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Traditional fermented soybean contains a variety of microflora. To obtain a comprehensive and accurate understanding of the microbial community structure and metabolic potential of fermented soybean, comparative metagenomics and metatranscriptomics were performed on a sample of fermented soybean in Yunnan Province. Metagenomic DNA and metatranscriptomic RNA were sequenced using Illumina HiseqTM2500, which yielded a total of 92,192,276 reads, with an average read length of 150 bp and 38,798,262 paired-end sequences, with an average length of 151 bp. The results show that Providencia stuartii was the most abundant species and the genes of carbohydrates (2296, 13.30%), protein metabolism (1530, 8.86%), and amino acids and amino acid derivatives (1423, 8.24%) were dominant. The expression levels of the genes belonging to amino acid transport and metabolism processes were the highest according to the reads per length of transcript in kilo-bases per million mapped reads (RPKM) values, followed by energy production and conversion and carbohydrate transport and metabolism. The metabolic pathways were primarily associated with carbohydrates, proteins and amino acids, which might be in accordance with the high levels of proteins and other nutrients in soybeans. Overall, these findings provide insights into the community structure and metabolic potential of the fermented soybean microbiome.

The goal of this study was to explore the regulatory mechanisms of phenyllactic acid (PLA) overaccumulation in Lactobacillus plantarum. The dynamics of PLA production revealed that 24 h was a suitable fermentation time, at which one of the largest differences in PLA content between strains S1 and YM-4-3 was 22.42 mg/L. Additionally, an optimization experiment showed that PLA production under the optimal condition (sample YM-4-3y) was up to 400.74 mg/L, 7.61-13.26 times as those of YM-4-3 and S1. Subsequently, an integrated analysis of genomic, transcriptomic and metabolomic data revealed that, YM-4-3 and YM-4-3y, compared with S1, although lacking a complete de novo biosynthetic pathway, increased PLA production by strengthening the core pathway and central carbon metabolism, and weakening the biosynthesis pathway of amino acids and their derivatives. These changes can provide sufficient precursors and compensate for or balance the energy consumed by the reinforced core pathway.

Background: Mothers are the primary source of bacteria for newborns, but it is unclear whether mother-to-newborn transmission occurs prior to, during or after birth. Similarly, the effect of the delivery mode on neonatal microorganisms has been the focus of controversy. Methods: Healthy maternal and neonatal pairs that underwent vaginal birth and caesarean section were enrolled in this study. Meconium, placenta, membrane and amniotic fluid samples for newborns and vaginal, rectal and oral samples for mothers were collected. All samples were amplified and sequenced by a 16S rRNA gene primer set targeting bacteria and archaea. Findings: A total of 550 samples from 36 mother-neonate pairs with vaginal births and 42 mother-neonate pairs with caesarean sections were included in this study. The negative controls showed that the data analysis in this study was not affected by contamination. There was a high diversity of microbial communities in the pregnancy environment of the foetus. Meconium samples could be divided into three distinct types that were not influenced by the delivery method. Interpretation: The distribution patterns of bacterial communities in the meconium, placenta, and foetal membranes were highly similar and had nothing to do with the mode of delivery. For approximately half of the placental microorganisms, the same sequence could be found in the vaginal, rectal, and oral samples of the mother. Keywords: Meconium, Microbiota, Delivery mode, Archaea

This work aims to uncover how glucose affected the production of phenyllactic acid (PLA) and p-hydroxyphenyllactic acid ( p-OH-PLA). The highest yields of PLA (68.53 mg/L) and p-OH-PLA (50.39 mg/L) were observed after Lactobacillus plantarum strain YM-4-3 fermentation in media containing 30 and 10 g/L glucose, respectively. Additionally, the antimicrobial activity of YM-4-3 against food-borne pathogens and the NADH/NAD+ ratio were positively correlated with the production of PLA and p-OH-PLA, respectively. In addition, a 2-oxoglutarate/malate translocator coding gene ( Omt1) was selected based on the qPCR results, and its knockout mutant, compared with the wild-type strain YM-4-3, showed that the PLA and p-OH-PLA production was decreased by 1.37-6.99 and 1.53-1.59 times, respectively. This result indicated that OMT1 was involved in the biosynthesis of PLA and p-OH-PLA. To conclude, this study suggests that glucose, NADH/NAD+ ratio and/or the Omt1 gene, PLA, and p-OH-PLA production, and antimicrobial activity contribute to a cause-and-effect relationship.

Lactobacillus (Lb.) plantarum is typically used as a starter culture in salt-fermented foods. Here we report 3-4% NaCl reducing the antimicrobial activity of Lb. plantarum strain YM-4-3, owing to the decrease of bacterial growth, plantaricin activity and expression levels of plantaricin biosynthesis-related genes (PBGs). Meanwhile, 1% NaCl promoted slightly the growth of YM-4-3 and up-regulated the expression of PBGs to the greatest level. The results from a spoilage experiment of fermented soybean products revealed that the 1% NaCl and YM-4-3 treatment group had the longest shelf life representing the minimum number of pathogenic bacteria and the lowest degree of mildew. Therefore, a combination of Lb. plantarum with a low concentration of salt, such as 1% NaCl, is a recommended condition for preparing fermented foods.

Intestinal bacteria are symbiotic microbiota within the human gut and are implicated in the occurrence and development of colorectal cancer (CRC). The current study investigated the changes in bacterial composition prior to and following surgery, as well as the differences in the bacterial community structure between cancer tissue and adjacent normal tissue. The diversity of the bacterial community and the composition of the bacteria were assessed. In addition, phylogenetic analysis and principle component analysis (PCA) were performed. The results revealed that cancer tissue and adjacent normal tissue exhibited similar bacterial compositions. However, a significant difference was identified in the composition of intestinal bacteria in stool samples collected from patients following surgery compared with stool samples collected prior to surgery. Each patient had their own unique intestinal bacterial community, likely due to a number of factors, including diet, genetic factors and health status. In addition, phylogenetic trees revealed that the most abundant operational taxonomic unit, 0001, was associated with Escherichia coli in all samples. Finally, PCA suggested that the bacterial community structure in all patient stools was similar following surgery. The current study provides information regarding the diversity of the intestinal bacterial community of patients with CRC and provides a basis for postoperative intestinal assessments.

The objective of this study was to evaluate the effects of a three-strain yogurt formulation in slow-transit constipation (STC) patients. Each individual in both treatment groups consumed 250 mL of the formulated yogurt daily for a week (7 days), and fecal samples were collected for gut microbiota and short-chain fatty acid (SCFA) analyses. A significant increase in the defection frequency (p<0.001) and bacterial diversity (p=0.027) at the 100% sequence homology level and a decrease in the concentrations of acetic acid (p=0.014), propionic acid (p=0.019), and butanoic acid (p=0.005) were observed after the STC patients consumed three-strain yogurt formulation. In addition, the consumption of the three-strain yogurt formulation significantly altered the composition of the intestinal bacteria in the STC patients. The relative abundances of 23 genera in the top dominating genera were altered significantly after the STC patients consumed the yogurt. In summary, the consumption of 250 mL day− the three-strain yogurt formulation described in this study can play a role in improving the symptoms of STC.

Tobacco brown spot, caused by Alternaria species, is a devastating tobacco disease. To explore the role of a group III histidine kinase (AlHK1) on A. longipes pathogenesis, the invasion progress of A. longipes was monitored. We found that the wild-type strain C-00 invaded faster than the AlHK1-disrupted strain HK∆4 in the early and middle infection stages and the reverse trend occurred in the late infection stage. Then, eight invasion transcriptomes were performed using RNA-Seq and 205 shared, 505 C-00 and 222 HK∆4 specific differentially expressed genes (DEGs) were identified. The annotation results showed seven antioxidant activity genes were specifically identified in the HKΔ4 DEGs. A subsequent experiment confirmed that HKΔ4 was more resistant to low concentrations oxidative stress than C-00. In addition, the results from 1) statistics for the number of DEGs, GO enriched terms, DEGs in clusters with rising trends, and 2) analyses of the expression patterns of some DEGs relevant for osmoadaptation and virulence showed that changes in C-00 infection existed mainly in the early and middle stages, while HKΔ4 infection arose mainly in the late stage. Our results reveal firstly the pathogenesis of A. longipes regulated by AlHK1 and provide useful insights into the fungal-plant interactions.

Folate is an important intermediate in cellular metabolism. However, because of a lack of key enzymes in the folate biosynthetic pathway, humans require supplementation with dietary folate. Some Lactobacillus plantarum strains have the ability to produce folate. To gain a better understanding of the folate biosynthetic pathway in the L. plantarum strain 4_3, which generates high folate yields, L. plantarum strain 4_3 was grown in folic acid casei medium (FACM) and fermented soybean, after obtaining a draft genome sequence. The pH values and folate yields were monitored during culturing, as were the transcriptomic profiles of cultured bacteria. The folate content increased for 12 h and then decreased before increasing again. All the genes involved in the de novo biosynthesis of folate were detected in both the genomic and transcriptomic data. The upregulation of the para-aminobenzoate biosynthesis pathway could explain the folate production in fermented soybean. Soybeans are a good substrate for the production of functional foods because of their well-suited cultivation and nutritional quality. The results of this study provide a good explanation for the high folate production observed during the fermentation of soybeans.

Hybrid histidine kinase (HHKs) are widespread in fungi, but their roles in the regulation of fungal adaptation to environmental stresses remain largely unclear. To elucidate this, we cloned HisK2301 from Rhodosporidium kratochvilovae strain YM25235, characterized HisK2301 as a novel HHK, and further investigated the role of HisK2301 by overexpressing it in YM25235. Our results revealed that HisK2301 can promote adaptation of YM25235 to cold, osmotic, and salt stresses. During cold stress, HisK2301 significantly enhanced the biosynthesis of polyunsaturated fatty acids (PUFA) and intracellular glycerol. HisK2301 also augmented the expression levels of Δ12/Δ15 fatty acid desaturase ( RKD12) and glycerol-3-phosphate dehydrogenase1 ( GPD1), which are responsible for PUFA and glycerol biosynthesis, respectively. To conclude, our findings give the first insight into the defense and mechanisms of HisK2301 in fungi against cold stress and suggest the potential use of the novel cold-adapted HHK HisK2301 in industrial processes, such as large-scale production of PUFA.

Due to small size, strong fluorescence and low cytotoxicity, fluorescent carbon dots (CDs) attract people's attention. The CDs-Ws derived from Weissella sp. Kl-3 with bright blue photoluminescent were obtained via hydrothermal method. The CDs-Ws could selectively label dead bacterial and yeast cells, and show the potential for the differentiation of live/dead microbe. It showed that the prepared CDs-Ws had multicolor fluorescence emission properties, excellent biocompatibility and low biotoxicity with cell and in vivo imaging. In addition, CDs-Ws sensitized by ampicillin sodium was employed as fluorescence nanosensor (CDs-Ws-Amp Na) to detect Cr(VI) and VB12 based on inner filter effet mechanism. The linear correction was obtained for VB12 detection in 0–25 μM with 51.50 nM detection limit, and the linear range was 0–50 μM with 106.57 nM detection limits for Cr(VI) by CDs-Ws-Amp Na. The fluorescent nanosensor was used for detection of Cr(VI) in water and VB12 in serum and milk. It shows excellent potential in bioimaging, Cr(VI) and VB12 detection.

The protein kinase HOG1 in high osmolarity glycerol pathway is one of mitogen-activated protein kinases and plays an important role in fungi cellular responses to external stress and stimuli. In this study, AlHOG1, a yeast HOG1 homolog, was isolated from tobacco pathogenic fungus Alternaria longipes and its disrupted mutants were generated using homologous recombination. Compared with the wild-type strain, the mutants grew slower under Minimal-Media, produced less conidia on Potato-Dextrose-Agar and showed a retardation phenotype in conidial germination rate. Colony color observation indicated that AlHOG1 most likely negatively regulated melanin production under nutrients-deficient or osmotic stress. The same action mode of AlHOG1 on hyphal growth in response to certain carbon or nitrogen sources was speculated. Additionally, the disrupted strains were sensitive to osmotic and oxidative stress, and showed increased resistance to dicarboximide, phenylpyrrole and carbendazim fungicides. Meanwhile, results from the comparative analysis between the AlHOG1- and the AlHK1 (encoding a group III histidine kinase)-disrupted mutants showed that AlHOG1 mediated-pathway was partly regulated by the upstream AlHK1 kinase for cellular resistance to salts osmotic stress and that AlHK1 was a primary regulator for cellular sugar and fungicides stress adaptation and likely modulated both AlHOG1-mediated pathway and other unknown mechanisms. Noteworthily, AlHOG1 but not AlHK1 was confirmed to be associated with high concentration glycerol adaptation, which is the first report to our knowledge. Overall, our results indicated that AlHOG1 was involved in multiple physiological processes in A. longipes, including mycelial and conidial development, melanin production, nutrients sensing and multi-stress responses.

A vertical flow constructed wetland was combined with a biological aerated filter to develop an ecological filter, and to obtain the optimal operating parameters: The hydraulic loading was 1.55 m 3 /(m 2 ·d), carbon–nitrogen ratio was 10, and gas–water ratio was 6. The experimental results demonstrated considerable removal efficiency of chemical oxygen demand (COD), ammonia nitrogen (NH 4 + -N), total nitrogen (TN), and total phosphorus (TP) in wastewater by the ecological filter, with average removal rates of 83.79%, 93.10%, 52.90%, and 79.07%, respectively. Concentration of NH 4 + -N after treatment met the level-A discharge standard of GB18918-2002. Compared with non-plant filter, the ecological filter improved average removal efficiency of COD, NH 4 + -N, TN, and TP by 13.03%, 25.30%, 14.80%, and 2.32%, respectively: thus, plants significantly contribute to the removal of organic pollutants and nitrogen. Through microporous aeration and O 2 secretion of plants, the ecological filter formed an aerobic–anaerobic–aerobic alternating environment; thus aerobic and anaerobic microbes were active and effectively removed organic pollutants. Meanwhile, nitrogen and phosphorus were directly assimilated by plants and as nutrients of microorganisms. Meanwhile, pollutants were removed through nitrification, denitrification, filtration, adsorption, and interception by the filler. High removal rates of pollutants on the ecological filter proved that it is an effective wastewater-treatment technology for decentralized wastewater of mountainous towns.

Lactobacillus plantarum is an important probiotic and is mostly isolated from fermented foods. We sequenced the genome of L. plantarum strain 5-2, which was derived from fermented soybean isolated from Yunnan province, China. The strain was determined to contain 3114 genes. Fourteen complete insertion sequence (IS) elements were found in 5-2 chromosome. There were 24 DNA replication proteins and 76 DNA repair proteins in the 5-2 genome. Consistent with the classification of L. plantarum as a facultative heterofermentative lactobacillus, the 5-2 genome encodes key enzymes required for the EMP (Embden-Meyerhof-Parnas) and phosphoketolase (PK) pathways. Several components of the secretion machinery are found in the 5-2 genome, which was compared with L. plantarum ST-III, JDM1 and WCFS1. Most of the specific proteins in the four genomes appeared to be related to their prophage elements.

Yond bap is a traditional fermented milk product from the Yunnan province in China. Yond baps are mostly produced with goat’s milk and occasionally with cow’s milk. As a traditional dairy product produced by fermentation, yond bap contains an abundant microflora. The microbes that play a role in the fermentation of goat milk form a specific community structure. In this work, 11 types of yond bap were characterized from four different regions in the Yunnan province. We employed bar-coded pyrosequencing of 16S rRNA to analyze the bacterial community structure in the yond baps. The results indicated that the bacterial community structures of the 11 yond baps were different. Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were detected in all the samples. Pseudomonas, a proteobacterium, was the predominant bacterial genus. Pseudomonas sequences were detected often and in most of the samples. Next, Streptococcaceae, Lactobacillaceae, and Lactococcus belonging to Streptococcaceae family played important roles in the fermentation of yond baps as the numbers of sequences belonging to these species were higher. The results demonstrate the presence of different bacterial community structures of yond baps from different regions in the Yunnan Province of China. This study provides information about the diversity of the microbial community of fermented food and a reliable theoretical foundation for improving the quality and flavor of yond baps.

The gut microbiota is known to have a considerable impact on health; some types of organisms, including bifidobacteria and lactobacilli, are considered to be ‘good’ colonizing bacteria, while other species are potentially pathogenic. The initial colonization of a newborn infant affects his/her health in the future. Recently, research has indicated that the fetus may actually be colonized with bacteria during gestation. Accordingly, this study was conducted to assess the similarities in the bacterial species detected in the infant’s first feces with samples obtained from the mother’s placenta and vagina., BACKGROUND: The gut microbiota plays an important role in human health. It is essential to understand how the composition of the gut microbiota in neonates is established. OBJECTIVES: To investigate the nature of the microbial community in the first feces of newborn infants compared with the mothers’ placentae and vaginas. METHODS: One infant who was delivered via Cesarean section was compared with an infant who was delivered vaginally. Bar-coded pyro-sequencing of 16S ribosomal RNA genes was used to investigate the bacterial community composition and structure of each site. RESULTS: Neonatal feces of both infants had similar bacterial communities, and they were similar to the mother’s placenta regardless of the method of delivery. The vaginal bacterial community differed between the two mothers, but not different sites within the vagina. The bacteria in the neonatal feces and the mothers’ placentae demonstrated considerably higher diversity compared with the vaginas. The family Lactobacillaceae dominated in the vaginal samples, while the most abundant family in the fecal and placental samples was Micrococcineae. CONCLUSIONS: These results may provide new directions for the study of infant gut microbial formation.

Quorum sensing (QS) is a means of cell-to-cell communication that regulates, via small signalling molecules, expression of a series of genes and controls multicellular behaviour in many bacterial species. The enzyme S-ribosylhomocysteine lyase (LuxS) transforms S-ribosylhomocysteine (SRH) into 4, 5-dihydroxy-2, 3-pentanedione (DPD), the precursor of the interspecies QS signalling molecule autoinducer-2 (AI-2). In this study, two LuxS-coding genes, luxS1 and luxS2, with 70% sequence identity were isolated from Lactobacillus plantarum YM-4-3, and overexpressed in Escherichia coli BL21 (DE3), and the protein products were purified successfully. After incubation of LuxS1 or LuxS2 with SRH, the reaction products were able to induce Vibrio harveyi BB170 bioluminescence, clearly demonstrating that both LuxS1 and LuxS2 synthesize AI-2 from SRH in vitro. Ellman's assay results revealed optimal temperatures for LuxS1 and LuxS2 of 45 and 37 °C, respectively, and their activities were stimulated or inhibited by several metal ions and chemical reagents. In addition, enzyme kinetics data showed that Km, Vmax and Kcat value of LuxS1 for the substrate (SRH) were higher than that of LuxS2. These results suggest that LuxS1 and LuxS2 mediate QS in a temperature-dependent manner and may play conserved roles in AI-2 synthesis but exhibit different activities in response to external environmental stress. To our knowledge, this paper is the first report of two luxS genes present in one bacterial genome and the subsequent comparative elucidation of their functions in AI-2 production. Collectively, our study provides a solid basis for future research concerning the AI-2/LuxS QS system in L. plantarum YM-4-3.