Allobaculum mucilyticum sp. nov. and Allobaculum fili sp. nov., isolated from the human intestinal tract

As part of a culturomics study to identify bacterial species associated with inflammatory bowel disease, a large collection of bacteria was isolated from patients with ulcerative colitis. Two of these isolates were tentatively identified as members of the family Erysipelotrichaceae. Following phylogenetic analysis based on 16S rRNA gene sequence and genome sequences, both strain 128^T and 539^T were found to be most closely related to Allobaculum stercoricanis, with G+C contents of 48.6 and 50.5 mol%, respectively, and the genome sizes of 2 864 314 and 2 580 362 base pairs, respectively. Strains 128^T and 539^T were strict anaerobe rods that grew in long chains between 37 and 42 °C. Scanning electron microscopy did not reveal flagella, fimbriae or visible endospores. Biochemical analysis showed nearly identical results for both strains with enzymatic activity of C4 and C8 esterases, acid phosphatase, naphthol-AS-BI-phosphohydrolase, β-glucuronidase, N-acetyl-β-glucosaminidase and arginine arylamidase. In addition, both strains produced indole and reduced nitrate. Major fatty acids were identified as C_18:1 ω9c (oleic acid, 64.06% in 128^T and 74.35% in 539^T), C_18:1 ω7c/C_18:1 ω9t/C_18:1 ω12t/UN17.834 (16.18 % in 128^T and 6.22% in 539^T) and C_16:0 (6.23% in 128^T and 7.37% in 538^T). Based on these analyses two novel species are proposed, Allobaculum mucilyticum sp. nov. with the type strain 128^T (=NCTC 14626^T=DSM 112815^T) and Allobaculum fili sp. nov. with the type strain 539^T (=NCTC 14627^T=DSM 112814^T).

Low abundance members of the gut microbiome exhibit high immunogenicity

Studies identifying bacterial members that dictate host phenotype have focused mainly on the dominant members, and the role of low abundance microbes in determining host phenotypes and pathogenesis of diseases remains unexplored. In this study, we compared the gut bacterial community of mice with wide-ranging microbial exposure to determine if low abundance bacteria vary based on microbial exposure or remain consistent. We noted that similar to the high abundance bacterial community, a core community of low abundance bacteria made up a significant portion of the gut microbiome irrespective of microbial exposure. To determine the role of low abundance bacteria in regulating community composition and host gene expression, we devised a microbiome dilution strategy to "delete" out low abundance bacteria and engrafted the diluted microbiomes into germ-free mice. Our approach successfully excluded low abundance bacteria from small and large intestinal bacterial communities and induced global changes in microbial community composition in the large intestine. Gene expression analysis of intestinal tissue revealed that loss of low abundance bacteria resulted in a drastic reduction in expression of multiple genes involved MHCII antigen presentation pathway and T-cell cytokine production in the small intestine. The effect of low abundance bacteria on MHCII expression was found to be specific to the intestinal epithelium at an early timepoint post-colonization and correlated with bacteria belonging to the family Erysipelotrichaceae. We conclude that low abundance bacteria have a significantly higher immuno-stimulatory effect compared to dominant bacteria and are thus potent drivers of early immune education in the gut.

Whole-Genome Shotgun Metagenomic Sequencing Reveals Distinct Gut Microbiome Signatures of Obese Cats

Overweight and obesity are growing health problems in domestic cats, increasing the risks of insulin resistance, lipid dyscrasias, neoplasia, cardiovascular disease, and decreasing longevity. The signature of obesity in the feline gut microbiota has not been studied at the whole-genome metagenomic level. We performed whole-genome shotgun metagenomic sequencing in the fecal samples of eight overweight/obese and eight normal cats housed in the same research environment. We obtained 271 Gbp of sequences and generated a 961-Mbp de novo reference contig assembly, with 1.14 million annotated microbial genes. In the obese cat microbiome, we discovered a significant reduction in microbial diversity (P < 0.01) and Firmicutes abundance (P = 0.005), as well as decreased Firmicutes/Bacteroidetes ratios (P = 0.02), which is the inverse of obese human/mouse microbiota. Linear discriminant analysis and quantitative PCR (qPCR) validation revealed significant increases of Bifidobacterium sp., Olsenella provencensis, Dialister sp.CAG:486, and Campylobacter upsaliensis as the hallmark of obese microbiota among 400 enriched species, whereas 1,525 bacterial species have decreased abundance in the obese microbiome. Phascolarctobacterium succinatutens and an uncharacterized Erysipelotrichaceae bacterium are highly abundant (>0.05%) in the normal gut with over 400-fold depletion in the obese microbiome. Fatty acid synthesis-related pathways are significantly overrepresented in the obese compared with the normal cat microbiome. In conclusion, we discovered dramatically decreased microbial diversity in obese cat gut microbiota, suggesting potential dysbiosis. A panel of seven significantly altered, highly abundant species can serve as a microbiome indicator of obesity. Our findings in the obese cat microbiome composition, abundance, and functional capacities provide new insights into feline obesity.

IMPORTANCE Obesity affects around 45% of domestic cats, and licensed drugs for treating feline obesity are lacking. Physical exercise and calorie restrictions are commonly used for weight loss but with limited efficacy. Through comprehensive analyses of normal and obese cat gut bacteria flora, we identified dramatic shifts in the obese gut microbiome, including four bacterial species significantly enriched and two species depleted in the obese cats. The key bacterial community and functional capacity alterations discovered from this study will inform new weight management strategies for obese cats, such as evaluations of specific diet formulas that alter the microbiome composition, and the development of prebiotics and probiotics that promote the increase of beneficial species and the depletion of obesity-associated species. Interestingly, these bacteria identified in our study were also reported to affect the weight loss success in human patients, suggesting translational potential in human obesity.

Relationship of Diet to Gut Microbiota and Inflammatory Biomarkers in People with HIV

While changes in microbiome composition have been associated with HIV, the effect of diet and its potential impact on inflammation remains unclear. Methods: Twenty-seven people living with HIV (PWH) on antiretroviral therapy (ART) were studied. A comprehensive dietary analysis was performed and two types of dietary patterns were determined. We explored the associations of each dietary pattern with gut microbiota and plasma inflammatory biomarkers. Results: We appreciated two dietary patterns, Mediterranean-like (MEL) and one Western-like (WEL). Compared to participants with the WEL pattern, participants with MEL pattern showed higher abundance of Lachnospira (p-value = 0.02) and lower levels of the inflammatory biomarkers D-dimer (p-value = 0.050) and soluble TNF-alpha receptor 2 (sTNFR2) (p-value = 0.049). Men who have sex with men (MSM) with MEL pattern had lower abundance of Erysipelotrichaceae (p-value < 0.001) and lower levels of D-dimer (p-value = 0.026) than MSM with WEL pattern. Conclusion: MEL pattern favours Lachnospira abundance, and protects against Erysipelotrichaceae abundance and higher levels of the inflammatory biomarkers D-dimer and sTNFR2, precursors of inflammatory processes in HIV-infected patients. Our study contributes to understanding the determinants of a healthier diet and its connections with gut microbiota and inflammation.

Electroacupuncture may alleviate behavioral defects via modulation of gut microbiota in a mouse model of Parkinson's disease

OBJECTIVE

Parkinson's disease (PD) is a chronic neurodegenerative disease involving non-motor symptoms, of which gastrointestinal disorders are the most common. In light of recent results, intestinal dysfunction may be involved in the pathogenesis of PD. Electroacupuncture (EA) has shown potential effects, although the underlying mechanism remains mostly unknown. We speculated that EA could relieve the behavioral defects of PD, and that this effect would be associated with modulation of the gut microbiota.

METHODS

Mice were randomly divided into three groups: control, PD + MA (manual acupuncture), and PD + EA. MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) was used to establish the mouse model of PD. Rotarod performance tests, open field tests, and pole tests were carried out to assess motor deficiencies. Immunohistochemistry was conducted to examine the survival of dopaminergic neurons. 16S ribosomal RNA (rRNA) gene sequencing was applied to investigate the alterations of the gut microbiome. Quantitative real-time polymerase chain reaction (PCR) was performed to characterize the messenger RNA (mRNA) levels of pro-inflammatory and anti-inflammatory cytokines.

RESULTS

We found that EA was able to alleviate the behavioral defects in the rotarod performance test and pole test, and partially rescue the significant loss of dopaminergic neurons in the substantia nigra (SN) chemically induced by MPTP in mice. Moreover, the PD + MA mice showed a tendency toward decreased intestinal microbial alpha diversity, while EA significantly reversed it. The abundance of Erysipelotrichaceae was significantly increased in PD + MA mice, and the alteration was also reversed by EA. In addition, the pro-inflammatory cytokines interleukin (IL)-6 and tumor necrosis factor (TNF)-α were substantially increased in the SN of PD + MA mice, an effect that was reversed by EA.

CONCLUSION

These results suggest that EA may alleviate behavioral defects via modulation of gut microbiota and suppression of inflammation in the SN of mice with PD, which provides new insights into the pathogenesis of PD and its treatment.

nov., isolated from healthy human feces

A Gram-positive, non-motile, rod-shaped facultative anaerobic bacterial strain SG502^T was isolated from healthy human fecal samples in Brookings, SD, USA. The comparison of the 16S rRNA gene placed the strain within the family Erysipelotrichaceae. Within this family, Clostridium innocuum ATCC 14501^T, Longicatena caecimuris strain PG-426-CC-2, Eubacterium dolichum DSM 3991^T and E. tortuosum DSM 3987^T(=ATCC 25548^T) were its closest taxa with 95.28%, 94.17%, 93.25%, and 92.75% 16S rRNA sequence identities respectively. The strain SG502^T placed itself close to C. innocuum in the 16S rRNA phylogeny. The members of genus Clostridium within family Erysipelotrichaceae was proposed to be reassigned to genus Erysipelatoclostridium to resolve the misclassification of genus Clostridium. Therefore, C. innocuum was also classified into this genus temporarily with the need to reclassify it in the future because of its difference in genomic properties. Similarly, genome sequencing of the strain and comparison with its 16S phylogenetic members and proposed members of the genus Erysipelatoclostridium, SG502^T warranted a separate genus even though its 16S rRNA similarity was >95% when comapred to C. innocuum. The strain was 71.8% similar at ANI, 19.8% [17.4–22.2%] at dDDH and 69.65% similar at AAI to its closest neighbor C. innocuum. The genome size was nearly 2,683,792 bp with 32.88 mol% G+C content, which is about half the size of C. innocuum genome and the G+C content revealed 10 mol% difference. Phenotypically, the optimal growth temperature and pH for the strain SG502^T were 37 °C and 7.0 respectively. Acetate was the major short-chain fatty acid product of the strain when grown in BHI-M medium. The major cellular fatty acids produced were C_18:1ω9c, C_18:0and C_16:0. Thus, based on the polyphasic analysis, for the type strain SG502^T (=DSM 107282^T= CCOS 1889^T), the name Dakotella fusiforme gen. nov., sp. nov., is proposed.

Faecalibacillus intestinalis gen. nov., sp. nov. and Faecalibacillus faecis sp. nov., isolated from human faeces

Two long-rod-shaped, Gram-stain-positive, obligately anaerobic and non-spore-forming strains, SNUG30099^T and SNUG30370^T, were isolated from faecal samples of healthy Korean subjects. The strains formed circular ivory-coloured colonies on Brain-heart infusion medium supplemented with 0.5% Difco yeast extract (YBHI) agar and cells were approximately 3.5-4.5×0.3-0.4 µm in size. Taxonomic analyses based on 16S rRNA gene sequences distinguished the strains from other species within the family Erysipelotrichaceae. The closest relative of strains SNUG30099^T and SNUG30370^T was Longibaculum muris (92.9 % and 93.6 % similarity, respectively), followed by Clostridium saccharogumia (92.3 % and 92.2 %). Phylogenetic inference also divided the strains into a unique branch that differed from other related strains that belong to the family Erysipelotrichaceae. DNA G+C contents based on the whole genome sequences of strains SNUG30099^T and SNUG30370^T were 29.2 and 30.2 mol%, respectively. Both novel strains possessed meso-diaminopimelic acid as the peptidoglycan, and phosphatidylethanolamine was observed as one of the major polar lipids. The major cellular fatty acid composition was different from those of other related taxa. In addition, the profile of biochemical activities advocated that the strains have distinct characteristics in comparison to other strains. Taken together, a novel genus, named Faecalibacillus gen. nov., is proposed, which includes the type species Faecalibacillus intestinalis sp. nov. for strain SNUG30099^T and Faecalibacillus faecis sp. nov. for strain SNUG30370^T. The type strains of these novel species are SNUG30099^T (=KCTC 15631^T=JCM 32256^T) and SNUG30370^T (=KCTC 15632^T=JCM 32257^T).

nov., a new member of the family Erysipelotrichaceae isolated from the small intestine of a swine

A strictly anaerobic, Gram-stain-positive, catalase-negative, non-motile, rod-shaped bacterium, designated SG0102^T, was isolated from the small intestine of a swine. Optimal growth occurred at 37°C and pH 7.0. Furthermore, growth was observed in the presence of up to 3% (w/v) NaCl but not at salinity levels higher than 4%. The comparative analysis of 16S rRNA gene sequences showed that strain SG0102^T was most closely related to Kandleria vitulina DSM 20405^T (93.3%), followed by Catenibacterium mitsuokai KCTC 5053^T (91.1%), Sharpea azabuensis KCTC 15217^T (91.0%), and Eggerthia catenaformis DSM 5348^T (89.6%). The average nucleotide identity values between strain SG0102^T and related species, K. vitulina DSM 20405^T, C. mitsuokai KCTC 5053^T, S. azabuensis KCTC 15217^T, and E. catenaformis DSM 5348^T, were 71.0, 69.3, 70.0, and 69.2%, respectively. The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SG0102^T belonged to the family Erysipelotrichaceae in the class Erysipelotrichia. The DNA G + C content of the strain SG0102^T was 39.5 mol%. The major cellular fatty acids (> 10%) of strain SG0102^T were C_16:0, C_16:0 dimethyl acetal, and C_18:2ω_9/12c. The cell wall peptidoglycan of strain SG0102^T contained the meso-diaminopimelic acid. The strain SG0102^T produced lactic acid as a major end product of fermentation. These distinct phenotypic and phylogenetic properties suggest that strain SG0102^T represents a novel species in a novel genus of the family Erysipelotrichaceae, for which the name Intestinibaculum porci gen. nov. sp. nov. is proposed. The type strain is SG0102^T (= KCTC 15725^T = NBRC 113396^T).

The Inhibitory Innate Immune Sensor NLRP12 Maintains a Threshold against Obesity by Regulating Gut Microbiota Homeostasis

In addition to high-fat diet (HFD) and inactivity, inflammation and microbiota composition contribute to obesity. Inhibitory immune receptors, such as NLRP12, dampen inflammation and are important for resolving inflammation, but their role in obesity is unknown. We show that obesity in humans correlates with reduced expression of adipose tissue NLRP12. Similarly, Nlrp12-/- mice show increased weight gain, adipose deposition, blood glucose, NF-κB/MAPK activation, and M1-macrophage polarization. Additionally, NLRP12 is required to mitigate HFD-induced inflammasome activation. Co-housing with wild-type animals, antibiotic treatment, or germ-free condition was sufficient to restrain inflammation, obesity, and insulin tolerance in Nlrp12-/- mice, implicating the microbiota. HFD-fed Nlrp12-/- mice display dysbiosis marked by increased obesity-associated Erysipelotrichaceae, but reduced Lachnospiraceae family and the associated enzymes required for short-chain fatty acid (SCFA) synthesis. Lachnospiraceae or SCFA administration attenuates obesity, inflammation, and dysbiosis. These findings reveal that Nlrp12 reduces HFD-induced obesity by maintaining beneficial microbiota.

Exploring the cockatiel (Nymphicus hollandicus) fecal microbiome, bacterial inhabitants of a worldwide pet

BACKGROUND

Cockatiels (Nymphicus hollandicus) were originally endemic to Australia; now they are popular pets with a global distribution. It is now possible to conduct detailed molecular studies on cultivable and uncultivable bacteria that are part of the intestinal microbiome of healthy animals. These studies show that bacteria are an essential part of the metabolic capacity of animals. There are few studies on bird microbiomes and, to the best of our knowledge, this is the first report on the cockatiel microbiome.

METHODS

In this paper, we analyzed the gut microbiome from fecal samples of three healthy adult cockatiels by massive sequencing of the 16S rRNA gene. Additionally, we compared the cockatiel fecal microbiomes with those of other bird species, including poultry and wild birds.

RESULTS

The vast majority of the bacteria found in cockatiels were Firmicutes, while Proteobacteria and Bacteroidetes were poorly represented. A total of 19,280 different OTUs were detected, of which 8,072 belonged to the Erysipelotrichaceae family.

DISCUSSION

It is relevant to study cockatiel the microbiomes of cockatiels owing to their wide geographic distribution and close human contact. This study serves as a reference for cockatiel bacterial diversity. Despite the large OTU numbers, the diversity is not even and is dominated by Firmicutes of the Erysipelotrichaceae family. Cockatiels and other wild birds are almost depleted of Bacteroidetes, which happen to be abundant in poultry-related birds, and this is probably associated with the intensive human manipulation of poultry bird diets. Some probable pathogenic bacteria, such as Clostridium and Serratia, appeared to be frequent inhabitants of the fecal microbiome of cockatiels, whereas other potential pathogens were not detected.

nov., two fermenting bacteria isolated from insect guts, and emended description of the family Erysipelotrichaceae

Two novel, obligately anaerobic Firmicutes from the family Erysipelotrichaceae were isolated from the intestinal tracts of a cockroach (strain ErySL, Shelfordella lateralis) and a scarab beetle larva (strain Pei061, Pachnoda ephippiata). Phylogenetic analysis indicated that the strains belong to a monophyletic group of hitherto uncultured bacteria from insect guts that are only distantly related to any described species (<90% 16S rRNA gene sequence similarity). Ultrastructural analysis revealed a Gram-positive cell envelope and, in the case of strain ErySL, a wide electron-lucent space between the cytoplasmic membrane and cell wall. In older cultures, cells formed pleomorphic rods with a thicker peptidoglycan layer. Both strains were obligately anaerobic and fermented glucose to formate, ethanol, and acetate as major products, but strain Pei061 tolerated up to 1% oxygen in the headspace. The same type of metabolism was observed with Erysipelothrix inopinata, except that the latter grew, albeit poorly, even under air. However, previous claims of a microaerophilic or facultatively anaerobic metabolism in the genus Erysipelothrix could not be substantiated. Based on phenotypic and phylogenetic evidence, we propose to classify the isolates as members of a new genus, Breznakia blatticola gen. nov. sp. nov. and Breznakia pachnodae sp. nov., with strain ErySL(T) (=DSM 28867(T)=JCM 30190(T)) and strain Pei061(T) (=DSM 16784(T)=JCM 30191(T)) as type strains, and provide an emended description of the family Erysipelotrichaceae.