Alkane-translocated cells of Rhodococcus strains utilize dissolved oxygen in the alkane phase of an aqueous-alkane two-phase culture.

To clarify the growth mechanisms of Rhodococcus in the alkane phase, we measured oxygen utilization in the alkane phase. The results showed that dissolved oxygen decreased significantly when viable cells were present in the alkane phase. The findings suggested that Rhodococcus strains can grow in alkanes and utilize the resident dissolved oxygen.

Mycobacterial DNA-binding protein 1 is critical for BCG survival in stressful environments and simultaneously regulates gene expression.

Survival of the live attenuated Bacillus Calmette-Guérin (BCG) vaccine amidst harsh host environments is key for BCG effectiveness as it allows continuous immune response induction and protection against tuberculosis. Mycobacterial DNA binding protein 1 (MDP1), a nucleoid associated protein, is essential in BCG. However, there is limited knowledge on the extent of MDP1 gene regulation and how this influences BCG survival.

Glycan-related genes in human gut microbiota exhibit differential distribution and diversity in carbohydrate degradation and glycan synthesis.

Interactions between humans and the gut microbiome occur by supplying nutrients to gut epithelial cells via short-chain fatty acids obtained from dietary carbohydrates or mucins and activating immunity via mucins' degradation. The degradation of carbohydrates derived from food is an important function for organisms to obtain energy. However, since humans possess only 17 genes encoding carbohydrate-degrading enzymes, the gut microbiome is responsible for degrading plant-derived polysaccharides.

Differential analysis of microbiomes in mucus and tissues obtained from colorectal cancer patients.

The outer mucus layer of the colorectal epithelium is easily removable and colonized by commensal microbiota, while the inner mucus layer is firmly attached to the epithelium and devoid of bacteria. Although the specific bacteria penetrating the inner mucus layer can contact epithelial cells and trigger cancer development, most studies ignore the degree of mucus adhesion at sampling. Therefore, we evaluated whether bacteria adhering to tissues could be identified by removing the outer mucus layer.

Unveiling microbiome profiles in human inner body fluids and tumor tissues with pancreatic or biliary tract cancer.

With the discovery of bacterial symbiosis in the tissues of various cancers, the study of the tumor microbiome is attracting a great deal of attention. Anatomically, since the gastrointestinal tract, liver, and pancreas form a continuous ductal structure, the microbiomes in the digestive juices of these organs may influence each other. Here, we report a series of microbiome data in tumor-associated tissues such as tumor, non-tumor, and lymph nodes, and body fluids such as saliva, gastric juice, pancreatic juice, bile, and feces of patients with pancreatic or biliary tract cancers.

Monitoring IgG against Mycobacterium tuberculosis proteins in an Asian elephant cured of tuberculosis that developed from long-term latency.

Tuberculosis (TB) is fatal in elephants, hence protecting elephants from TB is key not only in the conservation of this endangered animal, but also to prevent TB transmission from elephants to humans. Most human TB cases arise from long-term asymptomatic infections. Significant diagnostic challenges remain in the detection of both infection and disease development from latency in elephants due to their huge bodies.

Functional glyco-metagenomics elucidates the role of glycan-related genes in environments.

Background: Glycan-related genes play a fundamental role in various processes for energy acquisition and homeostasis maintenance while adapting to the environment in which the organism exists; however, their role in the microbiome in the environment is unclear.

Methods: Sequence alignment was performed between known glycan-related genes and complete genomes of microorganisms, and optimal parameters for identifying glycan-related genes were determined based on the alignments. Using the constructed scheme (> 90% of identity and > 25 aa of alignment length), glycan-related genes in various environments were identified from 198 different metagenome data.

Development of Novel PCR Assays for Improved Detection of Enterovirus D68.

Enterovirus D68 (EV-D68) causes a range of clinical manifestations, including asthma-like illness, severe respiratory disease, and acute flaccid myelitis. EV-D68 has caused worldwide outbreaks since 2014 and is now recognized as a reemerging infection in many countries. EV-D68-specific PCR assays are widely used for the diagnosis of EV-D68 infection; however, assay sensitivity is a concern because of genetic changes in recently circulated EV-D68.

Extracellular DNA of slow growers of mycobacteria and its contribution to biofilm formation and drug tolerance.

DNA is basically an intracellular molecule that stores genetic information and carries instructions for growth and reproduction in all cellular organisms. However, in some bacteria, DNA has additional roles outside the cells as extracellular DNA (eDNA), which is an essential component of biofilm formation and hence antibiotic tolerance. Mycobacteria include life-threating human pathogens, most of which are slow growers.

Higher genome mutation rates of Beijing lineage of Mycobacterium tuberculosis during human infection.

Mycobacterium tuberculosis (Mtb) strains of Beijing lineage have caused great concern because of their rapid emergence of drug resistance and worldwide spread. DNA mutation rates that reflect evolutional adaptation to host responses and the appearance of drug resistance have not been elucidated in human-infected Beijing strains. We tracked and obtained an original Mtb isolate of Beijing lineage from the 1999 tuberculosis outbreak in Japan, as well as five other isolates that spread in humans, and two isolates from the patient caused recurrence.

Innate Immune Responses in Serum and Cerebrospinal Fluid From Neonates and Infants Infected With Parechovirus-A3 or Enteroviruses.

Background: Parechovirus (PeV)-A3 and enteroviruses (EV) are the most common viruses causing sepsis and meningoencephalitis in neonates and young infants. Clinical manifestations of PeV-A3 infection are more severe than those of EV infection, and no pleocytosis with a positive polymerase chain reaction (PCR) result for PeV-A3 in cerebrospinal fluid (CSF) are characteristic findings. We hypothesized that innate immune responses to PeV-A3 and EV are distinct in serum and CSF.

Rice Endosperm Protein Administration to Juvenile Mice Regulates Gut Microbiota and Suppresses the Development of High-Fat Diet-Induced Obesity and Related Disorders in Adulthood.

Obesity and related disorders, which are increasing in adults worldwide, are closely linked to childhood diet and are associated with chronic inflammation. Rice endosperm protein (REP) intake during adulthood has been reported to improve lipid metabolism and suppress the progression of diabetic kidney disease in animal models. However, the effects of REP intake during childhood on adulthood health are unclear.

Mg(2+)-Dependent Control of the Spatial Arrangement of Rhodococcus erythropolis PR4 Cells in Aqueous-Alkane Two Phase Culture Containing n-Dodecane.

We recently reported that a close relationship exists between alkane carbon-chain length, cell growth, and translocation frequency in Rhodococcus. In the present study, we examined the regulation of the spatial arrangement of cells in aqueous-alkane two phase cultures. An analysis of the effects of minerals on cell localization revealed that changes in the concentration of MgSO4 in two phase cultures containing n-dodecane (C12) altered cell localization from translocation to adhesion and vice versa.

Rhodococcus rhodochrous ATCC12674 becomes alkane-tolerant upon GroEL2 overexpression and survives in the n-octane phase in two phase culture.

We recently reported that the overexpression of GroEL2 played an important role in increasing the alkane tolerance of Rhodococcus erythropolis PR4. In the present study, we examined the effects of the introduction of groEL2 on the alkane tolerance of other Rhodococcus strains. The introduction of groEL2 into Rhodococcus strains led to increased alkane tolerance.

Enhanced translocation and growth of Rhodococcus erythropolis PR4 in the alkane phase of aqueous-alkane two phase cultures were mediated by GroEL2 overexpression.

We previously reported that R. erythropolis PR4 translocated from the aqueous to the alkane phase, and then grew in two phase cultures to which long-chain alkanes had been added. This was considered to be beneficial for bioremediation.