional tests and mNGS of cell-free DNA (cfDNA) and whole-cell DNA (wcDNA) using BALF were simultaneously performed. mNGS of cfDNA showed higher detection rate (91.5%) and total coincidence rate (73.8%) than mNGS of wcDNA (83.1% and 63.9%) and conventional methods (26.9% and 30.8%). A total of 70 microbes were detected by mNGS of cfDNA, and most of them (60) were also identified by mNGS of wcDNA. The 31.8% (21/66) of fungi, 38.6% (27/70) of viruses, and 26.7% (8/30) of intracellular microbes can be only detected by mNGS of cfDNA, much higher than those [19.7% (13/66), 14.3% (10/70), and 6.7% (2/30)] only detected by mNGS of wcDNA. After in-depth analysis on these microbes with low loads set by reads per million (RPM), we found that more RPM and fungi/viruses/intracellular microbes were detected by mNGS of cfDNA than by mNGS of wcDNA. Besides, the abilities of mNGS using both cfDNA and wcDNA to detect microbes with high loads were similar. We highlighted the advantage of mNGS using cfDNA in detecting fungi, viruses, and intracellular microbes with low loads, and suggested that mNGS of cfDNA could be considered as the first choice for diagnosing pulmonary infections.

Metagenomic next-generation sequencing of cell-free and whole-cell DNA in diagnosing central nervous system infections.

Background: Central nervous system (CNS) infections pose a fatal risk to patients. However, the limited sample volumes of cerebrospinal fluid (CSF) and low detection efficiency seriously hinder the accurate detection of pathogens using conventional methods. Methods: We evaluated the performance of metagenomics next-generation sequencing (mNGS) in diagnosing CNS infections. CSF samples from 390 patients clinically diagnosed with CNS infections were used for the mNGS of cell-free DNA (cfDNA) (n =394) and whole-cell DNA (wcDNA) (n =150). Results: The sensitivity of mNGS using cfDNA was 60.2% (237/394, 95% confidence interval [CI] 55.1%-65.0%), higher than that of mNGS using wcDNA (32.0%, 95% [CI] 24.8%-40.2%, 48/150) and conventional methods (20.9%, 95% [CI] 16.2%-26.5%, 54/258) (P < 0.01, respectively). The accuracy of mNGS using cfDNA in positive samples was 82.6%. Most of viral (72.6%) and mycobacterial (68.8%) pathogens were only detected by the mNGS of cfDNA. Meningitis and encephalitis with Streptococcus pneumoniae infection might be more likely to result in critically ill diseases, while Human alphaherpesvirus 3 was prone to cause non-critically ill diseases. Conclusions: This is the first report on evaluating and emphasizing the importance of mNGS using CSF cfDNA in diagnosing CNS infections, and its extensive application in diagnosing CNS infections could be expected, especially for viral and mycobacterial CNS infections.

Environmental heterogeneity determines the response patterns of microbially mediated N-reduction processes to sulfamethoxazole in river sediments.

The widespread occurrence of antibiotics in aquatic ecosystems leads to potential ecological risks to organisms, in turn affecting microbially mediated processes. Here, we investigated the response of dominant N-reduction processes to the frequently detected antibiotic sulfamethoxazole (SMX) along the Chaobai River with regional environmental heterogeneity, including denitrification, anaerobic ammonium oxidation (anammox), dissimilatory nitrate reduction to ammonium (DNRA), and nitrous oxide (N2O) release. We found two divergent SMX response patterns for denitrification in contrasting scenarios of geochemical properties. In the context of low nitrate and carbon, SMX weakened denitrification with a slightly stimulation first. Whereas SMX directly inhibited denitrification when nitrate and carbon were sufficient. High SMX concentration suppressed anammox (26-72%) and DNRA activities (48-84%) via restraining the activities of anammox and DNRA bacteria. Notably, SMX increased the contribution of denitrification to N-reduction at the expense of DNRA to N-reduction, leading to a shift in nitrogen conversion towards denitrification. Additionally, SMX stimulated N2O emission (up to 91%) due to superior restraint on process of N2O reduction to N2 and an incline for N-reduction towards denitrification, thereby exacerbating greenhouse effect. Our results advance the understanding of how nitrogen cycling is affected by SMX in aquatic ecosystems with environmental heterogeneity.

Haloalkaliphilic denitrifiers-dependent sulfate-reducing bacteria thrive in nitrate-enriched environments.

As bridge in global cycles of carbon, nitrogen, and sulfur, sulfate-reducing bacteria (SRB) play more and more important role under various environments, especially the saline-alkali environments with significant increase in area caused by human activities. Sulfate reduction can be inhibited by environmental nitrate. However, how SRB cope with environmental nitrate stress in these extreme environments still remain unclear. Here, after a long-term enrichment of sediment from saline-alkali Qinghai Lake of China using anaerobic filter reactors, nitrate was added to evaluate the response of SRB. With the increase in nitrate concentrations, the inhibition on sulfate reduction was gradually observed. Interestingly, extension of hydraulic retention time can relieve the inhibition caused by high nitrate concentration. Mass balance analysis showed that nitrate reduction is prior to sulfate reduction. Further metatranscriptomic analysis shows that, genes of nitrite reductase (periplasmic cytochrome c nitrite reductase gene) and energy metabolisms (lactate dehydrogenase, formate dehydrogenase, pyruvate:ferredoxin-oxidoreductase, and fumarate reductase genes) in SRB was down-regulated, challenging the long-held opinion that up-regulation of these genes can relieve the nitrate inhibition. Most importantly, the nitrate addition activated the denitrification pathway in denitrifying bacteria (DB) via significantly up-regulating the expression of the corresponding genes (nitrite reductase, nitric oxide reductase c subunit, nitric oxide reductase activation protein and nitrous oxide reductase genes), quickly reducing the environmental nitrate and relieving the nitrate inhibition on SRB. Our findings unravel that in response to environmental nitrate stress, haloalkaliphilic SRB show dependency on DB, and expand our knowledge of microbial relationship during sulfur and nitrogen cycles.

The modified bilobed flap for reconstructing sacral decubitus ulcers.

BACKGROUND: Sacral pressure ulcers are associated with high morbidity and, in some cases, result in mortality from severe sepsis. Local flaps are frequently used for reconstruction of stage III and IV pressure ulcers. An ideal flap should be simple to design, have a reliable vascular supply and minimal donor site morbidity. Our study evaluates the use of a bilobed flap based on the superficial branch of the superior gluteal artery or the posterior branch of the fourth lumbar artery to reconstruct the sacral pressure ulcer. CASE PRESENTATION: We performed a retrospective analysis of paraplegic patients with sacral pressure ulcers treated with our bilobed flaps from January 2015 to December 2019. A description of our management, operative protocol, outcome and complications is outlined. Seven paraplegic patients (6 male, 1 female; average age 53.1 years) with sacral pressure ulcers were treated with our bilobed flap based on the superficial branch of the superior gluteal artery or the posterior branch of the fourth lumbar artery. The average size of the pressure ulcers was 7 × 5 cm (range 6.2 × 4.5 cm to 11 × 10 cm). All 7 flaps survived. The patients were followed up for 12 months without significant complications, such as flap necrosis or recurrence. CONCLUSIONS: The superficial branch of the superior gluteal artery or the posterior branch of the fourth lumbar artery reliably supplies the bilobed flap. The superior cluneal nerve can be included in the design. The technique is simple and reliable. It should be included in the reconstructive algorithm for the management of sacral pressure ulcers.

Comammox bacterial abundance, activity, and contribution in agricultural rhizosphere soils.

The newly identified complete ammonia oxidation (comammox), which is capable of oxidizing ammonia directly to nitrate, has complemented our knowledge of nitrification in the global nitrogen (N) cycle. However, understanding the contribution and ecological roles of comammox in complex soil environments is still in its infancy. Here, the community structure and function of comammox and the interactions with other ammonia oxidation processes in rhizosphere and non-rhizosphere soils of four different crop fields (maize, cotton, soybean, and millet) were investigated in summer and winter. The only identified comammox species Candidatus Nitrospira nitrificans was widely distributed in all sampled soils. Comammox bacterial abundance was lower than that of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). The measured comammox potential rate ranged from 0.01 ± 0.002 to 0.40 ± 0.02 mg N kg-1 d-1, contributing <19.2 and 22.1% to ammonia oxidation in summer and winter, the remainder being due to AOA and AOB. The potential rate and community composition of comammox bacteria were significantly different on a temporal scale, while crop species and soil types (rhizosphere and non-rhizosphere) showed no obvious influences. In terms of oxidation rates, AOA (1.2 ± 0.7 mg N kg-1 d-1) dominated the ammonia oxidation in agricultural soils over AOB (0.31 ± 0.1 mg N kg-1 d-1) and comammox (0.2 ± 0.1 mg N kg-1 d-1). Both anammox bacterial abundance and activity were below the detection limits, indicating a negligible contribution of anammox in agricultural rhizosphere soils. The identification of comammox bacterial abundance and activity in situ enriches our knowledge of nitrification in agricultural systems.

Nitrate reduction in the reed rhizosphere of a riparian zone: From functional genes to activity and contribution.

The increased nitrogen (N) fertilizer usage caused substantial nitrate (NO3-) leaching into groundwater and eutrophication in downstream aquatic systems. Riparian zones positioned as the link interfaces of terrestrial and aquatic environments are effective in NO3- removal. However, the microbial mechanisms regulating NO3- reduction in riparian zones are still unclear. In this study, four microbial NO3- reduction processes were explored in fine-scale riparian soil horizons by isotopic tracing technique, qPCR of functional gene, high-throughput amplicon sequencing, and phylogenetic molecular ecological network analysis. Interestingly, anaerobic ammonium oxidation (anammox) contributed to NO3- removal of up to 48.2% only in waterward sediments but not in landward soil. Denitrification was still the most significant contributor to NO3- reduction (32.0-91.8%) and N-losses (51.7-100%). Additionally, dissimilatory nitrate reduction to ammonium (DNRA) played a key role in NO3- reduction (4.4-67.5%) and was even comparable to denitrification. Community structure analysis of denitrifying, anammox, and DNRA bacterial communities targeting the related functional gene showed that spatial heterogeneity played a greater role than both temporal and soil type (rhizosphere and non-rhizosphere soil) variability in microbial community structuring. Denitrification and DNRA communities were diverse, and their activities did not depend on gene abundance but were significantly related to organic matter, suggesting that gene abundance alone was insufficient in assessing their activity in riparian zones. Based on networks, DNRA plays a keystone role among the microbial NO3- reducers. As the last line of defense in the interception of terrestrial NO3-, these findings contribute to our understanding of NO3- removal mechanisms in riparian zones, and could potentially be exploited to reduce the diffusion of NO3- pollution.

Robustness of anammox granular sludge treating low-strength sewage under various shock loadings: Microbial mechanism and little N2O emission.

With the increasing application of anammox for the treatment of high-strength industrial wastewater, application of anammox in municipal sewage has been gaining more attention. Sludge granulation in particular enhances the enrichment and retention of anammox bacteria in municipal sewage treatment systems. However, the performance of granular sludge under continuous and varying hydraulic loading shock remains little understood. In this study, the robustness of anammox granular sludge in treating low-strength municipal sewage under various shock loadings was investigated. Results showed that an upflow anaerobic sludge blanket (UASB) reactor with anammox granules performed well, with anammox specific activity up to 0.28 kg N/kg VSS/day and anti-loading shock capability up to 187.2 L/day during the 8-month testing period. The accumulation rate of N2O (<0.01 kg N/kg VSS/day) in the liquid phase was seven times higher than that of the gas phase, which could be mainly attributed to the incomplete denitrification and insufficient carbon source. However, only a small part of the produced N2O escaped into the atmosphere. High-throughput sequencing and molecular ecological network analyses also identified the bacterial diversity and community structure, indicating the potential resistance against loading shock. The composition and structural analyses showed that polysaccharides were an important functional component in the tightly bound extracellular polymeric substances (TB-EPS), which was the major EPS layer of anammox granules. Scanning electron microscopy (SEM) also showed that the gaps in between the anammox-clusters in the granules inhibit the flotation of the sludge and ensure efficient settling and retention of anammox granules.

Linking abundance and community of microbial N2O-producers and N2O-reducers with enzymatic N2O production potential in a riparian zone.

As aquatic-terrestrial ecotones, riparian zones are hotspots not only for denitrification but also for nitrous oxide (N2O) emission. Due to the potential role of nosZ II in N2O mitigation, emerging studies in terrestrial ecosystems have taken this newly reported N2O-reducer into account. However, our knowledge about the interactions between denitrification activities and both N2O-producers and reducers (especially for nosZ II) in aquatic ecosystems remains limited. In this study, we investigated spatiotemporal distributions of in situ N2O flux, potential N2O production rate, and potential denitrification rate, as well as of the related genes in a riparian zone of Baiyangdian Lake. Real-time quantitative PCR (qPCR) and high-throughput sequencing targeted functional genes were used to analyze the denitrifier communities. Results showed that great differences in microbial activities and abundances were observed between sites and seasons. Waterward sediments (constantly flooded area) had the lowest N2O production potential in both seasons. Not only the environmental factors (moisture content, NH4+ content and TOM) but also the community structure of N2O-producers and N2O-reducers (nirK/nirS and nosZ II/nosZ I ratios) could affect the potential N2O production rate. The abundance of the four functional genes in the winter was higher than in the summer, and the values all peaked at the occasionally flooded area in the winter. The dissimilarity in community composition was mainly driven by moisture content. Altogether, we propose that the N2O production potential was largely regulated by the community structure of N2O-producers and N2O-reducers in riparian zones. Increasing the constantly flooded area and reducing the occasionally flooded area of lake ecosystems may help reduce the level of denitrifier-produced N2O.

Anammox granular sludge in low-ammonium sewage treatment: Not bigger size driving better performance.

An integrated investigation to document high anammox abundance, activity and diversity in upflow anaerobic sludge blanket (UASB) reactor treating low-strength ammonium loading sewage was performed and showed that the optimal anammox granular sludge sizes could mitigate undesirable N2O emission. The enhanced anammox bacterial abundance, activity and specific anammox rate were achieved with optimal granules sludge sizes of 0.5-0.9 mm with multiple "Jettenia", "Brocadia", and "Anammoxoglobus" species. The tightly-bound extracellular polymeric substance (TB-EPS) was the main EPS layer found in anammox granular sludge, in which polysaccharides play an important structural role. Over this granular sludge sizes, the anammox bacterial abundance and activity did not significantly decrease, but N2O emission significantly increased. High throughput sequencing and ecological networks demonstrated the patterns of anammox and their co-occurring bacteria, with availability N2O-producer and N2O-reducer functional genes. Incomplete denitrification and insufficient carbon source mainly contributed to N2O production in granular sludge, as supported by results of stratification analysis.

Review of recent developments in determining volatile organic compounds in exhaled breath as biomarkers for lung cancer diagnosis.

Lung cancer is the most common cause of cancer deaths, its global incidence is rising, and continuing rises are predicted. The potential to diagnose lung cancers based on the determination of volatile organic compounds (VOCs) in human breath has been attracting increasing attention with the development of new techniques and methodologies. However, despite many reports of VOC profiling in lung cancer patients, little is known about how specific biomarkers relate to the biochemical pathways involved in lung cancer development, and there is still no reliable method for diagnosing lung cancer at the early stages. This review summarizes some of the latest methods used for monitoring biomarkers in lung cancer patients, which could be applicable for clinical diagnosis. Techniques for capturing and pre-concentrating biomarkers, and the technologies used for subsequently determining them, are also discussed.

Microbial communities in the native habitats of Agaricus sinodeliciosus from Xinjiang Province revealed by amplicon sequencing.

Agaricus sinodeliciosus is an edible species described from China and has been successfully cultivated. However, no studies have yet reported the influence factors implicated in the process of fructification. To better know abiotic and biotic factors, physiochemical characteristics and microbial communities were investigated in five different soil samples collected in the native habitats of specimens from northern Xinjiang, southern Xinjiang, and Zhejiang Province, respectively. There are major differences in texture and morphology among different specimens of A. sinodeliciosus from Xinjiang Province. A. sinodeliciosus from southern Xinjiang was the largest. Concentrations of DOC and TN and C/N ratio are not the main reason for the differences. Microbial communities were analyzed to find out mushroom growth promoting microbes (MGPM), which may lead to the differences. Functional microbes were picked out and can be divided into two categories. Microbes in the first category may belong to MGPM. There may be symbiotic relationships between microbes in the second category and A. sinodeliciosus. Certain analyses of microbial communities support the hypothesis that interactions between microbes and mushrooms would be implicated in morphological variation of the collected mushrooms. Redundancy analysis results indicate that high DOC/NH4+-N ratio and NH4+-N concentration can improve the yield of A. sinodeliciosus.

High production of fatty alcohols in Escherichia coli with fatty acid starvation.

BACKGROUND: Microbial biofuel synthesis attracting increasing attention. Great advances have been made in producing fatty alcohols from fatty acyl-CoAs and fatty acids in Escherichia coli. However, the low titers and limited knowledge regarding the basic characteristics of fatty alcohols, such as location and toxicity, have hampered large-scale industrialization. Further research is still needed. RESULTS: In this study, we designed a novel and efficient strategy to enhance fatty alcohol production by inducing fatty acid starvation. We report the first use of deletions of acyl-ACP thioesterases to enhance fatty alcohol production. Transcriptional analysis was conducted to investigate the mechanism of the designed strategy. Then, fatty alcohol production was further enhanced by deletion of genes from competing pathways. Fatty alcohols were shown to be extracellular products with low toxicity. The final strain, E. coli MGL2, produced fatty alcohols at the remarkable level of 6.33 g/L under fed-batch fermentation, representing the highest reported titer of fatty alcohols produced by microorganisms. CONCLUSIONS: Deletions of genes responsible for synthesis of fatty acids and competing products are promising strategies for fatty alcohol production. Our investigation of the location and toxicity of fatty alcohols suggest bright future for fatty alcohol production in E. coli.

Complete genome sequence of Thialkalivibrio versutus D301 isolated from Soda Lake in northern China, a typical strain with great ability to oxidize sulfide.

Thioalkalivibrio versutus D301 isolated from Soda Lake is a haloalkaliphilic and obligated chemolithoautotrophic Gram-negative bacterium. The strain has a good adaption to hyperhaline and highly alkaline environment and a powerful sulfur-oxidizing ability. Here, we present the complete genome sequence of T. versutus D301, providing insights into the genomic basis of its effects and facilitating its application in microbial desulfurization.

Desulfurization of immobilized sulfur-oxidizing bacteria, Thialkalivibrio versutus, by magnetic nanaoparticles under haloalkaliphilic conditions.

OBJECTIVES: As a haloalkaliphilic, sulfur-oxidizing bacteria, Thialkalivibrio versutus D301 can remove sulfide, thiosulfate and polysulfide in wastewater, we investigated how it might be reused when mixed with high concentrations of elemental sulfur. RESULTS: A process is described to immobilize T. versutus cells by using superparamagnetic Fe3O4 nanoparticles (NPs) under haloalkaliphilic conditions (i.e. pH 9.5, 0.5 M Na(+)). The saturation magnetization value (δs) of immobilized cells was 55.1 emu/g. The Fe3O4 NPs-coated cells had the similar sulfur oxidization activity to that of free cells, and they could be reused six batch cycles. Analysis of hydraulic diameters showed that bacterial cells were immobilized by Fe3O4 NPs due to the nano-size effects. CONCLUSIONS: Magnetic immobilization is a convenient technique for cell immobilization under haloalkaliphilic conditions and is a promising technology for large scale application.

Bacterial communities in haloalkaliphilic sulfate-reducing bioreactors under different electron donors revealed by 16S rRNA MiSeq sequencing.

Biological technology used to treat flue gas is useful to replace conventional treatment, but there is sulfide inhibition. However, no sulfide toxicity effect was observed in haloalkaliphilic bioreactors. The performance of the ethanol-fed bioreactor was better than that of lactate-, glucose-, and formate-fed bioreactor, respectively. To support this result strongly, Illumina MiSeq paired-end sequencing of 16S rRNA gene was applied to investigate the bacterial communities. A total of 389,971 effective sequences were obtained and all of them were assigned to 10,220 operational taxonomic units (OTUs) at a 97% similarity. Bacterial communities in the glucose-fed bioreactor showed the greatest richness and evenness. The highest relative abundance of sulfate-reducing bacteria (SRB) was found in the ethanol-fed bioreactor, which can explain why the performance of the ethanol-fed bioreactor was the best. Different types of SRB, sulfur-oxidizing bacteria, and sulfur-reducing bacteria were detected, indicating that sulfur may be cycled among these microorganisms. Because high-throughput 16S rRNA gene paired-end sequencing has improved resolution of bacterial community analysis, many rare microorganisms were detected, such as Halanaerobium, Halothiobacillus, Desulfonatronum, Syntrophobacter, and Fusibacter. 16S rRNA gene sequencing of these bacteria would provide more functional and phylogenetic information about the bacterial communities.

Efficient production of succinic acid from macroalgae hydrolysate by metabolically engineered Escherichia coli.

In this study, microbial production of succinic acid from macroalgae (i.e., Laminaria japonica) was investigated for the first time. The engineered Escherichia coli BS002 exhibited higher molar yield of succinic acid on mannitol (1.39±0.01mol/mol) than glucose (1.01±0.05mol/mol). After pretreatment and enzymatic hydrolysis, L. japonica hydrolysate was mainly glucose (10.31±0.32g/L) and mannitol (10.12±0.17g/L), which was used as the substrate for succinic acid fermentation with the recombinant BS002. A final 17.44±0.54g/L succinic acid was obtained from the hydrolysate after 72h dual-phase fermentation. The yield was as high as 1.24±0.08mol/mol total sugar, which reached 73% of the maximum theoretical yield. The results demonstrate that macroalgae biomass represents a novelty and economical alternative feedstock for biochemicals production.