First report of human infection by Rhodoplanes sp., Alphaproteobacteria in China

Application of nematicide avermectin enriched antibiotic-resistant bacteria and antibiotic resistance genes in farmland soil

The extensive use of antibiotics in medicine and agriculture has resulted in the accumulation of antibiotic-resistant microorganisms and antibiotic resistance genes (ARGs) in environments, which threaten human health and contaminate environment. Nematicide avermectin is widely applied to control root-knot nematodes. The effect of five-years application of avermectin on rhizosphere microbiome and resistome of sick tobacco plants in farmland were investigated in present study. The environmental risks of avermectin was assessed adequately. Metagenomic method was used to analyze antibiotic-resistant bacteria and antibiotic resistance genes in the avermectin-treated soil. The abundance and distribution of antibiotic-resistant bacteria and their antibiotic resistance genes were affected by avermectin application. The antibiotic resistant Proteobacteria occupied the highest percentage (36%) in rhizosphere soil and carried 530 ARGs. Opportunistic human pathogens carrying antibiotic resistance genes were enriched in the avermectin-treated soil. Avermectin application increased the counts of many types of antibiotic resistance genes. The relative abundances of genes adeF, BahA, fusH, ileS, and tlrB in the avermectin-treated soil were significantly greater than in the untreated control soil. Different resistance mechanisms were revealed in the avermectin-treated soil. The efflux of antibiotic (670 ARGs), inactivation of antibiotic (475 ARGs), and alteration of antibiotic target (267 ARGs) were the main resistance mechanisms. Rigid control the avermectin dose and use frequency and other pesticides can decrease soil antibiotic resistance genes and protect agricultural products' safety and public health. Overall, application of nematicide avermectin enriched antibiotic-resistant bacteria and antibiotic resistance genes in farmland soil, which should be on the alert for environment protection.

Effects of Plastic Debris on the Biofilm Bacterial Communities in Lake Water

Increasing discharge of plastic debris into aquatic ecosystems and the worsening ecological risks have received growing attention. Once released, plastic debris could serve as a new substrate for microbes in waters. The complex relationship between plastics and biofilms has aroused great interest. To confirm the hypothesis that the presence of plastic in water affects the composition of biofilm in natural state, in situ biofilm culture experiments were conducted in a lake for 40 days. The diversity of biofilm attached on natural (cobble stones (CS) and wood) and plastic substrates (Polyethylene terephthalate (PET) and Polymethyl methacrylate (PMMA)) were compared, and the community structure and composition were also analyzed. Results from high-throughput sequencing of 16S rRNA showed that the diversity and species richness of biofilm bacterial communities on natural substrate (observed species of 1353~1945, Simpson index of 0.977~0.989 and Shannon–Wiener diversity index of 7.42~8.60) were much higher than those on plastic substrates (observed species of 900~1146, Simpson index of 0.914~0.975 and Shannon–Wiener diversity index of 5.47~6.99). The NMDS analyses were used to confirm the taxonomic significance between different samples, and Anosim (p = 0.001, R = 0.892) and Adonis (p = 0.001, R = 808, F = 11.19) demonstrated that this classification was statistically rigorous. Different dominant bacterial communities were found on plastic and natural substrates. Alphaproteobacterial, Betaproteobacteria and Synechococcophycideae dominated on the plastic substrate, while Gammaproteobacteria, Phycisphaerae and Planctomycetia played the main role on the natural substrates. The bacterial community structure of the two substrates also showed significant difference which is consistent with previous studies using other polymer types. Our results shed light on the fact that plastic debris can serve as a new habitat for biofilm colonization, unlike natural substrates, pathogens and plastic-degrading microorganisms selectively attached to plastic substrates, which affected the bacterial community structure and composition in aquatic environment. This study provided a new insight into understanding the potential impacts of plastics serving as a new habitat for microbial communities in freshwater environments. Future research should focus on the potential impacts of plastic-attached biofilms in various aquatic environments and the whole life cycle of plastics (i.e., from plastic fragments to microplastics) and also microbial flock characteristics using microbial plastics in the natural environment should also be addressed.

Current Findings on Gut Microbiota Mediated Immune Modulation against Viral Diseases in Chicken

Chicken gastrointestinal tract is an important site of immune cell development that not only regulates gut microbiota but also maintains extra-intestinal immunity. Recent studies have emphasized the important roles of gut microbiota in shaping immunity against viral diseases in chicken. Microbial diversity and its integrity are the key elements for deriving immunity against invading viral pathogens. Commensal bacteria provide protection against pathogens through direct competition and by the production of antibodies and activation of different cytokines to modulate innate and adaptive immune responses. There are few economically important viral diseases of chicken that perturb the intestinal microbiota diversity. Disruption of microbial homeostasis (dysbiosis) associates with a variety of pathological states, which facilitate the establishment of acute viral infections in chickens. In this review, we summarize the calibrated interactions among the microbiota mediated immune modulation through the production of different interferons (IFNs) ILs, and virus-specific IgA and IgG, and their impact on the severity of viral infections in chickens. Here, it also shows that acute viral infection diminishes commensal bacteria such as Lactobacillus, Bifidobacterium, Firmicutes, and Blautia spp. populations and enhances the colonization of pathobionts, including E. coli, Shigella, and Clostridial spp., in infected chickens.

Newcastle Disease Virus Infection Interferes With the Formation of Intestinal Microflora in Newly Hatched Specific-Pathogen-Free Chicks

Newcastle disease virus (NDV) infection leads to disproportion of intestinal tract microbiol population in chickens. Whether vertical infection of NDV affects the formation of a healthy and diverse intestinal community in newly hatched chicks, which might further perturb the establishment of a normal intestinal mucosal immunity, is unclear. This study examined the effects of NDV infection of chick embryos on the formation of the intestinal microbiome of chicks at hatch using 16S rRNA genes pyrosequencing. Eleven-day-old specific-pathogen-free chicken eggs were inoculated via intra-allantoic way with Class I NDV strain. At hatch, chicks were randomly selected and their duodenal and cecal contents were extracted and examined for the composition of gut microflora by Illumina sequencing of the V3+V4 region of the 16S rRNA genes. The results showed that the duodenal flora possesses a greater sample richness and higher microbial diversity as compared with the ceca flora in newly hatched chicks. In addition, there is a clear association with loss of important bacterial population in concert with an enrichment of potentially pathogenic population and NDV infections, both in the duodenum and ceca. It is also increasingly observed that the NDV infection may be associated with the dysbiosis of gut flora. This study presented a profile of the early intestinal microbiota in specific-pathogen-free chicks at hatch and strongly indicates that NDV infection interferes with the formation of intestinal microbiome in newly hatched chicks.