Firmicutes Bacteria Research Articles

Structure of the Extracellular Region of the Bacterial Type VIIb Secretion System Subunit EsaA

Gram-positive bacteria use type VII secretion systems (T7SSs) to export effector proteins that manipulate the physiology of nearby prokaryotic and eukaryotic cells. Several mycobacterial T7SSs have established roles in virulence. By contrast, the genetically distinct T7SSb pathway found in Firmicutes bacteria more often functions to mediate bacterial competition. A lack of structural information on the T7SSb has limited the understanding of effector export by this protein secretion apparatus. Here, we present the 2.4Å crystal structure of the extracellular region of the T7SSb subunit EsaA from Streptococcus gallolyticus. Our structure reveals that homodimeric EsaA is an elongated, arrow-shaped protein with a surface-accessible "tip", which in some species of bacteria serves as a receptor for lytic bacteriophages. Because it is the only T7SSb subunit large enough to traverse the peptidoglycan layer of Firmicutes, we propose that EsaA plays a critical role in transporting effectors across the entirety of the Gram-positive cell envelope.

Transcriptome profile of carbon catabolite repression in an efficient l-(+)-lactic acid-producing bacterium Enterococcus mundtii QU25 grown in media with combinations of cellobiose, xylose, and glucose.

Enterococcus mundtii QU25, a non-dairy lactic acid bacterium of the phylum Firmicutes, is capable of simultaneously fermenting cellobiose and xylose, and is described as a promising strain for the industrial production of optically pure l-lactic acid (≥ 99.9%) via homo-fermentation of lignocellulosic hydrolysates. Generally, Firmicutes bacteria show preferential consumption of sugar (usually glucose), termed carbon catabolite repression (CCR), while hampering the catabolism of other sugars. In our previous study, QU25 exhibited apparent CCR in a glucose-xylose mixture phenotypically, and transcriptional repression of the xylose operon encoding initial xylose metabolism genes, likely occurred in a CcpA-dependent manner. QU25 did not exhibit CCR phenotypically in a cellobiose-xylose mixture. The aim of the current study is to elucidate the transcriptional change associated with the simultaneous utilization of cellobiose and xylose. To this end, we performed RNA-seq analysis in the exponential growth phase of E. mundtii QU25 cells grown in glucose, cellobiose, and/or xylose as either sole or co-carbon sources. Our transcriptomic data showed that the xylose operon was weakly repressed in cells grown in a cellobiose-xylose mixture compared with that in cells grown in a glucose-xylose mixture. Furthermore, the gene expression of talC, the sole gene encoding transaldolase, is expected to be repressed by CcpA-mediated CCR. QU25 metabolized xylose without using transaldolase, which is necessary for homolactic fermentation from pentoses using the pentose-phosphate pathway. Hence, the metabolism of xylose in the presence of cellobiose by QU25 may have been due to 1) sufficient amounts of proteins encoded by the xylose operon genes for xylose metabolism despite of the slight repression of the operon, and 2) bypassing of the pentose-phosphate pathway without the TalC activity. Accordingly, we have determined the targets of genetic modification in QU25 to metabolize cellobiose, xylose and glucose simultaneously for application of the lactic fermentation from lignocellulosic hydrolysates.

Gut microbiota and fecal metabolites in captive and wild North China leopard (Panthera pardus japonensis) by comparsion using 16\xa0s rRNA gene sequencing and LC/MS-based metabolomics

BackgroundGut microbes significantly contribute to nutrient digestion and absorption, intestinal health and immunity, and are essential for the survival and environmental adaptation of wild animals. However, there are few studies on the gut microbiota of captive and wild North China leopard (Panthera pardus japonensis).ResultsA total of 10 mainly bacterial phyla were identified in the fecal microbiota of North China leopard, Lachnoclostridium (p = 0.003), Peptoclostridium (p = 0.005), Bacteroides (p = 0.008), Fusobacterium (p = 0.017) and Collinsella (p = 0.019) were significantly higher than those of wild North China leopard. Distinct differences in the fecal metabolic phenotypes of captive and wild North China leopard were found, such as content of l-methionine, n-acetyl-l-tyrosine, pentadecanoic acid and oleic acid. Differentially abundant gut microbes were associated with fecal metabolites, especially the bacteria in Firmicutes and Bacteroidetes, involved in the metabolism of N-acetyl-L-alanine and D-quinovose.ConclusionThis study reports for the first time the differences in gut microbiota abundance between captive and wild North China leopard, as well as significant differences in fecal metabolic phenotypes between two groups.

Mild heat stress changes the microbiota diversity in the respiratory tract and the cecum of layer-type pullets

The present study aimed to research the effects of cyclic heat environment on the microbial diversity and structure of respiratory tract and cecum of chicken. A total of 360 layer-type pullets at 11 wk of age were subjected to different temperature treatments for 10 wk: constant 22°C; cyclic temperature 22°C to 24°C, 22°C to 26°C, 22°C to 28°C, 22°C to 30°C; the ambient temperature increased from 10:00, reached the set point within 1 h, and maintained until 18:00, thereafter the temperature was restored to 22°C; and the relative humidity was maintained at 60%. The result showed that feed intake of the chickens on ambient temperature 30°C group was significantly lower than that of the chickens on ambient temperature 24°C. The white blood cell, red blood cell, lymphocyte, hemoglobin, and pecked-cell volume content were highest at 24°C on 14, 16, and 18 wk. The ratio of CD3+CD4+/CD3+CD8+ T cells was lowest at 30°C. Meanwhile, the abundance of cecum bacteria in chickens at 30°C was lower than that at 24°C. Cyclic heat environment temperature treatment did not significantly affect the concentration of secretory immunoglobulin A in chicken bronchoalveolar lavage fluid (BALF) levels during 10 wk of trial. The diversity index analysis showed that the effect of 24°C on the cecum flora of chickens was optimal. Abundance of Firmicutes bacteria in the lung flora and cecum flora was lower at 30°C than at 24°C group. Similarly, the microorganism, Brevibacillus in the BALF was also significantly lower at 24°C. In conclusion, cyclic 24°C treatment was beneficial for the feed intake, blood routine indexes, microflora structure of the cecum, and respiratory tract in laying pullets.

English

Using phylogenetic analysis of the 16S rRNA gene 43 Gram-positive, spore-forming bacteria of the phylum Firmicutes were isolated, cultured and identified from five hot water springs in South Africa. Thirty-nine isolates belonged to the family Bacillaceae, genus Bacillus (n = 31) and genus Anoxybacillus (n = 8), while four isolates belonged to the family Paenibacillaceae, genus Brevibacillus. The majority of isolates fell into the Bacillus Bergey’s Group A together with Bacillus subtilis and Bacillus licheniformis. One isolate matched Bacillus panaciterrae which has not previously been described as a hot-spring isolate. Three unknown isolates from this study (BLAST <95% match) and three “uncultured Bacillus” clones of isolates from hot springs in India, China and Indonesia listed in NCBI Genbank, were included in the analysis. When bioinformatic tools: Basic Local Alignment Search Tool (BLAST), in silico amplified rDNA restriction analysis (ARDRA), guanine-cytosine (GC) percentage and phylogenetic analysis are used in combination, but not independently, differentiation between the complex Bacillus and closely related species was possible. Identification that relies solely on BLAST of the 16S rRNA sequence can be misleading. Key words: Bacillus, phylogeny, ARDRA, 16S rDNA, South Africa

Anaerobic chain elongation of cornstalk for MCFAs production via mixed culture: pH regulation

Anaerobic fermentation of waste biomass via microbial chain elongation for producing medium-chain fatty acids (MCFAs) is becoming an emerging and economically viable technology. However, due to the large abundant of microbial species and great diversity of microbial metabolic pathways in open cultures, how to achieve the high yields of MCFAs is an important topic. In this study, the effect of pH, as an important parameter for process control, on the production and composition of volatile fatty acids (VFAs) in two cycles of anaerobic chain elongation process with cornstalk as feedstock was investigated, and the 16S rRNA high throughput sequencing was employed to elucidate the mechanism of pH affecting chain elongation process. The results showed that pH significantly influenced the VFAs production and their spectra. At pH 5.6, the VFAs production was 10.0 g/L, which was increased to 15.9 g/L at pH 7.0, and was further increased to 18.8 g/L at pH 9.0. In addition, the metabolic pathways and the VFAs composition in anaerobic fermentation were greatly changed with pH regulation. Under acidic and neutral conditions (pHs of 5.6 and 7.0), the chain elongation was enhanced, and butyrate and caproate were the major products accounting for more than 80%. Specially, under the neutral condition, the caproate concentration reached (3.49±0.17) g/L. However, the pH of 9.0 seriously inhibited the chain elongation, and the major fermentation products were acetate (93.2%) and propionate (5.5%). The second-cycle fermentation with supplementing additional ethanol as an electron donor indicated that pH played the more important role in the chain elongation process for a high level MCFAs production. In the second cycle, the chain elongation reaction did not occur under the acidic conditions. However, when the pH was adjusted from 5.6 to 7.0, the chain elongation reaction was significantly stimulated, and the caproate concentration quickly increased from 1.88 to 11.8 g/L. The results of microbial community analysis showed that the fermentative bacteria of Firmicutes were the dominate population under the neutral pH condition accounting for 49.9%, which was far higher than those under the acidic and alkaline conditions. The strains relating to the chain elongation, such as Clostridium IV , Clostridium XI , Clostridium XIVa , Clostridium XIVb , Clostridium XVIII and Clostridium sensu stricto , were enriched under the neutral and acidic conditions, but not under the alkaline condition. It should be noted that the well-known pure culture bacteria relating to chain elongation, such as Clostridium Kluyveri , were not found in this study. In the second cycle, no significant difference on the relative abundance of strains relating to chain elongation was found between neutral and acidic conditions, suggesting that these strains could survive under the acidic conditions but their activity was inhibited. When the pH was adjusted from 5.6 to 7.0, their activities could quickly recover to produce caproate. The above findings provided an effective regulating strategy for selective production of MCFAs from waste biomass with open cultures of microbial consortia.

High-throughput sequencing analysis of the regulation of intestinal flora in giant pandas with indigestion using a probiotic agent LyPB

This study aimed to investigate the effect of LyPB on the intestinal microflora of giant pandas with indigestion, using high-throughput sequencing (HTS) technology. The species distribution and microfloral density and diversity before and after administration of the LyPB probiotic agent were analyzed. LyPB evidently has the ability to adjust the floral imbalance in the panda’s intestine. To test the effects of LyPB on the microflora of the panda gut, fecal samples were taken from a healthy giant panda (Anan) without administration of LyPB and from a dyspeptic giant panda Yangyang before and after LyPB administration. Compared with the sample obtained from healthy Anan (anan-c) and that obtained from dyspeptic Yangyang before LyPB administration (yangyang1), the sample taken from Yangyang (yangyang2) after LyPB administration displayed a significant increase in the operational taxonomic unit index. An increase in the Chao index indicated an increase in the microfloral richness, while an increase in the Shannon index indicated an increase in microfloral diversity. At phylum and genus levels, a significant increase was observed in the density of probiotic bacteria of phylum firmicutes, genus Streptococcus, while a drastic reduction in the density of Escherichia coli/Escherichia coli Shigella/bacteria of genus Shigella was observed. Data obtained in this study shows that LyPB preparations successfully improve the microbial structure within the panda’s intestinal canal by significantly increasing the effective microbial community and decreasing the number of pathogenic microbes.

Bacteriome and mycobiome and bacteriome-mycobiome interactions in head and neck squamous cell carcinoma.

The etiology of head and neck squamous cell carcinoma (HNSCC) is not fully understood. While risk factors such as positive human papilloma virus (HPV) status, smoking and tobacco use have been identified, they do not account for all cases of the disease. We aimed to characterize the bacteriome, mycobiome and mycobiome-bacteriome interactions of oral wash in HNSCC patients and to determine if they are distinct from those of the oral wash of matched non-HNSCC patients. Oral wash samples were collected from 46 individuals with HNSCC and 46 controls for microbiome analyses. We identified three fungal phyla and eleven bacterial phyla of which Ascomycota (fungi, 72%) and Firmicutes (bacteria, 39%) were the most dominant, respectively. A number of organisms were identified as being differentially abundant between oral wash samples from patients with HNSCC and oral wash samples from those without HNSCC. Of note, strains of Candida albicans and Rothia mucilaginosa were differentially abundant and Schizophyllum commune was depleted in those with HNSCC compared to oral wash from those without HNSCC. Our results suggest that the oral cavity of HNSCC patients harbors unique differences in the mycobiome, bacteriome, and microbiome interactions when compared to those of control patients.

Ursolic acid improves the bacterial community mapping of the intestinal tract in liver fibrosis mice.

Liver fibrosis often appears in chronic liver disease, with extracellular matrix (ECM) deposition as the main feature. Due to the presence of the liver-gut axis, the destruction of intestinal homeostasis is often accompanied by the development of liver fibrosis. The inconsistent ecological environment of different intestinal sites may lead to differences in the microbiota. The traditional Chinese medicine ursolic acid (UA) has been proven to protect the liver from fibrosis. We investigated the changes in the microbiota of different parts of the intestine during liver fibrosis and the effect of UA on these changes based on high-throughput sequencing technology. Sequencing results suggest that the diversity and abundance of intestinal microbiota decline and the composition of the microbiota is disordered, the potentially beneficial Firmicutes bacteria are reduced, and the pathways for functional prediction are changed in the ilea and anal faeces of liver fibrosis mice compared with normal mice. However, in UA-treated liver fibrosis mice, these disorders improved. It is worth noting that the bacterial changes in the ilea and anal faeces are not consistent. In conclusion, in liver fibrosis, the microbiota of different parts of the intestines have different degrees of disorder, and UA can improve this disorder. This may be a potential mechanism for UA to achieve anti-fibrosis. This study provides theoretical guidance for the UA targeting of intestinal microbiota for the treatment of liver fibrosis.

Nicotine exposure during pregnancy alters the maternal gut microbiome and both cecal and plasma short chain fatty acids in Sprague Dawley rats.

Children of mothers that smoke during pregnancy are more likely to be obese and develop high blood pressure, suggesting a developmental origin of these diseases. Evidence now suggests that an imbalance of the bacterial microbes in the gastrointestinal tract may also play an important role these diseases. Thus, the present study was undertaken to test the hypothesis that nicotine‐exposure during pregnancy alters the maternal gut‐microbiome, inducing gut dysbiosis that may be passed on to the child during birth and/or shifts in bacterial metabolites, such as short chain fatty acids (SCFAs), that the fetus is exposed to in utero. To test our hypothesis, age‐matched virgin and pregnant female rats were exposed to nicotine (6 mg/kg/day) or vehicle (saline) via osmotic mini pump, including days 6–18 of pregnancy. Cecal contents, tissue from the proximal colon, and plasma were collected on day 14 of treatment. A two‐way ANOVA (pregnant state x treatment) identified that pregnancy decreased the abundance of bacteria in the phyla Firmicutes, while increasing the abundance of Actinobacteria and Verrucomicrobia compared to virgin rats (P&lt;0.02). Nicotine exposure, independent of pregnancy, further increased the abundance of Actinobacteria (P&lt;0.03) and tended to increase the proportion of Firmicutes and decrease the abundance of Verrucomicrobia. Evaluation of cecal SCFAs identified that pregnancy upregulated the abundance of acetate and propionic acid (P&lt;0.02) and tended to upregulate butyric and hexanoic acid. Conversely, nicotine exposure, independent of pregnancy, decreased cecal acetate (P&lt;0.02), propionic acid (P&lt;0.007), and hexanoic acid (P&lt;0.009) concentrations. Similarly, plasma levels of acetate, propionic, butyric, and valeric acid were upregulated by pregnancy, and nicotine exposure, independent of pregnant state, reversed this trend (P&lt;0.05). Finally, gene expression in the proximal colon identified that pregnancy triggered an upregulation of multiple genes, including the protective enzyme 11‐beta HSD2, the sodium channel ENAC, Ffar2, the SCFA acetate and propionate transporter, the solute carrier SMCT1, and Tph2, the rate limiting enzyme for serotonin production (P&lt;0.05). Independent of pregnancy status, nicotine downregulated the expression of all five genes. These results confirm our hypothesis that nicotine exposure during pregnancy can significantly alter the maternal gut microbiome and affect fetal exposure to specific circulating factors linked to gut microbial metabolism. These findings provide a new link between changes in the maternal gut microbiome and the fetal origins of adult diseases.Support or Funding InformationFL DOH James and Esther King Biomedical Research Program 8JK06

Dairy product intake modifies gut microbiota composition among hyperinsulinemic individuals.

The objectives of this study were to investigate differences in gut microbiota (GM) composition after high dairy intake (HD) compared to adequate dairy intake (AD) and to correlate GM composition variations with the change in glycemic parameters in hyperinsulinemic subjects. In this crossover study, 10 hyperinsulinemic adults were randomized to HD (≥ 4 servings/day) or AD (≤ 2 servings/day) for 6weeks, separated by a 6-week washout period. Fasting insulin and glucose levels were measured after each intervention. Insulin resistance was calculated with the homeostasis model assessment of insulin resistance (HOMA-IR). GM was determined with 16S rRNA-based high-throughput sequencing at the end of each intervention. Paired t test, correlations and machine learning analyses were performed. Endpoint glycemic parameters were not different between HD and AD intake. After HD compared with AD intake, there was a decrease in the abundance of bacteria in Roseburia and Verrucomicrobia (p = 0.04 and p = 0.02, respectively) and a trend for an increase abundance in Faecalibacteria and Flavonifractor (p = 0.05 and p = 0.06, respectively). The changes in abundance of Coriobacteriia, Erysipelotrichia, and Flavonifractor were negatively correlated with the change in HOMA-IR between the AD and HD phases. Furthermore, a predictive GM signature, including Anaerotruncus, Flavonifractor, Ruminococcaceae, and Subdoligranulum, was related to HOMA-IR. Overall, these results suggest that HD modifies the abundance of specific butyrate-producing bacteria in Firmicutes and of bacteria in Verrucomicrobia in hyperinsulinemic individuals. In addition, the butyrate producing bacteria in Firmicutes phylum correlate negatively with insulin resistance.

Growth and intestinal health of the red claw crayfish, Cherax quadricarinatus, reared under different salinities

The purpose of this work was to examine immune regulation and the gut microbiota in the red claw crayfish, Cherax quadricarinatus, raised at four different salinities. Juvenile C. quadricarinatus (18.28 ± 0.03 g) individuals were exposed to four salinity levels 0, 5, 10 and 15 practical salinity units (psu) for 35 days. No significant differences in weight gain, specific growth rate, feed conversion ratio or survival were found among the animals in the four treatment groups, but a significantly higher condition factor was obtained in crayfish raised in water with a salinity of 5 psu than in control crayfish. The superoxide dismutase activity of crayfish reared in water at 5, 10 or 15 psu was significantly higher than that of control crayfish. Catalase activity and total glutathione concentrations were significantly higher in crayfish raised at salinities of 10 and 15 psu than in control crayfish. ProPO gene expression levels decreased significantly in the crayfish in the 5, 10 and 15 psu groups. Toll gene expression levels decreased significantly in the crayfish in the 5 psu and 10 psu groups but increased in crayfish in the 15 psu group compared with the control crayfish. Bacteria of the phylum Tenericutes and bacteria of the genus Candidatus_Bacilloplasma were significantly more abundant in the 5, 10 and 15 psu groups, while the abundance of bacteria in the phylum Firmicutes decreased markedly compared with that in the control. The 5 psu group displayed significantly higher values of the Chao1 and ACE richness estimators than the control group. Microbe-mediated functions predicted by PICRUSt showed that 76.94% of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including environmental information and metabolism, significantly increased in the crayfish in the 5, 10 and 15 psu groups. Taken together, the findings of this study provide guidance for the practical rearing of C. quadricarinatus in brackish water or seawater and contribute to research on stress physiology.

Rhizosphere Microbial Community Structure Is Selected by Habitat but Not Plant Species in Two Tropical Seagrass Beds.

Rhizosphere bacterial community structures and their determining drivers have been studied in a variety of marine and freshwater ecosystems for a range of plant species. However, there is still limited information about the influence of habitat on microbial communities in seagrass beds. This study aimed to determine which factors (habitat and plant species) have crucial roles on the rhizospheric bacteria associated with two tropical seagrass species (Thalassia hemprichii and Enhalus acoroides) that are dominant at Xincun Bay and Tanmen Harbor in Hainan Island, South China. Using Illumina HiSeq sequencing, we observed substantial differences in the bacterial richness, diversity, and relative abundances of taxa between the two habitats, which were characterized differently in sediment type and nutrient status. Rhizospheric bacteria from sandy sediment at the eutrophic Xincun Bay were dominated by Desulfobacteraceae and Helicobacteraceae, which are primarily involved in sulfate cycling, whereas rhizosphere microbes from the reef flat at oligotrophic Tanmen Harbor were dominated by Vibrionaceae and Woeseiaceae, which may play important roles in nitrogen and carbon fixing. Additionally, we speculated that host-specific effects of these two seagrass species may be covered under nutrient-rich conditions and in mixed community patches, emphasizing the importance of the nutrient status of the sediment and vegetation composition of the patches. In addition, our study confirmed that Proteobacteria was more adapted to the rhizosphere environment than to low-carbon conditions that occurred in bulk sediment, which was primarily dominated by well-known fermentative bacteria in the phylum Firmicutes.

Metagenomic Characterization of Intestinal Regions in Pigs With Contrasting Feed Efficiency.

Greater feed efficiency (FE) is critical in increasing profitability while reducing the environmental impact of pig production. Previous studies that identified swine FE-associated bacterial taxa were limited in either sampling sites or sequencing methods. This study characterized the microbiomes within the intestine of FE contrasting Duroc × (Landrace × Yorkshire) (DLY) pigs with a comprehensive representation of diverse sampling sites (ileum, cecum, and colon) and a metagenomic sequencing approach. A total of 226 pigs were ranked according to their FE between weaning to 140 day old, and six with extreme phenotypes were selected, three for each of the high and low groups. The results revealed that the cecum and colon had similar microbial taxonomic composition and function, and had higher capacity in polysaccharide metabolism than the ileum. We found in cecum that the high FE pigs had slightly higher richness and evenness in their micriobiota than the low FE pigs. We identified 12 phyla, 17 genera, and 39 species (e.g., Treponema porcinum, Treponema bryantii, and Firmicutes bacterium CAG:110) that were potentially associated with swine FE variation in cecum microbiota through LEfSe analysis. Species enriched in the cecum of the high FE pigs had a greater ability to utilize dietary polysaccharides and dietary protein according to the KEGG annotation. Analysis of antibiotic resistance based on the CARD database annotation indicated that the macB resistant gene might play an important role in shaping the microbial community in the cecum of pigs with contrasting FE. The bacteria from the genus Prevotella was highly enriched in the cecum of low FE pigs, which may impair the establishment of a more effective nutrient harvesting microbiota because of the interaction between Prevotella and other benefical microbes. These findings improved our understanding of the microbial compositions in the different gut locations of DLY pigs and identified many biomarkers associated with FE variation wich may be used to develop strategies to improve FE in pigs.

Improvement of biogas production in plug flow reactor using biogas slurry pretreated cornstalk

Biogas slurry pretreatment for enhancing the biomethanization of cornstalk was investigated. After pretreating 24 h with a volume proportion of biogas slurry and water of 4:1, the lignin reduction of cornstalk achieved 24.96%, while cellulose and hemicellulose decreased by 19.44%. Meanwhile, a large amount of volatile fatty acids were produced, which mainly composed of acetic acid. The fungi of Ascomycota and Neocallimastigomycota and bacteria of Bacteroidetes and Firmicutes cooperatively dominated the biogas slurry pretreatment. Subsequently, pretreated cornstalk was fermented in a semi-continuous anaerobic plug flow reactor for operated 120 d. The specific biogas and methane yield were up to 0.36 m3/kg VS and 0.21 m3/kg VS, respectively. The bacteria genera Clostridium III, Solibacillus, Sedimentibacter, Proteiniphilum, Petrimonas, Comamonas, and Ornatilinea were further enriched. Methanothrix and Methanobacterium became the dominant methanogen during the operation. These results provide an efficient and environmentally friendly approach for enhancing the lignocellulose to biogas.

Genomic landscape and genetic manipulation of the black soldier fly Hermetia illucens, a natural waste recycler.

The black soldier fly (BSF), Hermetia illucens (Diptera: Stratiomyidae), is renowned for its bioconversion of organic waste into a sustainable source of animal feed. We report a high-quality genome of 1.1 Gb and a consensus set of 16,770 gene models for this beneficial species. Compared to those of other dipteran species, the BSF genome has undergone a substantial expansion in functional modules related to septic adaptation, including immune system factors, olfactory receptors, and cytochrome P450s. We further profiled midgut transcriptomes and associated microbiomes of BSF larvae fed with representative types of organic waste. We find that the pathways related to digestive system and fighting infection are commonly enriched and that Firmicutes bacteria dominate the microbial community in BSF across all diets. To extend its potential practical applications, we further developed an efficient CRISPR/Cas9-based gene editing approach and implemented this to yield flightless and enhanced feeding capacity phenotypes, both of which could expand BSF production capabilities. Our study provides valuable genomic and technical resources for optimizing BSF lines for industrialization.

Enhanced anaerobic co-digestion of fat, oil, and grease by calcium addition: Boost of biomethane production and microbial community shift

This work focused on the application of calcium (0.1–1% w/v) to overcome the inhibition caused by the high loadings (2% v/v) of fat, oil, and grease (FOG) in the context of biomethane production, organic removal, and microbial community shift. Addition of 0.5% calcium showed maximum biomethane production (6-fold increase); biomethane production decreased following the addition of calcium (>0.5%). The highest organic removal rates were 83 and 89% upon the addition of 0.3 and 0.5% calcium, respectively. Addition of calcium facilitated the growth of bacteria of phylum Firmicutes from the Clostridium, Syntrophomonas, and Sedimentibacter genera. The population of members from the genus Methanosaeta increased after the addition of 0.5% calcium, which is one of the factors responsible for high biomethane production. This study demonstrated that addition of calcium is an attractive strategy to avoid the inhibition of the growth of anaerobic microflora due to the presence of high FOG concentrations.

Effects of oral florfenicol on intestinal structure, function and microbiota in mice.

Many kinds of antibiotics have effects on intestinal structure and function. In the current experimental study, we evaluate the effect of oral florfenicol on intestinal barrier in mice. Thirty adult male mice were randomly divided into two groups, the group none (N) and the group florfenicol (F), the mice in group F were orally administered florfenicol 100mg/kg body weight (BW) for 7days. At day 8, mice were euthanized and sampled for the analysis of alterations in genes and proteins from jejunum, jejunum morphology and microbiota analysis. Administration of florfenicol caused higher liver index (P < 0.05). In the jejunum, mucosa injury and villus rupture, compared with the group N, the villus length and V/C (villus length/crypt depth) in group F were marked decrease (P < 0.01). The transcription level of Muc2 and occludin in group F were significantly lower than those in group N (P < 0.01 or P < 0.05). The expression of APRIL, IL-17, IL-22, BAFF and sIgA on protein level were significantly down-regulated (P < 0.01 or P < 0.05), while the expression of IL-10, TGF-β, IL-6, IL-4 were significantly up-regulated (P < 0.01) in group F. The abundances of bacteria in Firmicutes and Lactobacillus decreased significantly (P < 0.01) in group F. Our results indicated that oral administration of florfenicol might have a negative impact on functions of intestinal mucosal barrier, immune system and the intestinal microbiota.

Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring

The composition of mammalian microbiota has been related with the host health status. In this study, we assessed the oral microbiome of 3 cetacean species most commonly found stranded in Iberian Atlantic waters (Delphinus delphis, Stenella coeruleoalba and Phocoena phocoena), using 16S rDNA-amplicon metabarcoding. All oral microbiomes were dominated by Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria bacteria, which were also predominant in the oral cavity of Tursiops truncatus. A Constrained Canonical Analysis (CCA) showed that the major factors shaping the composition of 38 oral microbiomes (p-value < 0.05) were: (i) animal species and (ii) age class, segregating adults and juveniles. The correlation analysis also grouped the microbiomes by animal stranding location and health status. Similar discriminatory patterns were detected using the data from a previous study on Tursiops truncatus, indicating that this correlation approach may facilitate data comparisons between different studies on several cetacean species. This study identified a total of 15 bacterial genera and 27 OTUs discriminating between the observed CCA groups, which can be further explored as microbiota fingerprints to develop (i) specific diagnostic assays for cetacean population conservation and (ii) bio-monitoring approaches to assess the health of marine ecosystems from the Iberian Atlantic basin, using cetaceans as bioindicators.

Expression and purification of affinity-tagged variants of the photochemical reaction center from Heliobacterium modesticaldum.

The heliobacterial photochemical reaction center (HbRC) from the chlorophototrophic Firmicutes bacterium Heliobacterium modesticaldum is the only homodimeric type I RC whose structure is known. Using genetic techniques recently established in our lab, we have developed a rapid heterologous expression system for the HbRC core polypeptide PshA. Our system relies on rescue of the non-chlorophototrophic ∆pshA::cbp2p-aph3 strain of Hbt. modesticaldum by expression of a heterologous pshA gene from a replicating shuttle vector. In addition, we constructed two tagged variants of PshA, one with an N-terminal octahistidine tag and one with an internal hexahistidine tag, which facilitate rapid purification of pure, active HbRC cores in milligram quantities. We constructed a suite of shuttle vectors bearing untagged or tagged versions of pshA driven by various promoters. Surprisingly, we found that the eno and gapDH_2 promoters from Clostridium thermocellum drive better expression of pshA than fragments of DNA derived from the region upstream of the pshA locus on the Hbt. modesticaldum genome. This "pshA rescue" strategy also provided a useful window into how Hbt. modesticaldum regulates pigment synthesis and growth rate when chlorophototrophic output decreases.