Lactobacillus sakei was increased in obesity group.
In this study, we enrolled 88 adults with obesity and 64 healthy control subjects without obesity. No significant difference was found between the obesity and control groups, with respect to age, gender, and social habits, except for diet.; higher intake of daily calories, calorie-adjusted fat, and calorie-adjusted saturated fat was found in the obesity group (Table S1). In order to compare the abundance and composition of Lactobacillus species between the two groups, we quantified the relative abundance of Lactobacillus in their faeces, using real-time polymerase chain reaction (PCR), and found no difference between the two groups (Fig. 1a). Considering the high diversity across Lactobacillus species to obscure the relationship between obesity and Lactobacillus, we performed species-specific PCR analysis next. Obesity group was more often colonised with L. sakei than the control group (Fig. 1b). There was no significant difference in the prevalence of other Lactobacillus species between the two groups (Fig. 1b).
Relationship between fat consumption and L. sakei abundance
Since higher fat consumption was seen in the obesity group than in the control group, we analysed the relationship between fat consumption and L. sakei abundance. High fat consumption is one of the main reasons of obesity, and affects the composition of gut microbiota, independent of the development of obesity[29, 30]. We categorised all participants into four groups according to the quartiles of fat consumption. Notably, participants in the highest fat-consumption group were approximately 3.1 times (odds ratio [OR]: 3.21, confidence interval [CI]: 2.03–4.57) more likely to have L. sakei strain in their faeces than those in the lowest fat-intake group, after adjusting for age, gender, and body mass index (BMI) (Fig. 1c). Saturated fatty acids increase the reactive oxygen species (ROS) levels in gut[11, 12] and L. sakei contains haem-dependent catalase, despite most Lactobacillus species being catalase negative[26, 31]. Hence, we hypothesised that the catalase activity of L. sakei might be a mechanistic underpinning of the relationship between high-fat diet and L. sakei. To investigate this hypothesis, we measured ROS levels in the faeces of each participant. We could find a trend of increased ROS levels in the faeces from obesity group compared to that from the control group (p = 0.06) (Fig. 1d). When categorising the participants according to fat intake, ROS levels in faeces were found to increase significantly with increase of fat intake, after adjusting for BMI (Fig. 1e). It, therefore, suggested that higher levels of ROS might arise from fat intake, rather than from obesity itself.
Lactobacillus sakei strain was isolated from the faeces of obese subjects
To further investigate the characteristics of L. sakei, related to high-fat diet-induced ROS, we isolated L. sakei strain from the faeces of obese subjects. Fresh faeces from 15 subjects in the obesity group were used for this purpose. Lactobacillus-specific culture, for confirming the presence of L. sakei-specific katA gene, and 16S rRNA gene sequencing, were used for isolation. Only one strain of L. sakei was isolated from one subject, and we named it L. sakei ob4.1. Severe obesity (BMI 32.15 kg/m2) and high fat consumption (37.28 g/1000 kcal/day) were found in the host of L. sakei ob4.1 (Table S2).
L. sakei ob4.1 showed higher resistance to oxidative stress than L. sakei DSM 20017
Since our data suggested high fat intake to increase ROS levels in the faeces, we aimed to explore the resistance of L. sakei ob4.1 against oxidative stress.
L. sakei is known to show high diversity, regarding catalase activity, across the strains[19]. For comparison, we chose L. sakei DSM 20017 as a reference strain, (isolated from rice wine), whose whole genome information was available[32]. For negative control, we used L. rhamnosus GG (ATCC53103), which contained no catalase gene[33]. Survival of each strain was assessed under oxidative stress, generated by either H2O2 or aeration. The short-term survival ratio of L. sakei ob4.1 was significantly higher than that of L. sakei DSM 20017 in presence of each concentration of H2O2 (5, 10, 15, and 30 mM) (Fig. 2a, b). Long-term survival of Lactobacillus strains, under aerobic conditions, was evaluated next. After 24 h of aerobic growth, survival of L. sakei ob4.1 was approximately 100 times higher than that of L. sakei DSM 20017 (Fig. 2c). Next, we measured the adhesion ability of L. sakei strains, with or without oxidative stress. Compared to L. rhamnosus GG, which is known to have great adhesion ability, both the L. sakei strains showed similar adhesion properties without H2O2. However, after H2O2 treatment, L. sakei ob4.1 was the only strain that could maintain adhesion ability (Fig. 2d).
Functional and comparative genomic analysis of L. sakei ob4.1
In order to understand the genetic basis of the higher resistance of L. sakei ob4.1 to oxidative stress, we sequenced the genome of L. sakei ob4.1 and compared it with that of L. sakei DSM 20017. L. sakei ob4.1 was found to have larger genome (2.03 Mbp) than L. sakei DSM 20017 (1.91 Mbp) (Supplementary Fig. 1a). Maximal Unique Matches algorithm[34] was used to align the two strains, and high degree of dissimilarity was observed between them (Supplementary Fig. 1b). Next, we performed genome-based clustering analysis using L. sakei ob4.1, L. sakei DSM 20017, and 15 other representative L. sakei strains (Supplementary data 1). L. sakei ob4.1 and DSM 20017 were relatively distant from each other, with average nucleotide identity (ANI) of 98.73% (Supplementary Fig. 2). It indicated that the two strains were from different phylogenetic lineages within the L. sakei species. We next investigated the strain-specific genes. A total of 207 genes were present in L. sakei ob4.1, though not in L. sakei DSM 20017 (Supplementary Fig. 1c). We next investigated the genes involved in oxidative stress, in L. sakei strains, from among those that associated with higher catalase activity of L. sakei ob4.1. However, we could not find any difference in the presence or absence of genes involved in oxidative stress, across the L. sakei strains (Supplementary data 2). Each L. sakei strain contained one catalase gene (KatA), and 98.5% identity was found across amino acid sequences of the catalase (Supplementary Fig. 1d).
L. sakei 4.1 had higher catalase expression and activity under oxidative stress
We could not identify genetic factors that explained the higher resistance of L. sakei ob4.1 to oxidative stress. However, considering that catalase activity is regulated by oxidative stress at gene transcription and protein synthesis levels in various Lactobacillus species[31, 35], we investigated the effect of oxidative stress on katA mRNA level and catalase enzymatic activity in L. sakei strains. Increased katA mRNA expression was detected in both strains, grown in aerobic conditions rather than in anaerobic conditions, as well as in strains treated with hydrogen peroxide. However, the increase was significantly higher in L. sakei ob4.1 (Fig. 3a). Next, we measured the catalase activities of Lactobacillus strains. Significantly higher increase of catalase activity was found in L. sakei ob4.1 grown in aerobic conditions (Fig. 3b). These results collectively suggested that resistance of L. sakei ob4.1 to oxidative stress could be regulated by the extent of oxidative stress at the transcriptional level, rather than at the genetic levels.
L. sakei ob4.1 strain reduced palmitate-induced inflammation in colon epithelium
In order to identify the roles of L. sakei ob4.1 strain in host colon epithelium, we focused on the anti-inflammatory properties of L. sakei ob4.1 in colon epithelial cells. The characteristics of L. sakei are diverse across the strains, with only a few strains showing anti-inflammatory properties[36–38]. In comparative genomic analysis, L. sakei ob4.1 had the highest similarity with L. sakei proBio65 strain (Supplementary Fig. 2), which was isolated from fermented vegetable (kimchi) and is used as a probiotic strain with anti-inflammatory effects[37]. First, we stimulated Caco-2 cells with a saturated fatty acid (palmitate). Palmitate stimulation significantly increased ROS levels in colon epithelium (Fig. 4a), and gene expression of proinflammatory cytokines like IL-6 (Fig. 4b) and TNF-alpha (Fig. 4c). When treated with live cells, L. sakei ob4.1 strain decreased gene expression of pro-inflammatory cytokines significantly, comparable to L. rhamnosus GG (Fig. 4b, c). ROS levels were sustained high after treatment with L. sakei strain (Fig. 4a). When treated with heat-killed cells, L. sakei ob4.1 and L. sakei DSM 20017 showed no significant change while L. rhamnosus GG maintained the anti-inflammatory functions (Supplementary Fig. 3a, b). When Caco-2 cells were treated with different doses of Lactobacillus strains, we found anti-inflammatory properties to be dose-dependent, both in L. sakei ob4.1 and DSM 20017 (Supplementary Fig. 3c,d).These results suggested that maintenance of cell viability is essential for anti-inflammatory properties of L. sakei strains, and that the latter could be mediated by a yet unknown mechanism, not by reduction of ROS in colon epithelium.
L. sakei ob4.1 showed high colonisation and reduced colon inflammation in high-fat diet-induced obese mice
To investigate the interaction between L. sakei ob4.1 strain and host colon in vivo, mice maintained on a high-fat (60%) or low-fat (10%) diet for 2 weeks were inoculated independently with 1 × 108 CFU/mouse of spontaneous rifampin-resistant L. sakei strains. After 2 days of gavage, bacterial numbers in the colon contents were counted. L. sakei ob4.1-inoculated mice on a high-fat diet shed L. sakei significantly in the colon contents compared to L. sakei DSM 20017-inoculated mice on a high-fat diet (Fig. 5a). Total number of Lactobacillus was not different between the strains, in mice maintained on low-fat diet (Fig. 5a). This result was consistent with the higher attachment ability of L. sakei ob4.1 in palmitate-treated Caco-2 cells. When we investigated whether L. sakei ob4.1 had anti-inflammatory properties in high-fat-induced obese mice, if administrated as a probiotic, the mice on high-fat diet exhibited significantly higher colon mucosal ROS levels (Fig. 5c). Furthermore, reduced colon length (Fig. 5d) and increased expression levels of inflammatory markers of colon mucosa (Fig. 4e, f) were found in the high-fat-fed mice. Following 4 weeks of treatment with L. sakei ob4.1 or L. sakei DSM 20017, body weight did not change in the mice, with either low-fat diet or high-fat diet (Fig. 5b). Neither of L. sakei ob4.1 or L. sakei DSM 20017 decreased ROS levels in colonic mucosa (Fig. 5c), although L. sakei ob4.1 significantly increased the colon length (Fig. 5d) and decreased inflammatory marker expression in high-fat-fed mice (Fig. 5e). Together, these results show that effects of L. sakei ob4.1 observed in our obese mouse model are similar to those in the palmitate-induced colon epithelial cells.