Relative Abundance Levels Research Articles

Nisin and Nisin Probiotic Disrupt Oral Pathogenic Biofilms and Restore Their Microbiome Composition towards Healthy Control Levels in a Peri-Implantitis Setting.

Peri-implantitis is characterized by chronic inflammation of the peri-implant supporting tissues that progressively and irreversibly leads to bone loss and, consequently, implant loss. Similar to periodontal disease, oral dysbiosis is thought to be a driver of peri-implantitis. However, managing peri-implantitis with traditional treatment methods, such as nonsurgical debridement or surgery, is not always successful. Thus, novel strategies have been proposed to address these shortcomings. One strategy is the use of probiotics as antimicrobial agents since they are considered safe for humans and the environment. Specifically, the probiotic Lactococcus lactis produces nisin, which has been used worldwide for food preservation. The objective of this study was to determine whether nisin and the wild-type (WT) nisin-producing L. lactis probiotic can disrupt oral pathogenic biofilms and promote a healthier oral microbiome within these oral biofilms on titanium discs. Using confocal imaging and 16S rRNA sequencing, this study revealed that nisin and WT L. lactis probiotic disrupt oral pathogenic biofilms in a peri-implantitis setting in vitro. More specifically, nisin decreased the viability of the pathogen-spiked biofilms dose-dependently from 62.53 ± 3.69% to 54.26 ± 3.35% and 44.88 ± 2.98%, respectively. Similarly, 105 CFU/mL of WT L. lactis significantly decreased biofilm viability to 52.45 ± 3.41%. Further, both treatments shift the composition, relative abundance, and diversity levels of these biofilms towards healthy control levels. A total of 1 µg/mL of nisin and 103 CFU/mL of WT L. lactis were able to revert the pathogen-mediated changes in the Proteobacteria (from 80.5 ± 2.9% to 75.6 ± 2.0%, 78.0 ± 2.8%, and 75.1 ± 5.3%, respectively) and Firmicutes (from 11.6 ± 1.6% to 15.4 ± 1.3%, 13.8 ± 1.8%, and 13.7 ± 2.6%, respectively) phyla back towards control levels. Thus, nisin and its nisin-producing L. lactis probiotic may be useful in treating peri-implantitis by promoting healthier oral biofilms, which may be useful for improving patient oral health.

Comparison and Correlation Analysis of Immune Function and Gut Microbiota of Broiler Chickens Raised in Double-Layer Cages and Litter Floor Pens.

ABSTRACTThis study aimed to compare the immune function and gut microbiota between double-layer caged and litter floor pen-raised broiler chickens. Eighty meaty male chicks were selected and divided into cage group and litter floor group, with 20 replicates in each group. The broilers were raised in the same chicken house. The rearing density of the two rearing systems was same. The broilers were sampled on days 13 and 34. The results showed that compared with the cage group, the litter floor broilers had worse growth performance (23.24% increase in feed conversion ratio) in the early stage; better slaughter performance at day 42; stronger peripheral immune function (including higher lysozyme activity, T-cell ratio, Th-cell ratio, Tc-cell ratio, CD4/CD8, IL-10, B-cell ratio, IgG and IgA levels; and spleen immune-related gene expression); and stronger intestinal immune function (including higher ileum CD80, AvBD2, Mucin2, NF-κB, IL-8, IFN-γ/IL-4, and IgA mRNA expression levels and ileal mucosa sIgA levels). Compared with the cage group, the alpha diversity of ileum microbiota of the litter floor broilers was higher, and the relative abundance levels of litter breeding bacteria (Facklamia, Globicatella, and Jeotgalicoccus) and potential pathogenic bacteria (Streptococcus and Staphylococcus) were higher (P < 0.05). Through Spearman correlation analysis, it was found that enriched microbes in the ileum of litter floor broilers were positively correlated with immune function. In summary, compared with cage broilers, litter floor broilers had more potential pathogenic bacteria and litter breeding bacteria in the ileum, which may be one of the important reasons for the stronger immune function status.IMPORTANCE In China, the three-dimensional rearing system (cage) for broilers has gradually become a trend. In production, it was found that the incidence of disease in broiler chickens raised in cage systems was significantly higher than that of ground litter. Given that broilers raised on ground litter systems may be exposed to more environmental microbes, it is important to understand whether the rearing environment affects the function and status of the host immune system by altering the gut microbiota. In this study, rearing environment-derived gut microbes associated with stronger immune function in ground litter broilers were provided, which will provide new insights into strategies to target gut microbes to promote immune function and status in broilers raised in cages.

Tanggap Parasitoid Braconidae (Hymenoptera) Terhadap Hama Invasif Liriomyza trifolii (Burgess) (Diptera: Agromyzidae) pada Tanaman Sayuran dan Hias di Bali

Response of Braconid Parasitoid Against Invasive Pest, Liriomyza trifolii (Burgess) (Diptera: Agromyzidae) on Vegetable and Ornamental Crops in Bali. Research on the respopnse of Braconid parasitoids to the invasive pest, Liriomyza trifolii that attacks ornamental plants and vegetables in Bali, was carried out from September 2020 to March 2021. This study aimed to determine the type and abundance of parasitoid populations that responded to Liriomyza trifolii on host plants in the field. In addition, this study also aims to evaluate the level of parasitization of each parasitoid against L. trifolii. This study used a purposive sampling method by taking leaf samples that showed active symptoms of Liriomyza larvae in the leaves of plants. The research focused on vegetables and ornamental plants cultivated in lowlands &lt;500 meters above sea level (masl), mediumlands 500-1000 meters above sea level and highlands&gt; 1000 meters above sea level. The results showed that there were two species of Braconid parasitoids that responded to Liriomyza trifolii in the field, namely Opius dissitus and Opius cromatomiyae. The relative abundance and degree of parasitization of the two parasitoids showed variation between host plant species and altitude. The relative abundance of O. dissituse was high in chrysanthemum (10.81%) at an altitude of &gt;1000 masl and low in long beans (0.53%) at an altitude of &lt;500 masl. The highest relative abundance of O. cromatomiyae was in marigold flowers (51.18%) at an altitude of &lt;500 masl and the lowest was in chrysanthemum (44.83%) at an altitude of &gt; 1000 masl. The highest level of parasitization of O. dissitus was found in pakcoy plants (50.00%) at an altitude of &gt;1000 masl and the lowest was in mustard plants (6.06%) at an altitude of &lt;500 masl. The highest level of parasitization of O. cromatomiyae was in celery (33.33%) at an altitude &lt;500 masl and the lowest was in tomato plants (25.00%) at an altitude&gt; 1000 masl. Both species of Braconid parasitoids have high potential as biological control agents for L. trifolii as indicated by their relative abundance and high levels of parasitization against these invasive pests.

High salinity slowed organic acid production from acidogenic fermentation of kitchen wastewater by shaping functional bacterial community

The high salinity of kitchen wastewater might have adverse effects on the production of short-chain fatty acids (SCFAs) in anaerobic fermentation. The effects and mechanisms of salinity on SCFA production in the anaerobic fermentation of kitchen wastewater were studied by varying the salt concentration, as follows: 0 g/L (S0), 2 g/L (S2), 6 g/L (S6), 10 g/L (S10), 15 g/L (S15), and 20 g/L (S20). Experimental results showed that hypersaline conditions (>10 g NaCl/L) accelerated the release of soluble proteins at the initial stage of anaerobic fermentation. They also significantly prohibited the hydrolysis and degradation of soluble proteins and carbohydrates. Compared with low salinity tests, the SCFA concentrations under hypersaline conditions (>10 g NaCl/L) only reached approximately 43% of the highest concentration on day 10, although the SCFA concentrations in all tests were very close on day 10 (14 g COD/L). High salinity delayed the production of n-butyric acid but did not change the composition of the total SCFAs. High salinity enriched Enterococcus and Bifidobacterium, the relative abundance levels of which reached 27.57% and 49.71%, respectively, before the depletion of substrate. High salinity showed a negative correlation with the relative abundance of the genera Clostridium_sensu_stricto_1, Prevotella and unclassified_f_Oscillospiraceae which are responsible for SCFA production. This study provided a theoretical basis for the fficient utilization of kitchen wastewater.

Pollution Characteristics and Driving Factors of Antibiotic Resistance Genes in Dexing Copper Mine

Environmental antibiotic resistance genes (ARGs) are a type of emerging pollutant that has been widely concerning. However, investigations into the contamination of ARGs in mining areas have been scarce. Here, the types, abundances, and influencing factors of ARGs and mobile genetic elements (MGEs) were investigated in soil/sediment of the Dexing copper mine area in June 2019 by using high-throughput quantitative polymerase chain reaction (HT-qPCR). Furthermore, the influence of heavy metals and MGEs factors on ARGs was studied using the multivariate statistical analysis method. The results showed that there were a variety of ARGs in the Dexing copper mining area, and the maximum detected number of ARGs was 70. At the relative abundance level, the relative abundance of individual sites reached 0.085. In the Dexing copper mine, multidrug, MLSB, β-lactamases, tetracycline, and aminoglycoside resistance genes were the dominant ARG classes based on their numbers. The efflux pump was the most dominant resistance mechanism, followed by antibiotic deactivation and cellular protection. There was a significant positive correlation between the abundance of ARGs and MGEs (P<0.05), and TnpA04 and Inti1 were the most important MEGs in Dexing copper mine samples, indicating that horizontal gene transfer might be an important mechanism for the spread of environmental ARGs. The results of Pearson correlation analysis and RDA analysis showed that the content of Cu was significantly positively correlated with the detected numbers and abundance of ARGs (P<0.05), suggesting that the high content of Cu in the Dexing copper mining area might be an important driving factor for the formation of ARGs.

Gut Microbiota Diversity and Overweight/Obesity in Infancy: Results from a Nested Case-control Study.

Childhood obesity is a major health concern worldwide. Previous studies have explored the relationship between obesity and gut microbiota. However, the results from such studies remain contradictory. In the present nested case-control study, based on a twin birth cohort study, the relationship between gut microbiota diversity and overweight/obesity in 1- and 6-month-old infants was explored. Twins were enrolled when one child had normal weight and the other child was overweight/obese at six months old. For both infants, stool samples were collected at 1 and 6 months of age. Finally, 12 twins were enrolled in the study. The gut microbiota was identified by 16S rRNA gene sequencing in the V3-V4 area. Six of the twins were monozygotic. The results revealed that the microbiota communities of monozygotic twins were similar to those of dizygotic twins. The relative abundance (RA) of microbiota of 1-month-old twins was significantly higher than that of 6-month-old twins. However, the microbiota diversity of 1-month-old twins was significantly lower than that of 6-month-old twins. In addition, 6-month-old twins had significantly higher RA levels of Bifidobacterium and Lachnospiracea incertae sedis than 1-month-old twins. The 6-month-old group had significantly lower RA levels of Veillonella, Klebsiella, Akkermansia, Streptococcus, or Staphylococcus than the 1-month-old group. At six months, the RA level of Clostridium sensu stricto was higher in the overweight/obesity group than the normal-weight group. These findings imply that changes in gut microbiota diversity during infancy may contribute to the development of obesity in early infancy.

Sexual Dimorphism, Length-Weight Relationships, Fecundity, and Diet of the Striped Eel Catfish &amp;lt;i&amp;gt;Plotosus lineatus&amp;lt;/i&amp;gt; (Plotosidae) on Taiwan’s Southwest Coast

This study of feeding guild fish from the same coast of subtropics helps to suggest conservation of fishery resources. A total of 2,537 specimens of Plotosus lineatus (Plotosidae) were collected from July 2013 to March 2019 on the coast of Taiwan. The average total body length (TL) was 23.7 cm ± 4.7 cm and 20.3 cm ± 2.9 cm, and the average body weight (W) was 94.1 g ± 59.6 g and 56.6 g ± 30.8 g among 174 males and 630 females, respectively. The LWRs of male and female were ln(W)M = 3.2914 × ln (TL) − 6.0395, and ln(W)F = 3.0917 × ln(TL) − 5.3629. The male specimens were large than female in TL and W. The average OSW/TL ratios were 0.722 ± 0.044 and 0.649 ± 0.029 among 41 male and 49 female specimens, respectively. The OSW of the male head was wider than that of the female head (F = 91.5; p P. lineatus exhibits significant sexual dimorphism. The average eggs number of each female was 2375.6 eggs/individual ± 1140.9 eggs/individual (N = 161). The major prey of P. lineatus were shrimps, crabs, and fishes; the total relative frequencies of occurrence of the prey were 57.1%, 32.6%, and 37.2%, respectively (N = 282), and their total relative abundance levels were 40.2%, 26.3%, and 25.8%, respectively (N = 445). Proper scientific knowledge management will improve the development of fisheries.

Spatiotemporal Distribution of Two Euschistus spp. Stink Bugs (Hemiptera: Pentatomidae) in Southeastern Farmscapes.

Stink bugs (Hemiptera: Pentatomidae) are ubiquitous, cryptic, phytophagous pests that are found in many crops. In agroecosystems, individuals disperse from adjacent noncrop hosts and tend to aggregate or cluster within fields. In this study, we characterized the distribution of Euschistus servus (Say) and Euschistus tristigmus (Say) (Hemiptera: Pentatomidae) over 2 yr at three southeastern United States farmscapes. Stink bugs were captured in pheromone-baited traps, and Spatial Analysis by Distance Indices (SADIE) used to identify the location of significant aggregations by habitat type and season. Euschistus servus adults were more likely to be captured in pecan orchards, cotton, other crops, or unmanaged habitats than in woodland habitats. Significant aggregations of E. servus were detected in a variety of habitats including pecan, corn, cotton, peanut, and tobacco, as well as fallow and hay fields, pastures, and hedgerows. Fewer adult E. tristigmus were captured than E. servus adults, and E. tristigmus adults were typically trapped and aggregated in woodland habitats. The resulting data provide an important understanding regarding the seasonal movement and relative abundance levels of stink bug populations, which are critical to the development of integrated pest management strategies.

Application of Metabolomics to Identify Potential Biomarkers for the Early Diagnosis of Coronary Heart Disease.

Coronary heart disease (CHD) is one of the leading causes of deaths globally. Identification of serum metabolic biomarkers for its early diagnosis is thus much desirable. Serum samples were collected from healthy controls (n = 86) and patients with CHD (n = 166) and subjected to untargeted and targeted metabolomics analyses. Subsequently, potential biomarkers were detected and screened, and a clinical model was developed for diagnosing CHD. Four dysregulated metabolites, namely PC(17:0/0:0), oxyneurine, acetylcarnitine, and isoundecylic acid, were identified. Isoundecylic acid was not found in Human Metabolome Database, so we could not validate differences in its relative abundance levels. Further, the clinical model combining serum oxyneurine, triglyceride, and weight was found to be more robust than that based on PC(17:0/0:0), oxyneurine, and acetylcarnitine (AUC = 0.731 vs. 0.579, sensitivity = 83.0 vs. 75.5%, and specificity = 64.0 vs. 46.5%). Our findings indicated that serum metabolomics is an effective method to identify differential metabolites and that serum oxyneurine, triglyceride, and weight appear to be promising biomarkers for the early diagnosis of CHD.

Effects of a traditional Chinese medicine formula containing the Coix seed and Lotus seed on the intestinal morphology and microbiota of local piglets

A traditional Chinese medicine formula based on the Coix seed and Lotus seed has been used as a general treatment of malnutrition, excessive fatigue, dysfunction of the spleen and stomach, and disorders of water transport in humans in China. However, there is limited information on its effects on the gut microbiota of piglets in vivo. In this study, the mix of Coix seed and Lotus were added the diet of forty weaned piglets (local piglets), and then evaluated it’s affected on the gut microbiota of piglets and on the relations within the gut bacterial community. The results indicated that this traditional Chinese medicine formula (LM) and the extract of the traditional Chinese medicine formula (LMT) downregulated pH of succus gastricus and raised pH of the ileum, and LMT obviously decreased the feed conversion ratio. Further study showed LMT and LM also significantly increased the thick and long of gastrointestinal villi. And then, 16S ribosomal DNA sequencing revealed that groups LMT and LM have higher relative abundance of the genus Lactobacillus in the colon, succus gastricus, and jejunum, which are beneficial bacteria sold as dietary supplements to aid digestion or to augment health. Meanwhile, the relative abundance levels of Prevotellaceae, Alloprevotella, and Prevotella in the colon and Clostridium in succus gastricus and jejunum were lower. These experiments highlight the usefulness of the traditional Chinese medicine formula based on the Coix seed and Lotus seed for decreasing pH in succus gastricus, for improving the structure of intestinal villi and gut microflora, and then for achieving improvements in pig production performance.

Nanofiber could deliver lactic acid bacteria to the intestine of ruminant in vitro experiment.

This study investigates the use of nanofiber microcapsules produced by electrostatic spinning as a carrier for the delivery of lactic acid bacteria (LAB) to the intestine of ruminants. We hypothesized that the LAB encapsulated into nanofiber microcapsules can be delivered to a ruminant's intestinal tract with little effect on the rumen fermentation and related bacteria. The in vitro experiment included three treatments: control group; 0.01g Lactobacillus acidophilus NCFM (L. acidophilus NCFM) encapsulated in nanofiber microcapsules by electrostatic spinning group (ELAN, 2.0×1011 CFU/g); and 0.01g L. acidophilus NCFM powder group (LANP, 2.0×1011 CFU/g), each incubated with 30ml of buffer rumen fluid for 48h to determine the effect on rumen fermentation, then the abundance of L. acidophilus NCFM in the intestine was estimated using the modified in vitro three-step procedure. Treatment responses were statistically analysed using one-way ANOVA. The results showed that compared to the control, the ELAN group had a significant increase in pH (p<0.05), while the LANP group had a non-significant decrease in pH (p>0.05). LANP and ELAN groups had no significant influence on total volatile fatty acid and individual volatile fatty acids (p>0.05), apart from isobutyric acid of both groups, which reduced (p<0.05). ELAN group had a decreasing trend of gas production and dry matter digestion, while the LANP group increased them significantly (p<0.05). During the 16h and 48h rumen incubation, compared with control, there was no significant change in all bacteria in the ELAN group (p>0.05), while the LANP group increased the relative abundance levels of S. bovis, S. ruminantium, M. elsdenii, F. succinogenes, B. fibrisolvens, Lactobacillus, L. acidophilus NCFM (p<0.05). In the intestinal part, compared with control, the relative abundance of L. acidophilus NCFM in the ELAN group increased significantly (p<0.05), while the result was not observed in the LANP group. We concluded based on our findings that L. acidophilus NCFM could be protected by nanofiber microcapsules and delivered to the intestinal site with little influence on the rumen fermentation and bacterial community, suggesting nanofiber microcapsules prepared by electrospinning technology could be used as a carrier for rumen-protected study.

Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses

BackgroundAbortion in horses leads to economic and welfare losses to the equine industry. Most cases of equine abortions are sporadic, and the cause is often unknown. This study aimed to detect potential abortigenic pathogens in equine abortion cases in Australia using metagenomic deep sequencing methods.ResultsAfter sequencing and analysis, a total of 68 and 86 phyla were detected in the material originating from 49 equine abortion samples and 8 samples from normal deliveries, respectively. Most phyla were present in both groups, with the exception of Chlamydiae that were only present in abortion samples. Around 2886 genera were present in the abortion samples and samples from normal deliveries at a cut off value of 0.001% of relative abundance. Significant differences in species diversity between aborted and normal tissues was observed. Several potential abortigenic pathogens were identified at a high level of relative abundance in a number of the abortion cases, including Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Streptococcus equi subspecies zooepidemicus, Pantoea agglomerans, Acinetobacter lwoffii, Acinetobacter calcoaceticus and Chlamydia psittaci.ConclusionsThis work revealed the presence of several potentially abortigenic pathogens in aborted specimens. No novel potential abortigenic agents were detected. The ability to screen samples for multiple pathogens that may not have been specifically targeted broadens the frontiers of diagnostic potential. The future use of metagenomic approaches for diagnostic purposes is likely to be facilitated by further improvements in deep sequencing technologies.

A new approach to suppress methane emissions from rice cropping systems using ethephon

Rice is the main staple food for more than half of the world's population. Yet, rice cultivation is subjected to criticism because of its important role in methane (CH4) emissions. Although several agronomic practices such as controlled irrigation and conservation tillage have been widely adopted to mitigate CH4 emissions from rice cultivation, the benefits gained by these practices are highly dependent on site-specific soil and climate conditions, and often offset by yield reduction. The use of plant growth regulating compounds having the potential to increase the crop yield and mitigate CH4 emissions may be an innovative approach to sustainable agriculture. Ethylene (C2H4), a plant growth regulator is known to have a strong inhibitory effect on methanogenesis. However, due to gaseous form and low water solubility, C2H4 has not been used to suppress methanogenesis in paddy fields. To develop C2H4 as a prospective soil amendment for reducing methane (CH4) emissions, ethephon (2-Chloroethylphosphonic acid), a precursor of C2H4 was tested. We found that ethephon reduced CH4 formation by 43%, similar to other well known methanogenic inhibitors (2-Bromoethanesulfonate, 2-Chlomoethanesulfonate, 2-Mercaptoethanesulfonate). However, ethephon rapidly hydrolyzed to C2H4 and methanogenic activity recuperated completely after C2H4 removal. To slow down the release of C2H4, ethephon was mixed with bio-degradable polymers such as cellulose acetate and applied to paddy soils. We found that compared with the control, the C2H4 release of ethephon slowed down to 90 days, and the CH4 emissions were reduced by 90%. The application of ethephon at lower concentrations did not significantly alter bacterial communities, their relative abundance, and the abundance of methanotrophs, but it significantly reduced archaeal communities and the relative abundance and expression level of methanogens in paddy soils. Results suggest that cellulose acetate-mixed ethephon has great promise to suppress CH4 emissions in rice paddies while ensuring sustainable yields.

The “neighbor avoidance effect” of microplastics on bacterial and fungal diversity and communities in different soil horizons

Microplastics are a new type of environmental pollutant, and pose a serious threat to soil ecosystems. It is important to study microplastics effects on soil microorganisms to better understand their effects on terrestrial ecosystems. Therefore, we collected soil and microplastic samples from corn, pepper, peanut and cucumber fields in Shunyi District, Beijing, China, and used Illumina MiSeq high-throughput sequencing technology to analyze bacterial and fungal community composition and diversity. We focused on microplastic surface and its surrounding “rhizosphere-like” soil in the 0–10 cm (humus) and 10–20 cm (eluvial) deep horizons. Microbial richness and diversity on microplastic surface were significantly lower than those in surrounding “rhizosphere-like” soil, and microbial richness and diversity were reduced to a greater extent in the humus horizon than in the eluvial horizon. Microplastics likely enriched the microbes involved in their biodegradation. The relative abundance levels of Cyanobacteria and Basidiomycota on microplastic surfaces were significantly higher than those in surrounding “rhizosphere-like” soil, while the relative abundance levels of Acidobacteria, Chloreflexi, and Mortierellomycota were higher in “rhizosphere-like” soil. Furthermore, the relative abundance levels of pathways related to human diseases, animal pathogen, and fungal parasites were significantly higher on microplastic surfaces than in “rhizosphere-like” soil. These results show that the microbial diversity, richness, community structure and function between microplastic surfaces and surrounding “rhizosphere-like” soil are significantly different, leading to a “rhizosphere-like neighbor avoidance effect” between microplastic surfaces and the surrounding soil.

Identification of altered cell signaling pathways using proteomic profiling in stable and progressive chronic lymphocytic leukemia

Chronic lymphocytic leukemia (CLL) is characterized by significant biologic and clinical heterogeneity. This study was designed to explore CLL B-cells' proteomic profile in order to identify biologic processes affected at an early stage and during disease evolution as stable or progressive. Purified B cells from 11 untreated CLL patients were tested at two time points by liquid chromatography-tandem mass spectrometry. Patients included in the study evolved to either progressive (n=6) or stable disease (n=5). First, at an early stage of the disease (Binet stage A), based on the relative abundance levels of 389 differentially expressed proteins (DEPs), samples were separated into stable and progressive clusters with the main differentiating factor being the RNA splicing pathway. Next, in order to test how the DEPs affect RNA splicing, a RNA-Seq study was conducted showing 4217 differentially spliced genes between the two clusters. Distinct longitudinal evolutions were observed with predominantly proteomic modifications in the stable CLL group and spliced genes in the progressive CLL group. Splicing events were shown to be six times more frequent in the progressive CLL group. The main aberrant biologic processes controlled by DEPs and spliced genes in the progressive group were cytoskeletal organization, Wnt/β-catenin signaling, and mitochondrial and inositol phosphate metabolism with a downstream impact on CLL B-cell survival and migration. This study suggests that proteomic profiles at the early stage of CLL can discriminate progressive from stable disease and that RNA splicing dysregulation underlies CLL evolution, which opens new perspectives in terms of biomarkers and therapy.

Bacterial Community Changes in Penaeus vannamei Boone, 1931 Surface and Rearing Water During Enterocytozoon hepatopenaei Infection

White faeces syndrome is one of the major disease problems in shrimp aquaculture, resulting in enormous economic losses to farmers. Although white faeces syndrome is usually associated with Enterocytozoon hepatopenaei (EHP) infections, it may not be the sole cause for the occurrence of white faecal strings on the pond water surface. There is limited information on the microbial dynamics in a pond affected by white faeces syndrome. Hence, this study aimed at the bacterial community changes occurring on the surface of shrimp Penaeus vannamei Boone, 1931 afflicted by the white faeces syndrome and the pond water in which it was reared. The pond water and the shrimp surface shared &gt;45 % of the operational taxonomic units (OTUs), reflecting the influence of water quality on the bacterial community composition on the shrimp surface. Among these, the Proteobacteria formed the principal phyla and remained unaltered throughout the culture period. Bacteroidetes formed the second largest group across samples, followed by Cyanobacteria, Actinobacteria, Planctomycetes, Verrucomicrobia and Chloroflexi. The relative abundance levels of health indicator bacterial families such as Thiotrichaceae,Microbacteriaceae and Chitinophagaceae showed significant fluctuations on the shrimp surface. Disease indicators such as Rickettsiaceae, Mycobacteriaceae showed an increase in numbers on the shrimp surface. PICRUSt functional predictions revealed higher abundances of genes involved in metabolism and genetic information processing. The study provides valuable findings on the bacterial communities of rearing water and shrimp surface associated with white faeces syndrome.

Improvement of Gut Barrier Function by Potato Anthocyanins Is Dependent on Gut Microbiota

Abstract Objectives Ulcerative colitis (UC) is characterized by chronic colonic inflammation, impaired barrier function and gut bacterial dysbiosis. Anthocyanin-containing potatoes have been shown to maintain the intestinal barrier function in colitic mice. However, the role of gut microbiota in the anti-colitic effects of anthocyanin-containing potatoes is not clear. This study evaluated the gut barrier protective efficacy of purple- and red-fleshed potatoes using a DSS-induced murine model of colitis with the intact and antibiotic-depleted microbiota. Methods Four-week-old mice (C57BL6) were randomized into four groups, receiving a standard control diet, or a 20% purple-/red-fleshed potato (PP/RP) supplemented diet. A broad-spectrum antibiotic cocktail was used to deplete the gut bacteria. After eight weeks, mice were treated with 2% DSS in their drinking water for five days to induce colitis. The polyphenol composition of potatoes was analyzed by LC-MS/MS. Intestinal permeability was measured using FITC-dextran. Colonic myeloperoxidase (MPO) activities were determined using the o-dianisidine dihydrochloride method. The fecal short-chain fatty acids (SCFA) content of mice was measured by GC-FID. RT-PCR was used to analyze the relative gene expression levels of cytokines and bacterial abundance. Results The predominant anthocyanin detected in RP was pelargonidin (93.13%). Whereas petunidin (75.57%) and malvidin (21.05%) were the two major anthocyanins present in PP. Administration of antibiotics resulted in a reduction in fecal SCFA. Antibiotic-treated mice were more prone to the DSS-induced increase in gut permeability. Anthocyanin-containing potato diets alleviated DSS-induced colonic damage, elevation in histology score and gut permeability only in non-antibiotic mice. RP alone suppressed the elevated colonic MPO activity and the gene expression levels of MUC2 in mice with intact gut microbiota. Conclusions In summary, anthocyanin-containing potatoes alleviated colitis-associated colonic epithelial damage and increased gut permeability in intact microbiota mice but not in microbiota-ablated mice. This suggests that the gut microbiome is essential for the gut barrier protective activity of anthocyanin-containing potatoes. Funding Sources USDA-NIFA awards 2016–67,017-29,285 and 2019–67,017-29,258.

Sowing enriched pastures for extensive livestock enhances the abundance of birds and arthropods in Mediterranean grasslands

A great number of farmland wildlife species has shown a sharp population decline in European countries, mainly caused by changes in agricultural practices leading to habitat alterations. Within this scenario, the identification of agricultural practices providing economic benefits to farmers and, at the same time, favoring higher biodiversity levels is a key challenge. This is especially interesting in Mediterranean livestock farming environments where bird numbers decrease due to intensification. Aiming at assessing the benefit to biological diversity of certain types of management practices in grasslands, we experimentally planted enriched pastures. Through a monitoring program of the bird and arthropod communities performed in Extremadura (W Spain) during 2 years (2016–2018), we compared relative richness of birds, abundance, and density values of birds and arthropods between treatment (three plots with enriched pastures) and control areas (six plots of natural grasslands). We found that enriched pastures had higher levels of relative abundance and density of wildlife with respect to natural grasslands and provided a greater variability and availability of trophic resources to birds. Habitat use by birds and arthropods not only depended on the type of pastures but also on the season, the study area, the presence of livestock and the vegetation height. Sowing enriched pastures constitutes a proactive measure stimulating biodiversity in Mediterranean extensive livestock farms that is also beneficial at the socioeconomic level. Therefore, co-financing this measure within the framework of subsidies from the Common Agricultural Policy of the European Union, as well as its inclusion in the future operational programs approved by the authorities, are essential.

Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn\u2019s disease

BackgroundThis study aims to characterize, the gut and oral microbiome in Asian subjects with Crohn’s disease (CD) using whole genome shotgun sequencing, thereby allowing for strain-level comparison.MethodsA case–control study with age, sex and ethnicity matched healthy controls was conducted. CD subjects were limited to well-controlled patients without oral manifestations. Fecal and saliva samples were collected for characterization of gut and oral microbiome respectively. Microbial DNA were extracted, libraries prepared and sequenced reads profiled. Taxonomic diversity, taxonomic association, strain typing and microbial gene pathway analyses were conducted.ResultsThe study recruited 25 subjects with CD and 25 healthy controls. The oral microbe Streptococcus salivarius was found to be enriched and of concordant strains in the gut and oral microbiome of Crohn’s disease subjects. This was more likely in CD subjects with higher Crohn’s Disease Activity Index (184.3 ± 2.9 vs 67.1 ± 82.5, p = 0.012) and active disease status (Diarrhoea/abdominal pain/blood-in-stool/fever and fatigue) (p = 0.016). Gut species found to be significantly depleted in CD compared to control (Relative abundance: Median[Range]) include: Faecalibacterium prausnitzii (0.03[0.00–4.56] vs 13.69[5.32–18.71], p = 0.010), Roseburia inulinivorans (0.00[0.00–0.03] vs 0.21[0.01–0.53], p = 0.010) and Alistipes senegalensis (0.00[0.00–0.00] vs 0.00[0.00–0.02], p = 0.029). While Clostridium nexile (0.00[0.00–0.12] vs 0.00[0.00–0.00], p = 0.038) and Ruminococcus gnavus (0.43[0.02–0.33] vs 0.00[0.00–0.13], p = 0.043) were found to be enriched. C. nexile enrichment was not found in CD subjects of European descent. Microbial arginine (Linear-discriminant-analysis: 3.162, p = 0.001) and isoprene (Linear-discriminant-analysis: 3.058, p < 0.001) pathways were found at a higher relative abundance level in gut microbiome of Crohn’s disease.ConclusionsThere was evidence of ectopic gut colonization by oral bacteria, especially during the active phase of CD. Previously studied gut microbial differences were detected, in addition to novel associations which could have resulted from geographical/ethnic differences to subjects of European descent. Differences in microbial pathways provide possible targets for microbiome modification.

Differences in the gut microbiota between young and elderly persons in Korea

The gut microbiota differs among countries owing to the prevailing diet composition. For the characterization of the gut microbiota of Koreans at different ages in future studies, e.g., in an in vitro human digestion model, we tried to investigate whether the gut microbiota differs between the young and elderly in Korea. Two hundred fecal samples were collected: 100 from elderly people (over 65 years old) at geriatric nursing hospitals and 100 from young people (university students, 20-25 years old) in Gyeonggi province, Korea. The composition of the gut microbiota in these fecal samples was analyzed by next-generation sequencing methods. There were significant differences in the taxonomic composition of the microbiota (the top 10 most abundant taxa) between the young and elderly people in Korea, especially in terms of relative abundance levels of bacteria in phyla Firmicutes, Proteobacteria, Tenericutes, and Fusobacteria (P < 001). The gut microbiota of young people contained higher relative abundance of Lactobacillus than did the microbiota of elderly people, while the microbiota of elderly people manifested higher relative abundance of Escherichia. Even though the sample size may not be large enough for this study to be representative of the entire population of Korea, the study still provides data that are suggestive of differences in the gut microbiota between young and elderly people in Korea. Furthermore, our findings may be applied to develop an improved age-based in vitro model of digestion of Koreans for future research.