Crohn's disease therapy with Dietzia: the end of anti-inflammatory drugs

Differences in the gut and pharyngeal microbiomes before and after treatment of an acute exacerbation of chronic obstructive pulmonary disease

This study investigated the gut microbiota and pharyngeal microbiome before and after treatment of an acute exacerbation of chronic obstructive pulmonary disease (AECOPD). The abundance and diversity of microorganisms in the gut and pharynx were examined in 24 patients before and after treatment of AECOPD. Enzyme-linked immunosorbent assay was used to detect inflammatory factors in venous blood and 16S rDNA sequencing was performed. The concentration of short-chain fatty acids (SCFAs) in fecal samples was measured by chromatography-mass spectrometry. The results indicated that the diversity and richness of the gut microbiota decreased post-treatment. The linear discriminant analysis effect size (LEfSe) algorithm revealed an increase in the abundance of f_Dietziaceae, g_Dietzia, g_Megasphaera, g_Robinsoniella, s_Salivarius, and s_Peoriensis in the gut after treatment. There was also a post-treatment decrease in the richness of the pharyngeal microbiome. LEfSe revealed a high abundance of p_Actinobacteria, f_Bacteriodaceae, o_Thermales, g_Bacteroides, and g_Thermus in the pharynx before treatment, and an increased abundance of o_Enterobacterales, f_Enterobacteriaceae, f_Ruminococcaceae, and g_Faecalibacterium after treatment. There were no post-treatment changes in SCFA levels. However, the serum C-reactive protein level decreased after treatment. Levels of other inflammatory factors, including tumor necrosis factor-alpha, interleukin (IL)-1β, IL-6, IL-10, transforming growth factor-beta, IL-23, IL-17, and interferon-gamma, were consistent before and after treatment. In this study, changes in the gut microbiota and pharyngeal microbiome occurred after treatment for AECOPD, with no changes in levels of SCFAs or inflammatory factors, except for a decrease in the C-reactive protein level.

Microbiome and metabolome reveal beneficial effects of baicalin on broiler growth performance and intestinal health

Normal function and health of the intestinal tract were necessary for the growth and development of broilers. Baicalin (BA) possessed a variety of biological activities. The objective of this study was to examine the impact of BA on the growth performance, intestinal barrier function, intestinal microbiota, and mucosal metabolism in broilers. A total of 720 21-day-old broilers were randomly allocated into 3 groups and fed with either basal diet (Con group) or basal diet supplemented with 6 or 12 mg/kg baicalin (BA6 and BA12 groups) for a continuous feeding period of 40 days. Results showed that BA had a trend towards improving (P = 0.086) the 60-day body weight of broilers, and the BA12 group exhibited significantly higher (P < 0.05) average daily gain from day 39 to 60 compared to the Con group. Additionally, in the BA12 group, the ratio of villus height to crypt depth and the expression levels of tight junction protein-related genes significantly increased (P < 0.05), while intestinal permeability significantly decreased (P < 0.05). Supplementation with 12 mg/kg BA significantly enhanced antioxidant capacity, promoted (P < 0.05) crypt proliferation, increased (P < 0.05) immunoglobulin levels, upregulated (P < 0.05) IL-2 and IL-8 mRNA levels, and downregulated (P < 0.05) IL-4 and TGF-β2 mRNA levels. Metabolomics analysis revealed that BA improved the metabolic characteristics of intestinal mucosa, significantly upregulating pathways associated with ascorbate and aldarate metabolism, glyoxylate and dicarboxylate metabolism, phosphatidylinositol signaling system, alpha-linolenic acid metabolism, and galactose metabolism. 16S rRNA sequencing results indicated that BA increased the richness of intestinal microbiota community and the relative abundance of Actinobacteria phylum, while reducing the relative abundance of contains mobile elements, potentially pathogenic, and facultatively anaerobic. Overall, 12 mg/kg BA improved intestinal health by modulating intestinal barrier function, antioxidant capacity, immunity, intestinal microbiota, and intestinal mucosal metabolism levels, ultimately enhancing broiler growth performance.

Intestine microbiota and SCFAs response in naturally Cryptosporidium-infected plateau yaks

Diarrhea is a severe bovine disease, globally prevalent in farm animals with a decrease in milk production and a low fertility rate. Cryptosporidium spp. are important zoonotic agents of bovine diarrhea. However, little is known about microbiota and short-chain fatty acids (SCFAs) changes in yaks infected with Cryptosporidium spp. Therefore, we performed 16S rRNA sequencing and detected the concentrations of SCFAs in Cryptosporidium-infected yaks. Results showed that over 80,000 raw and 70,000 filtered sequences were prevalent in yak samples. Shannon (p<0.01) and Simpson (p<0.01) were both significantly higher in Cryptosporidium-infected yaks. A total of 1072 amplicon sequence variants were shared in healthy and infected yaks. There were 11 phyla and 58 genera that differ significantly between the two yak groups. A total of 235 enzymes with a significant difference in abundance (p<0.001) were found between healthy and infected yaks. KEGG L3 analysis discovered that the abundance of 43 pathways was significantly higher, while 49 pathways were significantly lower in Cryptosporidium-infected yaks. The concentration of acetic acid (p<0.05), propionic acid (p<0.05), isobutyric acid (p<0.05), butyric acid (p<0.05), and isovaleric acid was noticeably lower in infected yaks, respectively. The findings of the study revealed that Cryptosporidium infection causes gut dysbiosis and results in a significant drop in the SCFAs concentrations in yaks with severe diarrhea, which may give new insights regarding the prevention and treatment of diarrhea in livestock.

The Roles of the Two-Component System, MtrAB, in Response to Diverse Cell Envelope Stresses in Dietzia sp. DQ12-45-1b

Two-component systems (TCSs) act as common regulatory systems allowing bacteria to detect and respond to multiple environmental stimuli, including cell envelope stress. The MtrAB TCS of Actinobacteria is critical for cell wall homeostasis, cell proliferation, osmoprotection, and antibiotic resistance, and thus is found to be highly conserved across this phylum. However, how precisely the MtrAB TCS regulates cellular homeostasis in response to environmental stress remains unclear. Here, we show that the MtrAB TCS plays an important role in the tolerance to different types of cell envelope stresses, including environmental stresses (i.e., oxidative stress, lysozyme, SDS, osmotic pressure, and alkaline pH stresses) and envelope-targeting antibiotics (i.e., isoniazid, ethambutol, glycopeptide, and β-lactam antibiotics) in Dietzia sp. DQ12-45-1b. An mtrAB mutant strain exhibited slower growth compared to the wild-type strain and was characterized by abnormal cell shapes when exposed to various environmental stresses. Moreover, deletion of mtrAB resulted in decreased resistance to isoniazid, ethambutol, and β-lactam antibiotics. Further, Cleavage under targets and tagmentation sequencing (CUT&Tag-seq) and electrophoretic mobility shift assays (EMSAs) revealed that MtrA binds the promoters of genes involved in peptidoglycan biosynthesis (ldtB, ldtA, murJ), hydrolysis (GJR88_03483, GJR88_4713), and cell division (ftsE). Together, our findings demonstrated that the MtrAB TCS is essential for the survival of Dietzia sp. DQ12-45-1b under various cell envelope stresses, primarily by controlling multiple downstream cellular pathways. Our work suggests that TCSs act as global sensors and regulators in maintaining cellular homeostasis, such as during episodes of various environmental stresses. The present study should shed light on the understanding of mechanisms for bacterial adaptivity to extreme environments.

IMPORTANCE The multilayered cell envelope is the first line of bacterial defense against various extreme environments. Bacteria utilize a large number of sensing and regulatory systems to maintain cell envelope homeostasis under multiple stress conditions. The two-component system (TCS) is the main sensing and responding apparatus for environmental adaptation. The MtrAB TCS highly conserved in Actinobacteria is critical for cell wall homeostasis, cell proliferation, osmoprotection, and antibiotic resistance. However, how MtrAB works with regard to signals impacting changes to the cell envelope is not fully understood. Here, we found that in the Actinobacterium Dietzia sp. DQ12-45-1b, a TCS named MtrAB is pivotal for ensuring normal cell growth as well as maintaining proper cell morphology in response to various cell envelope stresses, namely, by regulating the expression of cell envelope-related genes. Our findings should greatly advance our understanding of the adaptive mechanisms responsible for maintaining cell integrity in times of sustained environmental shocks.

Autochthonous Lactic Acid Bacteria Isolated From Dairy Cow Feces Exhibiting Promising Probiotic Properties and in vitro Antibacterial Activity Against Foodborne Pathogens in Cattle

Bovine enteric bacterial pathogens are a major cause of health decline in agricultural cattle populations. The identification of host-derived microbiota with probiotic characteristics is key for the development of treatments utilizing pathogen displacement and recolonization by commensal flora. In this study, intestinal microbiota in fecal samples from four Holstein dairy cows were analyzed using 16S ribosomal RNA gene next-generation sequencing, leading to the identification of three Lactobacillus isolates (Lactobacillus gasseri, Lactobacillus reuteri, and Lactobacillus salivarius). By taking advantage of the preferential growth in acidified culture media, bacterial characteristics examination, and restriction fragment length polymorphism analysis of 16S rRNA genes, the three lactic acid bacteria (LAB) strains were successfully isolated. The three LAB isolates possess the prerequisite growth tolerances for probiotic functionality, as well as exhibit effective antimicrobial potency against enteric bacterial pathogens of cattle, including Escherichia coli O157:H7, Mycobacterium avium subspecies paratuberculosis, and Salmonella species (Salmonella enteritidis, Salmonella typhimurium, and Salmonella Dublin). Moreover, the LAB isolates showed significant adhesion to cattle intestine, implying greater survivability potential due to their species specificity when administered in the same host species. The LAB isolates were sensitive to most antibiotics with notable resistances of L. gasseri to streptomycin and L. salivarius to kanamycin. Genes attributed to specific antibiotic resistances demonstrated a low risk of lateral transfer in a conjugation study. Our in vitro results demonstrate the promising probiotic characteristics of these newly identified Lactobacillus strains and their considerable potential to serve as probiotics feed supplements for cows.

Single-Homology-Arm Linear DNA Recombination by the Nonhomologous End Joining Pathway as a Novel and Simple Gene Inactivation Method: a Proof-of-Concept Study in Dietzia sp. Strain DQ12-45-1b

Nonhomologous end joining (NHEJ) is critical for genome stability because of its roles in double-strand break repair. Ku and ligase D (LigD) are the crucial proteins in this process, and strains expressing Ku and LigD can cyclize linear DNA in vivo Here, we established a proof-of-concept single-homology-arm linear DNA recombination for gene inactivation or genome editing by which cyclization of linear DNA in vivo by NHEJ could be used to generate nonreplicable circular DNA and could allow allelic exchanges between the circular DNA and the chromosome. We achieved this approach in Dietzia sp. strain DQ12-45-1b, which expresses Ku and LigD homologs and presents NHEJ activity. By transforming the strain with a linear DNA single homolog to the sequence in the chromosome, we mutated the genome. This method did not require the screening of suitable plasmids and was easy and time-effective. Bioinformatic analysis showed that more than 20% of prokaryotic organisms contain Ku and LigD, suggesting the wide distribution of NHEJ activities. Moreover, an Escherichia coli strain also showed NHEJ activity when the Ku and LigD of Dietzia sp. DQ12-45-1b were introduced and expressed in it. Therefore, this method may be a widely applicable genome editing tool for diverse prokaryotic organisms, especially for nonmodel microorganisms.IMPORTANCE Many nonmodel Gram-positive bacteria lack efficient genetic manipulation systems, but they express genes encoding Ku and LigD. The NHEJ pathway in Dietzia sp. DQ12-45-1b was evaluated and was used to successfully knock out 11 genes in the genome. Since bioinformatic studies revealed that the putative genes encoding Ku and LigD ubiquitously exist in phylogenetically diverse bacteria and archaea, the single-homology-arm linear DNA recombination by the NHEJ pathway could be a potentially applicable genetic manipulation method for diverse nonmodel prokaryotic organisms.