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Polycystic ovary syndrome (PCOS) is a common endocrine disease in females that is characterized by hyperandrogenemia, chronic anovulation, and polycystic ovaries. However, the exact etiology and pathogenesis of PCOS are still unknown. The aim of this study was to clarify the bacterial, stress status, and metabolic differences in the gut microbiomes of healthy individuals and patients with high body mass index (BMI) PCOS (PCOS-HB) and normal BMI PCOS (PCOS-LB), respectively. Here, we compared the gut microbiota characteristics of PCOS-HB, PCOS-LB, and healthy controls by 16S rRNA gene sequencing, FK506-binding protein 5 (FKBP5) DNA methylation and plasma metabolite determination. Clinical parameter comparisons indicated that PCOS patients had higher concentrations of total testosterone, androstenedione, dehydroepiandrosterone sulfate, luteinizing hormone, and HOMA-IR while lower FKBP5 DNA methylation. Significant differences in bacterial diversity and community were observed between the PCOS and healthy groups but not between the PCOS-HB and PCOS-LB groups. Bacterial species number was negatively correlated with insulin concentrations (both under fasting status and 120 min after glucose load) and HOMA-IR but positively related to FKBP5 DNA methylation. Compared to the healthy group, both PCOS groups had significant changes in bacterial genera, including Prevotella_9, Dorea, Maihella, and Slackia, and plasma metabolites, including estrone sulfate, lysophosphatidyl choline 18:2, and phosphatidylcholine (22:6e/19:1). The correlation network revealed the complicated interaction of the clinical index, bacterial genus, stress indices, and metabolites. Our work links the stress responses and gut microbiota characteristics of PCOS disease, which might afford perspectives to understand the progression of PCOS.

BACKGROUND & AIMS: Fecal microbiota transplantation (FMT) is a therapy that can induce clinical remission in ulcerative colitis. FMT through enema or colonoscopy brings pain to patients. In this study, we aimed to assess the efficiency of FMT via capsules in UC and determine the specific factors related to the response to clinical remission. METHODS We conducted a single-blind trial in Zhongshan Hospital of Xiamen University, China. 21 patients were randomized to accept FMT, and 4 were assigned to the placebo. Patients in the FMT group received capsules filled with healthy donor fecal material and those in the placebo group received capsules filled with glycerol. We performed 16s ribosomal RNA gene sequencing and shotgun metagenomics in fecal samples and analyzed serum samples for metabolome features. RESULTS FMT via capsules could receive favorable levels of therapeutic success in UC. 3 FMTs in 1 week induced clinical remission in 57.1% (12 of 21) and clinical response in 76.2% (16 of 21). Gut bacterial richness after FMT was increased in the patients who achieved remission. The increased relative abundance of Alistipes sp, O. splanchnicus, and F. prausnitzii was the strongest predictor of clinical remission. Patients in remission after FMT had enrichment of Alistipes sp, O. splanchnicus and had increased levels of indolelactic acid. Patients who did not achieve remission had enrichment of Escherichia coli and Klebsiella and increased levels of 12,13-DiHOME and lipopolysaccharide biosynthesis. CONCLUSIONS We had demonstrated the efficacy of FMT via capsules in active UC. We found that FMT could promote gut microbiome reconstruction, reduce the invasion of harmful bacteria and the synthesis of LPS, and accelerate the metabolism of indoleacetic acid by increasing the abundance of specific bacteria to alleviate intestinal inflammation. These findings may raise a new way in the design of FMT therapy for UC. ClinicalTrails.gov (NCT03426683).

For a long time, gut bacteria have been recognized for their important roles in the occurrence and progression of gastrointestinal diseases like colorectal cancer, and the ever-increasing amounts of microbiome data combined with other high-quality clinical and imaging datasets are leading the study of gastrointestinal diseases into an era of biomedical big data. The "omics" technologies used for microbiome analysis continuously evolve, and the machine learning or artificial intelligence technologies are key to extract the relevant information from microbiome data. This review intends to provide a focused summary of recent research and applications of microbiome big data and to discuss the use of artificial intelligence to combat gastrointestinal diseases.

Denitrification is an important global N cycle process. The gene encoding NosZ that converts nitrous oxide (N2O) to N2 has been widely used as a biomarker to study denitrifying communities. However, conventional PCR primers target a limited range of the genetically diverse Clade I nosZ, and the amplicons are too long for sequencing on current NGS platforms. To address these issues, we developed a new PCR primer set that amplifies a 355-bp region of Clade I nosZ and captures broader taxonomic coverage than conventional primers in in silico tests. When compared with the widely used nosZF_nosZR_Rich_2003 set using the same soil samples and the same sequencing depth, the new set retrieved genes from four times more unique species, with consistently higher general diversity-based metrics. The new primer set performed well with different sequencing platforms (Ion Torrent and Illumina), and among a wide variety of soils from polar to tropical, desert to agricultural, and surface to a very low biomass subsoil, with significant differences in denitrifying community diversity and composition. This new primer set for Clade I together with the primers recently reported for Clade II by Chee-Sanford et al. (J Microbiol Meth 172:105908, 2020) provides a more comprehensive assessment of denitrifier gene hosts, their ecological patterns, and the degree of novelty in retrieved gene sequences.

Background Although recent studies have indicated that intestinal microbiota dweller are involved in the pathogenesis of allergy rhinitis (AR), the influence of gut microbiota on AR adult has not been fully elucidated yet. Hence, we carried out this study to uncover the distinctive bacterial taxa that differentiate allergy rhinitis patients from healthy individuals. Feces samples from thirty three AR patients and thirty one healthy individuals were analyzed by 16S rRNA gene sequencing. Results Results showed that the bacterial diversity in AR group was significantly higher than that of the non-AR group. Bacterial communities between AR and non-AR group were significantly differentiated as revealed by Principal coordinates analysis (PCoA) and the variation within non-AR were higher than that of the counterpart. Firmicutes, Fusobacteria, Actinobacteria, Cyanobacteria and Chloroflexi were the significantly differed phyla taxa and the top significantly distinguished bacterial genus included Prevotella_9, Phascolarctobacterium, Roseburia, Megamonas, Alistipes, Lachnoclostridium and Fusobacterium. The higher network complexity in AR group were dominated by taxa belonging to Firmicutes. The predicted function, alpha linolenic acid metabolism and bacterial invasion of epithelial cells pathway were higher in non-AR group while gonadotropin-releasing hormone (GnRH) signaling pathway, Fc γ-R mediated phagocytosis and endocytosis were higher in AR patients. Although the bacterial diversity between moderate and severe AR patients showed no significant difference, the significant correlation between featured genus and total nasal symptom score or rhinoconjunctivitis quality of life questionnaire, such as Butyricicoccus and Eisenbergiella, revealed the potential to intervene the AR status by means of gut microbiota. Conclusions In conclusion, patients with allergy rhinitis had distinguished gut microbiota characteritics in comparison with healthy controls. The results suggest that gut microbiota might play crucial roles in influencing the course and different symptoms of AR. Trial registration ChiCTR, ChiCTR1900028613. Registered 29 December 2019, https://www.chictr.org.cn/showproj.aspx?proj=47650.

Reduced bone mineral density (BMD) is associated with an altered microbiota in senile osteoporosis. However, the relationship among gut microbiota, BMD and bone metabolic indexes remains unknown in postmenopausal osteoporosis. In this study, fecal microbiota profiles for 106 postmenopausal individuals with osteopenia (n=33) or osteoporosis (n=42) or with normal BMD (n=31) were determined. An integrated 16S rRNA gene sequencing and LC-MS-based metabolomics approach was applied to explore the association of estrogen-reduced osteoporosis with the gut microbiota and fecal metabolic phenotype. Adjustments were made using several statistical models for potential confounding variables identified from the literature. The results demonstrated decreased bacterial richness and diversity in postmenopausal osteoporosis. Additionally, showed significant differences in abundance levels among phyla and genera in the gut microbial community were found. Moreover, postmenopausal osteopenia-enriched N-acetylmannosamine correlated negatively with BMD, and distinguishing metabolites were closely associated with gut bacterial variation. Both serum procollagen type I N propeptide (P1NP) and C-terminal telopeptide of type I collagen (CTX-1) correlated positively with osteopenia-enriched Allisonella, Klebsiella and Megasphaera. However, we did not find a significant correlation between bacterial diversity and estrogen. These observations will lead to a better understanding of the relationship between bone homeostasis and the microbiota in postmenopausal osteoporosis.

An amendment to this paper has been published and can be accessed via the original article.

Background Hepatitis B Virus (HBV) is one of the most common epidemic viruses worldwide. The serological antigen transfusion of chronic HBV infection is still an urgent problem to be solved. Previous results had shown that fecal microbiota transplantation (FMT) has great potential in the treatment of refractory HBV. Immune clearance of HBV is age-related in both human and mice models. Therefore, we aimed to explore the relationship between the microbiota and HBV chronic tendency. Methods Adult (12 weeks old) and young (6 weeks old) C3H mice were hydrodynamically injected with 10 μg pAAV/HBV1.2 plasmid via the tail vein. We gavaged young mice of FMT group three times with Feces from the adult mouse before the tail injection as FMT group, while young mice gavaged with the sterile water served as control (each group, N=5). The serum HBs-Ag level was monitoring weekly after the injection. Results Rapid HBs-Ag clearance occurred in the adult mice while the control young mice still remained chronic infections. Interestingly, young mice gavaged stool from adult mice showed a large decrease in serum HBs-Ag (p Conclusions FMT can enhance the capability of the liver to resist the chronic progression of HBV infection. Further research on this phenomenon and its underlying mechanisms may pave a new path for the treatment of HBV.

Background Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis(UC). We aim to establish the efficacy of multidonor, easy way FMT by capsules in active UC, and identify the factors associated with response to therapy. Methods We conducted a prospective trial in Zhongshan Hospital Affiliated to Xiamen University, Xiamen, China. A total of 28 adults with active UC (Mayo score 4–11) were enrolled in this trial, followed by capsules 3 days one week. One donor’s fecal microbiota was made into one capsule, and fecal microbiota transplantation was each derived from two or three unrelated donors. The primary outcome was steroid-free clinical remission with endoscopic remission or response. We performed 16S rDNA stool analysis to access associated microbial changes. Based on LC-MS/MS technology metabonomic researches were carried out to study metablome of the serum. Results The primary outcome with clinical remission was achieved in 16 out of 28 patients (57.14%), and 11 out of 22 patients(50%) had the musical healing. No adverse events were identified in these patients. The effects have no significant relationship with the age, gender, severity and extent of disease.FMT increased microbial diversity and altered composition. After FMT, unlike non-responders, the intestinal flora structure of responders was close to the donor, and the significant change began 1 week after transplantation. After FMT, responders had enrichment of Alloprevotella compared with non-responders and had increased levels of taurochenodeoxycholate and taurocholate. Escherichia-Shigella were decreased after FMT in responders, but no change in non-responders. The correlation analysis between the differential metabolites and the differential flora showed that the bile acid-related metabolites were positively correlated with the abundance of Alloprevotella and Prevotella_9. Conclusions Intensive-dosing, multidonor, FMT by capsules induces clinical remission in active ulcerative colitis and is associated with the changes of intestinal flora. Alloprecotella and bile acid-related metabolites were related to curative effect. The enrichment of Alloprevotella after FMT may be able to treat ulcerative colitis by regulating bile acid metabolism, improving mucosal permeability and regulating immunity. Future work should focus on the multi center verification and the relationship of immunity and gut microbiome.

With the increasing researches on the role of gut microbiota in human health and disease, appropriate storage method of fecal samples at ambient temperature would conveniently guarantee the precise and reliable microbiota results. Nevertheless, less choice of stabilizer that is cost-efficient and feasible to be used in longer preservation period obstructed the large-scale metagenomics studies. Here, we evaluated the efficacy of a guanidine isothiocyanate-based reagent method EffcGut and compared it with the other already used storage method by means of 16S rRNA gene sequencing technology. We found that guanidine isothiocyanate-based reagent method at ambient temperature was not inferior to OMNIgene·GUT OM-200 and it could retain the similar bacterial community as that of −80 °C within 24 weeks. Furthermore, bacterial diversity and community structure difference were compared among different sample fraction (supernatant, suspension and precipitate) preserved in EffcGut and −80 °C. We found that supernatant under the preservation of EffcGut retained the similar community structure and composition as that of the low temperature preservation method.

The isolation of microorganisms able to break the cell wall of algal species would contribute to the release of starch and lipid molecules for biofuel production. In this study, a special plaque-forming bacterium, forming plaques of about 2 cm in diameter, was found to target the diatom Phaeodactylum tricornutum . To monitor the dynamic effects of the bacterium on P. tricornutum , samples from both normal algal cultures and lysates were analyzed by fluorescence microscopy and denaturing gradient gel electrophoresis. The DGGE results showed that there was no different band between normal algal cultures and lysate samples, suggesting the bacterium's low abundance. Several different culture mediums were tried, and the obtained bacteria from the lysates were further investigated using the plaque-forming method. Finally, one isolated bacterium grown on culture medium containing P. tricornutum cells showed the special lytic activity. The results from sequence and phylogenetic analysis show that this bacterium belongs to the genus of Labrenzia in the family Rhodobacteraceae . This study demonstrates the isolation of a lytic bacterium that has a potential for biofuel production through P. tricornutum ‘cracking’.

Prorocentrum donghaiense blooms occur frequently in the Yangtze River estuary and the adjacent East China Sea. These blooms have damaged marine ecosystems and caused enormous economic losses over the past 2 decades. Thus, highly efficient, low-cost, ecofriendly approaches must be developed to control P. donghaiense blooms. In this study, a bacterial strain (strain Y42) was identified as Paracoccus sp. and was used to lyse P. donghaiense. The supernatant of the strain Y42 culture was able to lyse P. donghaiense, and the algicidal activity of this Y42 supernatant was stable with different temperatures and durations of light exposure and over a wide pH range. In addition to P. donghaiense, Y42 showed high algicidal activity against Alexandrium minutum, Scrippsiella trochoidea, and Skeletonema costatum, suggesting that it targets primarily Pyrrophyta. To clarify the algicidal effects of Y42, we assessed algal lysis and determined the chlorophyll a contents, photosynthetic activity, and malondialdehyde contents of P. donghaiense after exposure to the Y42 supernatant. Scanning electron microscopy and transmission electron microscopy analyses showed that the Y42 supernatant disrupted membrane integrity and caused algal cell breakage at the megacytic zone. Photosynthetic pigment loss and significant declines in both photosynthetic efficiency and the electron transport rate indicated that the Y42 supernatant damaged the photosynthetic system of P. donghaiense. Malondialdehyde overproduction indicated that the Y42 supernatant caused lipid peroxidation and oxidative damage to membrane systems in the algal cell, ultimately leading to death. The findings of this study reveal the potential of Y42 to remove algal cells from P. donghaiense blooms. IMPORTANCE P. donghaiense is one of the most common dinoflagellate species that form harmful algal blooms, which frequently cause serious ecological pollution and pose health hazards to humans and other animals. Screening for bacteria with high algicidal activity against P. donghaiense and studying their algicidal processes and characteristics will contribute to an understanding of their algicidal effects and provide a theoretical basis for preventing algal blooms and reducing their harm to the environment. This study reports the algicidal activity and characteristics of Paracoccus against P. donghaiense. The stability of the algicidal activity of Paracoccus in different environments (including different temperature, pH, and sunlight conditions) indicates its potential for use in the control of P. donghaiense blooms.

Background Increasing evidence suggests that the gut microbiota has evolved as a new important player in the pathogenesis of hepatitis B virus-induced chronic liver disease, including chronic hepatitis, cirrhosis. However, the composition and structure alteration of the gut microbiota associated with the stage and progression of HBV infection remains unknown. Hence, the aim of the study is to elucidate the microbial influence which contributes to the microbial shift of HBV patients in different stages. Methods All subjects enrolled had clinic test performed in the Zhongshan Hospital, Xiamen University. A total of 62 subjects were finally selected for inclusion in this study, including 7 healthy individuals, 13 HBeAg negative chronic HBV infection patients (HNCHI), 6 HBeAg negative chronic hepatitis B patients (HNCHB), 5 HBeAg positive chronic hepatitis B patients (HPCHB) and 31 decompensated cirrhosis after hepatitis B patients (DCAHB) matched in age, gender and body mass index (BMI). Stools from all subjects were collected to extract DNA, then for 16S rDNA high-throughput sequencing and further compared by the bacterial diversity, community and structure, differential taxa analysis. Results DCAHB patients showed decreased gut bacterial diversity and more unique OTU numbers compared to the other four groups, suggesting that DCAHB is distinctive, which could further be confirmed by the PCA analysis. In phyla level, the relative abundance of Fusobacteria and Proteobacteria increased while Firmicutes content decreased from the health, HNCHI, HNCHB, HPCHB to DCAHB group. In genus level, the high level of Streptococcus, Veillonella, Enterobacteriaceae, Lactobacillus and Haemophilus, while decreased Clostridiaceae, Phascolarctobacterium, Coprococcus and Ruminococcaceae in DCAHB conform the disease progression state. In addition, LEfSe analysis reveals that Bacteroides fragilis, Bacteroides eggerthii, Veillonella dispar, Streptococcus anginosus, Corprococcus eutactus and Akkermansia muciniphila could serve as target microorganism for the further investigation. Conclusions These compositional and structural changes in the gut microbiota in varied stage HBV patients suggest the potential contributions of gut microbiota to the progression of HBV infection and thus provide new insight into gut microbiota-targeted interventions to improve the prognosis of this disease.

Background Serum HBsAg decline is an index for the effectiveness of antiviral treatment hepatitis B virus (HBV) e-antigen (HBeAg)-negative chronic hepatitis B (CHB) patients. Unfortunately, for entecavir (ETV), HBsAg decline or clearance only occurs in a minority of patients even after decades of antiviral therapy. Our previous study showed that Faecal microbiota transplantation (FMT) was able to induce HBeAg clearance in patients with positive HBeAg after long-term antiviral therapy. However, the effect of FMT on HBeAg negative CHB patients after long-term antiviral therapy is still unclear. Thus, we reported a case-controlled, open-label pilot trial of FMT for HBeAg negative CHB patients. Methods We recruited 10 patients who remained HBsAg positive following >1 years of ongoing ETV antiviral therapy. 5 of them were enrolled in the FMT arm while other 5 were enrolled in the control arm. All patients went on their previous antiviral therapy. We performed FMT via nasojejunal tube for the FMT arm every 2 weeks. The faecal microbial community was analysed using Illumina Hisequencing of 16S rDNA and bioinformatics methods. Serum HBsAg and endotoxin levels were monitored every 2 weeks. Results Serum HBsAg declined gradually after each time of FMT in the FMT arm compared to control arm. FMT induced serum HBsAg decline up to 55.27%±8.52% in the trial group accompanied with serum endotoxin decline while serum HBsAg in the control group increased 38.07% which may closely be related to drug resistance. 16S rDNA analysis of the stools showed that gut microbiota in the FMT group transformed towards the donors. In particular, the proportion of Bifidobacterium, Streptococcus, Clostridium, Clostridiaceae, Blautia, Coprococcus and Megamonas in the gut microbiota of the FMT group decreased significantly towards the donors while the proportion of Bacteroides, Butyricimonas, Odoribacter, Prevotella, Parabacteroides, Anaerostipes, Oscillospira, Ruminococcaceae and Sutterella increased towards the donors. Conclusions This study suggested that HBsAg decline in the serum of HBeAg negative CHB patients were detected after several times of FMT accompanied with serum endotoxin decline and the gut microbiota prone to the donors. Gut microbiota may be a new target for the treatment of HBeAg negative CHB.

A Gram-staining-negative, orange-pigmented, non-motile, aerobic bacterial strain, designated GYP20T, was isolated from a culture of the alga Picochlorum sp., a promising feedstock for biodiesel production, which was isolated from the India Ocean. Growth was observed at temperatures from 20 to 37 °C, salinities from 0 to 3 % and pH from 5 to 9.Mg 2+ and Ca2+ ions were required for growth. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strain was a member of the genus Phaeodactylibacter, which belongs to the family Saprospiraceae. Strain GYP20T was most closely related to Phaeodactylibacter xiamenensis KD52T (95.5 % sequence similarity). The major fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3. The predominant respiratory quinone was menaquinone-7 (MK-7). The polar lipids of strain GYP20T were found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unidentified glycolipids, two unidentified phospholipids and three unidentified aminolipids. According to its morphology, physiology, fatty acid composition and 16S rRNA sequence data, the novel strain most appropriately belongs to the genus Phaeodactylibacter, but can readily be distinguished from Phaeodactylibacter xiamenensis GYP20T. The name Phaeodactylibacter luteus sp. nov. is proposed with the type strain GYP20T ( = MCCC 1F01222T = KCTC 42180T).

Harmful algal blooms (HABs) could be deemed hazardous materials in aquatic environment. Alexandrium tamarense is a toxic HAB causing alga, which causes serious economic losses and health problems. In this study, the bacterium Deinococcus xianganeasis Y35 produced a new algicide, showing a high algicidal effect on A. tamarense. The algicidal compound was identified as deinoxanthin, a red pigment, based on high resolution mass spectrometry and NMR after the active compound was isolated and purified. Deinoxanthin exhibited an obvious inhibitory effect on algal growth, and showed algicidal activity against A. tamarense with an EC50 of 5.636 mu g/mL with 12 h treatment time. Based on the unique structure and characteristics of deinoxanthin, the content of reactive oxygen species (ROS) increased after 0.5 h exposure, the structure of organelles including chloroplasts and mitochondria were seriously damaged. All these results firstly confirmed that deinoxanthin as the efficient and eco-environmental algicidal compound has potential to be used for controlling harmful algal blooms through overproduction of ROS. (C) 2015 Elsevier B.V. All rights reserved.

In recent years, Microcystis aeruginosa blooms have occurred throughout the world, causing huge economic losses and destroying aquatic ecosystems. It is necessary to develop effective and ecofriendly methods to control M. aeruginosa blooms. Here, we report a high algicidal activity of prodigiosin (PG) against M. aeruginosa as well as the algicidal mechanism. PG showed high algicidal activity against M. aeruginosa, with a 50% lethal dose (LD50) of 5.87 μg/mL in 72 h. A combination of methods, including propidium iodide and Annexin V-fluorescein staining assays and light and electron microscopy indicated the existence of two modes of cell death with features similar to those in eukaryotic programmed cell death: necrotic-like and apoptotic-like. Biochemical and physiological analyses showed that PG generates reactive oxygen species (ROS), which induce lipid peroxidation, damage the membrane system and destroy the function of the photosystem. A proteomics analysis revealed that many proteins were differentially expressed in response to PG stress and that most of these proteins were involved in important metabolic processes, which may trigger necrotic-like or apoptotic-like cell death. The present study sheds light on the multiple toxicity mechanisms of PG on M. aeruginosa and its potential for controlling the occurrence of M. aeruginosa blooms in lakes.

Experiments were conducted to find out the molecular features, infection process of a special alga plaque-forming microorganism and its potential influence on the biomass of Chlorella vulgaris during the infection process. Direct contact between the algal cell and the bacterium may be the primary steps needed for the bacterium to lyse the alga. Addition of C. vulgaris cells into f/2 medium allowed us obtain the object bacterium. The 16S rRNA gene sequence comparisons results showed that the plaque-forming bacterium kept the closest relationship with Labrenzia aggregata IAM 12614(T) at 98.90%. The existence of the bacterium could influence both the dry weight and lipid content of C. vulgaris. This study demonstrated that direct cell wall disruption of C. vulgaris by the bacterium would be a potentially effective method to utilize the biomass of microalgae.

A Gram-stain-negative, elongated rod-shaped, motile by gliding, green-pigmented, aerobic bacterial strain, designated LY03T, was isolated from lake water in Xiamen, Fujian Province, China. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the genus Chitinimonas , which belongs to the family Burkholderiaceae . Strain LY03T was most closely related to Chitinimonas taiwanensis LMG 22011T (96.02 % 16S rRNA gene sequence similarity), followed by Chitinimonas koreensis KACC 11467T (94.85 %), and the three strains formed a distinct lineage from other strains in the phylogenetic analyses. Optimum conditions for growth were 37 °C, pH 7–9 and without NaCl. The major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and C10 : 0 3-OH. The DNA G+C content of strain LY03T was 63.6 mol% and the major respiratory quinone was ubiquinone-8 (Q-8). The polar lipids were found to consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown polar lipids and unidentified phospholipids. Differential phenotypic properties and phylogenetic distinctiveness distinguished strain LY03T from all other members of the genus Chitinimonas . On the basis of its morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain LY03T represents a novel species of the genus Chitinimonas , for which the name Chitinimonas prasina sp. nov. is proposed. The type strain is LY03T ( = MCCC 1F01209T = KCTC 32574T).

Toxicity of algicidal extracts from Mangrovimonas yunxiaonensis strain LY01 on Alexandrium tamarense were measured through studying the algicidal procedure, nuclear damage and transcription of related genes. Medium components were optimized to improve algicidal activity, and characteristics of algicidal extracts were determined. Transmission electron microscope analysis revealed that the cell structure was broken. Cell membrane integrity destruction and nuclear structure degradation were monitored using confocal laser scanning microscope, and the rbcS, hsp and proliferating cell nuclear antigen (PCNA) gene expressions were studied. Results showed that 1.0% tryptone, 0.4% glucose and 0.8% MgCl2 were the optimal nutrient sources. The algicidal extracts were heat and pH stable, non-protein and less than 1kD. Cell membrane and nuclear structure integrity were lost, and the transcription of the rbcS and PCNA genes were significantly inhibited and there was up-regulation of hsp gene expression during the exposure procedure. The algicidal extracts destroyed the cell membrane and nuclear structure integrity, inhibited related gene expression and, eventually, lead to the inhibition of algal growth. All the results may elaborate firstly the cell death process and nuclear damage in A. tamarense which was induced by algicidal extracts, and the algicidal extracts could be potentially used as bacterial control of HABs in future.

A novel Gram-stain-negative, horseshoe-shaped, non-motile bacterium, designated strain KD51T, forming colonies coloured pink by carotenoid pigments, was isolated from aggregates of the alga Chlorella autotrophica collected from the coastal sea off the city of Xiamen, Fujian Province, China. 16S rRNA gene sequence comparison showed that strain KD51T was a member of the genus Cyclobacterium , forming a distinct lineage with Cyclobacterium lianum HY9T. The 16S rRNA gene sequence similarity between strain KD51T and the type strains of species of the genus Cyclobacterium ranged from 92.1 % to 95.2 %. Growth occurred at 4–40 °C (optimum, 28 °C), in the presence of 3–9 % NaCl (optimum, 3–5 %) and at pH 6–10 (optimum, pH 7.5). The dominant fatty acids (>20 %) of strain KD51T were iso-C15 : 0 (32.2 %) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c; 22.2 %). The DNA G+C content was 41.7 mol% and the only respiratory quinone was menaquinone-7. On the basis of phenotypic data and phylogenetic inference, strain KD51T represents a novel species of the genus Cyclobacterium , for which the name Cyclobacterium xiamenense sp. nov. is proposed. The type strain is KD51T ( = CGMCC 1.12432T = KCTC 32253T). An emended description of the genus Cyclobacterium is also proposed.

A Gram-stain-negative, elongated rod-shaped, yellow-pigmented, aerobic bacterial strain, designated WJ-1T, was isolated from coastal seawater in Xiamen, Fujian province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain WJ-1T fell within the genus Tenacibaculum and was most closely associated with Tenacibaculum aestuarii SMK-4T (96.7 % 16S rRNA gene sequence similarity); lower similarities were shown to other members of the genus Tenacibaculum ( Tenacibaculum litopenaei B-IT (96.0 %), Tenacibaculum geojense YCS-6T (94.5 %) and Tenacibaculum jejuense CNURIC 013T (95.4 %). Growth was observed at temperatures from 16 to 38 °C, at salinities from 2 to 4 % and at pH 6–9. The major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 0 3-OH. The DNA G+C content of strain WJ-1T was 33.2 mol% and the major respiratory quinone was menaquinone-6 (MK-6). Differential phenotypic properties and phylogenetic distinctiveness in this study distinguished strain WJ-1T from all other members of the genus Tenacibaculum . According to the morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain WJ-1T represents a novel species of the genus Tenacibaculum , for which the name Tenacibaculum xiamenense sp. nov. is proposed. The type strain is WJ-1T ( = CGMCC 1.12378T = LMG 27422T).

Chitinase producing bacteria can involve extensively in nutrient cycling and energy flow in the aquatic environment through degradation and utilization of chitin. It is well known that diatoms cells are encased by box-like frustules composed of chitin. Thus the chitin containing of diatoms shall be a natural target of chitinase producing bacteria, however, the interaction between these two organismic groups has not been studied thus far. Therefore, in this study, the algicidal mechanism of one chitinase producing bacterium (strain LY03) on Thalassiosira pseudonana was investigated. The algicidal range and algicidal mode of strain LY03 were first studied and then bacterial viability, chemotactic ability and direct interaction characteristic between bacteria and diatom were also confirmed. Finally, the characteristic of the intracellular algicidal substance was identified and the algicidal mechanism was determined whereby algicidal bacterial cells showed chemotaxis to algal cells, fastened themselves on algal cells with their flagella and then produced chitinase to degrade algal cell walls and eventually caused algal lysis and death. It is the first time to investigate the interaction between chitinase producing bacteria and diatoms and this novel special interaction mode was confirmed in this study, which will be helpful in protection and utilization of diatoms resources.

Algicidal microbes could effectively remove the harmful algae from the waters. In this study, we were concerned with the ecological influence of an algicide extracted from Streptomyces alboflavus RPS, which could completely lyse the Phaeocystis globosa cells within two days. In microcosms, 4 μg/mL of the microbial algicide could efficiently remove P. globosa cells without suppressing other aquatic organisms. Bioluminescent assays confirmed that the toxicity of microbial algicide at this concentration was negligible. Interestingly, the toxicity of P. globosa exudates was also significantly reduced after being treated with the algicide. Further experiments revealed that the microbial algicide could instantly increase the permeability of the plasma membrane and disturb the photosynthetic system, followed by the deformation of organelles, vacuolization and increasing oxidative stress. The pre-incubation of N-acetyl cysteine (NAC) verified that the rapid damages to the plasma membrane and photosynthetic system caused the algal death in the early phase and the increasing oxidative stress killed the rest. The late accumulation and possible release of CAT also explained the decreasing toxicity of the algal culture. These results indicated that this microbial algicide has great potential in controlling the growth of P. globosa on site.

In this study, bioflocculant from Cobetia marina L03 could be used for effective harvesting of the microalgae Chlorella vulgaris via flocculation-flotation. A flotation efficiency of 92.7% was observed when 20 mg L(-1) bioflocculant was tested for flocculating the microalgal cells with 5mM CaCl2. The bioflocculant was stable at wide ranges of pH and temperature, which is advantageous for its application under various conditions. Chemical analysis of the bioflocculant indicated that it is composed of 31.6% total sugar and 0.2% protein (w/w). This bioflocculant has potential for the high-efficiency harvesting of microalgae and may be useful in reducing one of the barriers to microalgal biofuel production.

Phaeocystis globosa blooms in eutrophication waters can cause severely damage in marine ecosystem and consequently influence human activities. This study investigated the effect and role of an algicidal actinomycete (Streptomyces sp. JS01) on the elimination process of P. globosa. JS01 supernatant could alter algal cell membrane permeability in 4 h when analyzed with flow cytometry. Reactive oxygen species (ROS) levels were 7.2 times higher than that at 0 h following exposure to JS01 supernatant for 8 h, which indicated that algal cells suffered from oxidative damage. The Fv/Fm value which could reflect photosystem II (PS II) electron flow status also decreased. Real-time PCR showed that the expression of the photosynthesis related genes psbA and rbcS were suppressed by JS01 supernatant, which might induce damage to PS II. Our results demonstrated that JS01 supernatant can change algal membrane permeability in a short time and then affect photosynthesis process, which might block the PS II electron transport chain to produce excessive ROS. This experiment demonstrated that Streptomyces sp. JS01 could eliminate harmful algae in marine waters efficiently and may be function as a harmful algal bloom controller material.

A Gram-staining-negative, orange-pigmented, aerobic bacterial strain, designated KA37T, was isolated from a mangrove sediment sample collected from Yunxiao mangrove National Nature Reserve, Fujian Province, China. Growth was observed at 4–37 °C, 0–3 % (w/v) NaCl and pH 5–10. Mg2+ ions were required for growth. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the genus Erythrobacter, which belongs to the family Erythrobacteraceae. Strain KA37T was most closely related to Erythrobacter gangjinensis KCTC 22330T (96.9 % sequence similarity), followed by Erythrobacter marinus KCTC 23554T (96.8 %); similarity to other members of the genus was below 96.6 %. The major fatty acids were C17 : 1ω6c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Strain KA37T did not produce bacteriochlorophyll a. The predominant respiratory quinone was ubiquinone 10 (Q-10). The polar lipids of strain KA37T were sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, five unknown lipids and one unidentified phospholipid. According to its morphology, physiology, fatty acid composition and 16S rRNA sequence, the novel strain most appropriately belongs to the genus Erythrobacter, but can be distinguished readily from species of the genus Erythrobacter with validly published names. The name Erythrobacter luteus sp. nov. is proposed, with strain KA37T ( = MCCC 1F01227T = KCTC 42179T) as the type strain.

A novel Gram-staining-negative, aerobic, rod-shaped, non-motile, yellow bacterium designated strain KD53T, was isolated from a culture of the alga Phaeodactylum tricornutum from Xiamen, Fujian Province, China. 16S rRNA gene sequence comparison showed that strain KD53T was a member of the Roseobacter clade within the family Rhodobacteraceae , forming a distinct lineage with species of the genus Mameliella . The 16S rRNA gene sequence similarities between strain KD53T and other strains examined were all less than 97.0 %. Strain KD53T was found to grow optimally at 28 °C, at pH 7.5–8.0 and in the presence of 3 % (w/v) NaCl. The dominant fatty acids of strain KD53T were C18 : 1ω6c and/or C18 : 1ω7c, C18 : 0 and C16 : 0. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 65 mol% and the major respiratory quinone was ubiquinone 10 (Q-10). On the basis of phenotypic data and phylogenetic inference, strain KD53T represents a novel member of the genus Mameliella , then the name Mameliella phaeodactyli sp. nov. is proposed. The type strain is KD53T ( = MCCC 1K00273T = KCTC 42178T).

Phaeodactylibacter xiamenensis KD52 is a novel bacterium isolated from a culture of the alga Phaeodactylum tricornutum in Xiamen, Fujian Province, China. Here, we present the first draft genome sequence of this strain, which will provide an opportunity to further understand the functional genes related to signing for nutrition from the host algae and the molecular mechanisms underlying its beneficial properties.