Thursday, March 23, 2023

Lactobacillus, Bifidobacterium and other emerging probiotics

In the past few decades, Lactobacillus and Bifidobacterium genera were the main bacteria to be used as probiotics. One of the reasons for such attention was that these bacteria have the ability to thrive aerobically and are simple to package for sale. Cass Nelson-Dooley and Tony Hoffman of Metametrix (acquired by Genova Diagnostics in 2012) talked about these probiotics in MEBO interviews in 2009, emphasizing that high levels of Lactobacillus could be bad in some cases. Diets rich in simple carbs, poor absorption and small intestinal pockets can feed and trap excess Lactobacillus. Adding probiotics Bifidobacteria or Saccharomyces boulardii and prebiotic fiber to the diet could, in their opinion, help the MEBO population. D-lactate was one of the tests they offered that measured the level of this byproduct of bacterial fermentation, indicating an overgrowth of bacteria in the small intestine. According to our early clinical studies, D-lactate, however, was elevated in less than 20% of MEBO and PATM populations. 

Even though Lactobacillus is only a minor member of the human colonic microbiota, the proportions of those bacteria are frequently either positively or negatively correlated with human disease and chronic conditions. Although it generally is not considered a pathogen, it can cause disease in compromised hosts, including bacterial endocarditis, pleuropulmonary infections, gastrointestinal abscesses, urinary tract infection, conjunctivitis, dental caries, and endometritis. Lactobacillus bacteremia, presumably secondary to bacterial translocation from the gastrointestinal tract, has been reported in a patient with severe intestinal inflammation caused by ulcerative colitis. A decrease in genus Faecalibacterium and increase in Lactobacillaceae has been previously reported in patients with constipation. Compared to healthy individuals, pediatric and adult Crohn's disease (CD) patients had an increased relative abundance of Lactobacillus species. In both cases, Lactobacillus enrichment coincided with depletion of F. prausnitzii - that could represent a good candidate as next-generation probiotic.

The percentages of Bifidobacterium and the Lactobacillus group presented a decreasing trend in patients with quiescent ulcerative colitis (UC) compared to active UC, although no significant differences were observed. Excessive amounts of Bifidobacteria can have negative effects on the body, such as in the case of Bifidobacterium breve bacteremia caused by excessive probiotic supplementation in infants with gastrointestinal conditions. On the other hand, Lactobacillus, Bifidobacterium and F. prausnitzii are depleted in IBS patients, resulting in lower SCFA concentrations (short-chain fatty acids, which are organic acids produced by gut bacteria during fermentation of indigestible foods) compared with healthy individuals. Maternal prenatal stress could also cause lower levels of Lactobacillus and Bifidobacterium and keep them low even later in life. With lower levels of Bifidobacterium, celiac patients have an imbalance in the intestinal microbiota, regardless of pH, even while on a gluten-free diet. 

Data from our microbiome study (NCT03582826: Microbial Basis of Systemic Malodor and "People Allergic To Me" Conditions  - ClinicalTrials.gov) show that while there was a general trend of increasing levels of Bifidobacteria and Lactobacillus in individuals who achieve remission, less than 10% of participants needed to boost levels of both species to improve their condition. In line with previous knowledge, in MEBO/PATM population, Bifidobacteria (one of the first microbes to colonize the human gastrointestinal tract) was more common in younger individuals. About one third of the participants experienced lesser symptoms when increasing levels of their gut Bifidobacteria, another third benefited from more Lactobacillus and the remaining third felt better when increasing levels of Faecalibacterium prausnitzii (a butyrate-producing anaerobe typically associated with good health). Changes in the levels of these bacteria corresponding to recovering are overlayed on Figure 5 from our paper published in JMIR dermatology. It was illustrating changes in microbial diversity vs abundances of selected bacterial species associated with odor (CSS) for 12 female (F1-F12) and 10 male (M1-M19) participants who self-reported both flare-ups (beginning of the arrow) and improvements (end of the arrow). We added text boxes showing whether the levels of F. prausnitzii (F), Bifidobacterium (B) and Lactobacillus (L) are increasing (🡹) , decreasing (🡻) or fluctuating (🡺) as symptoms resolve. It is obvious that individuals with the highest bacterial diversity don't benefit from increasing levels of probiotic diversity, while those with low diversity levels do need more probiotic microbes in their system. The figure demonstrates the complexity of these bacterial perturbations and emphasizes the need to consider more than just three species when predicting which treatment will work best for reducing MEBO and PATM symptoms. 

As we mentioned in the previous blog post, Lactobacillus is the main genera responsible for odors of the uncooked food waste. Some strains of Lactobacillus produce lactic acid, which can contribute to a more acidic environment in the gut. This can be beneficial for some people, but for others it can exacerbate odor issues. Bifidobacteria could also produce organic acids such as acetic acid and lactic acid in addition to short-chain fatty acids (SCFAs) like butyrate, which can have anti-inflammatory effects and promote gut health, but some people may find it unpleasantly smelling. F. prausnitzii produces a range of metabolites including one of the worst smelling compounds Putrescine. F. prausnitzii  plays important role in balancing immunity. Its butyrate production has been correlated to the capacity to induce IL-10, an anti-inflammatory cytokine, in peripheral blood mononuclear cells (PBMC) but not to the ability to block IL-8 secretion in TNF-α-stimulated HT-29 cells. In COVID-19, Faecalibacterium prausnitzii has been inversely correlated with disease severity. 

Research has shown that the gut microbiome is far more complex than previously thought, with hundreds of bacterial species interacting in a delicate balance.  Therefore, focusing solely on Lactobacillus and Bifidobacterium, or any other bacterium, may not be enough to promote a healthy gut microbiome for everyone. Besides, different strains of bacteria within the same species can have different effects on the body.

After more than a century of research, the following species are identified as the primary probiotic species of Lactobacillus species: L.acidophilus, L.casei, L.fermentum, L.gasseri, L.johnsonii, L.paracasei, L. plantarum, L. rhamnosus, and L. salivarius. For Bifidobacteria these are: B.adolescentis, B.animalis, B.bifidum, B.breve, and B.longum. We are learning more about strains of these species. Novel probiotic strain Bifidobacterium bifidum CECT 7366 is active against the pathogenic bacterium Helicobacter pylori - and so are variations of Saccharomyces Boulardii and Lactobacilli johnsonii. Another strain L. plantarum 299v can directly interfere with E. coli colonization and improve the immunological status of the intestinal mucosa although these results have not yet been confirmed in humans. Lactobacillus GR-1 and B-54 or RC-14 strains in the vagina has been shown to reduce the risk of urinary tract infections. Mileti et al. found that Lactobacillus paracasei displayed a delay in the development of colitis and a decreased severity of disease but that L. plantarum and L. rhamnosus GG exacerbated the development of dextran sodium sulfate (DSS)-induced colitis. Bifidobacterium supplemented with various fiber additives can prevent the growth of Clostridium difficile, while Lactobacillus salivarius protects the broiler chicks from Salmonella infections. Several strains of other species promising as probiotics are from Roseburia spp., Akkermansia spp., and Faecalibacterium spp. Probiotic potential risk score (PPRS) allowed to classify 84 Faecalibacterium prausnitzii strains  into low-, medium-, and high-risk groups. 15 strains identified as low-risk strains are prioritized for clinical application. 

Unfortunately, the extreme oxygen sensitivity of F. prausnitzii imposes practical challenges to the production, transportation, storage, and manufacturing of probiotic products to be evaluated in a clinical setting. Instead, we have to turn to prebiotics - a type of dietary fiber - in our food . F. prausnitzii's growth is promoted by inulin, inositol (vitamin B8) and fructo-oligosaccharides, chicory roots, wheat, onion, banana, garlic, and leek, wheat, rye, rice, barley, oat, and sorghum, and gold kiwifruit

Gut microbiota can be also influenced by phytochemicals. In one study, black raspberry (BR) reduced the serum levels of trimethylamine-N-oxide and cholesterol in rats fed excessive choline with a high-fat diet (HFC). The authors hypothesized that since gut microbiota plays a crucial role in the production of trimethylamine and microbial metabolites, BR could influence gut microbial composition. Their study examined microbiomes and metabolomes of rats and showed that the BR supplementation enriched Bifidobacterium and reduced Clostridium cluster XIVa. 

While we have made significant progress in understanding the role of probiotics and prebiotics in supporting our gut health, it's important to recognize that there is still a great deal that we don't know. It's becoming increasingly clear that a personalized approach to prebiotic and probiotic use may be necessary to achieve optimal health outcomes. This approach involves paying attention to how different foods make you feel and adjusting your diet accordingly, while eating a diverse and balanced diet that incorporates a variety of whole foods and phytochemicals, staying hydrated, getting enough sleep and exercise, and managing stress levels. Focusing on overall health and well-being will help to support the body's natural ability to maintain a healthy microbiome and avoid dysbiosis-related health issues.



REFERENCES


Din AU, Hassan A, Zhu Y, Yin T, Gregersen H, Wang G. Amelioration of TMAO through probiotics and its potential role in atherosclerosis. Applied Microbiology and Biotechnology. 2019 Dec;103:9217-28.

Pacifico L, Osborn JF, Bonci E, Romaggioli S, Baldini R, Chiesa C. Probiotics for the treatment of Helicobacter pylori infection in children. World J Gastroenterol 2014; 20(3): 673-683 [PMID: 24574741 DOI: 10.3748/wjg.v20.i3.673] 

Lim T, Lee K, Kim RH, Ryu J, Cha KH, Park SY, Koo SY, Hwang KT. Effects of black raspberry extract on gut microbiota, microbial metabolites, and expressions of the genes involved in cholesterol and bile acid metabolisms in rats fed excessive choline with a high-fat diet. Food Sci Biotechnol. 2023 Feb 13;32(4):577-587. doi: 10.1007/s10068-023-01267-4. PMID: 36911337; PMCID: PMC9992478.

Heeney DD, Gareau MG, Marco ML. Intestinal Lactobacillus in health and disease, a driver or just along for the ride?. Current opinion in biotechnology. 2018 Feb 1;49:140-7.

Martín R, Miquel S, Benevides L, Bridonneau C, Robert V, Hudault S, Chain F, Berteau O, Azevedo V, Chatel JM, Sokol H. Functional characterization of novel Faecalibacterium prausnitzii strains isolated from healthy volunteers: a step forward in the use of F. prausnitzii as a next-generation probiotic. Frontiers in microbiology. 2017 Jun 30;8:1226.

Nalbandian A, Sehgal K, Gupta A, Madhavan MV, McGroder C, Stevens JS, Cook JR, Nordvig AS, Shalev D, Sehrawat TS, Ahluwalia N. Post-acute COVID-19 syndrome. Nature medicine. 2021 Apr;27(4):601-15.

Bai Z, Zhang N, Jin Y, Chen L, Mao Y, Sun L, Fang F, Liu Y, Han M, Li G. Comprehensive analysis of 84 Faecalibacterium prausnitzii strains uncovers their genetic diversity, functional characteristics, and potential risks. Frontiers in Cellular and Infection Microbiology. 2023 Jan 4;12:1924.

Gabashvili I.S. Cutaneous Bacteria in the Gut Microbiome as Biomarkers of Systemic Malodor and People Are Allergic to Me (PATM) Conditions: Insights From a Virtually Conducted Clinical Trial. JMIR Dermatol 2020;3(1):e10508 URL: https://derma.jmir.org/2020/1/e10508 DOI: 10.2196/10508

Wednesday, January 25, 2023

Food, Hormones and Odor Pollution

While there is not enough research on human odors, there are plenty of studies that can be related to this topic. Scientific papers published in January are about goats, fish, fermented food and biological waste. 

It is worth examining some of the latest findings and how they may be translated into take-home messages for humans.

1. Intermittent fasting could improve body odor. 

At least for fish. The study aimed to investigate the response of intestinal microbiota during 3 weeks’ starvation of largemouth bass (Micropterus salmoides), found that food deprivation helped to improve the odor of an economically important freshwater fish by reducing earthy-musty off-flavor compounds such as geosmin and 2-methylisoborneol. The study revealed that certain actinobacteria such as Microbacterium and Nocardioides were able to grow better than Mycoplasma, Pseudomonas, Acinetobacter, and Microbacterium when the fish were in a fasted state. This suggests that intermittent fasting may help to improve body odor by promoting the growth of beneficial bacteria and reducing the growth of odor-causing bacteria. However, more research is needed to confirm these findings in human studies. Besides, our own data show that people smell worse when starving themselves and it is a good idea to not go overboard. 

2. Adding fiber to diet and reducing stress levels can improve body odor. 

Korean native black goats (KNBG) are able to adapt to a wide variety of climatic conditions and foraging preferences. Twenty-four KNBG (48.6 ± 1.4 kg) were randomly allocated to one of four treatments featuring different dietary forage (high in fiber) to concentrate ratio (high forage [HF, 80:20] and low forage [LF, 20:80]), and a castration treatment (castration [CA] vs. non-castration [NCA] - aka higher levels of sex hormones, stress hormones). The animals were maintained on a free-choice feed and water regimen.

The intensity of a strong “goaty” flavor was remarkably enhanced when non-castrated KNBG were fed with the low forage diet. Better smelling goats had more hydrocarbons and ketones while worse smelling ones were higher in aliphatic aldehydes, possibly owing to the activity of testosterone, androsterone, and skatole. For volatile compounds, dichloromethane (chloroform-like odor) and m-xylene (plastic odor) were reported to be linked with the “strong lamb odor” influenced by dietary selection. 

A healthy gut microbiome may positively influence sex hormones by regulating the appetite and reducing insulin resistance. Acute psychosocial stress, on the other hand, causes unhealthy fluctuations in sex hormone levels.  

Here are a few tables compiled from the goat diet/hormones article:

Microbe GenusCompounds positively correlatedCompounds negatively correlated.
FlexilineaC16:0 (Palmitic acid, oily smell)C18:2n6 (Methyl linoleate, oily odor), C18:3n3 (Linoleic acid, oily, low odor), PUFA
IhubacterC16:0 (Palmitic acid, oily smell)C18:2n6, C18:3n3 (Linoleic acid), PUFA
Ruminococcus-C16:0 (Palmitic acid, oily smell)
ChristensenellaC18:0 (Stearic acid), PUFAC16:1n7 (Palmitoleic Acid, Cardioprotective - smells like Old Books)
LachnoclostridiumC18:1n9 Oleic acid)C18:2n6, C18:3n3 (Linoleic acid),, PUFA
Treponema-C18:0 (Stearic acid), C18:3n3 (Linoleic acid), C20:4n6 (Arachidonic acid: from marine, at low concentrations, to intense orange-citrus and animal-like odor)
SucciniclasticumC18:1n7 (Vaccenic acid), C18:3n3 (Linoleic acid)-
DesulfovibrioC18:1n7 (Vaccenic acid)-
Blautia-C18:2n6 (Linolelaidic acid)
Rhabdanaerobium-C18:3n3 (Linoleic acid)
Gracilibacter-C18:3n3 (Linoleic acid)
Butyrivibrio-C18:3n3 (Linoleic acid)
ParaprevotellaC20:4n6, C22:4n6-
IntestinimonasC22:4n6-

This table summarizes the relationship between meat fatty- composition and rumen bacteria at the genus level. 

Higher levels of carbohydrates may promote the persistence and flavor formation of Z. rouxii (Zygosaccharomyces, a genus of yeasts in the family Saccharomycetaceae) in the moromi soy sauce, and it changes its aroma profile. Not sure if it is to the better or worse. 

3. Acinetobacter is associated with fish odor and the odor of biowaste. It is also associated with odor in MEBO and PATM populations - this is one of not yet published results of our microbiome study  (in addition to skin bacteria)

A study to be published in print in the February issue of "Science of The Total Environment", examined odor profiles of cooked and uncooked food waste.

Odor pollution often occurs in the initial decomposition stage of municipal biowaste, including throwing/collection and transportation. However, this aspect of odor impact from municipal biowaste has not been well studied. In Nie and colleagues' experiments, a practical dustbin (120 L) equipped with flux chamber and filled with three types of municipal biowaste was used to simulate garbage storage conditions. The result indicated that the emission rate of odor pollutants for uncooked food waste (UFW) represented a nearly linear growth trend, reaching the maximum (3963 ± 149 μg kg−1 DM h−1) at 72 h. Cooked food waste (CFW) increased rapidly from 8 h to 24 h, and then remain fluctuated, reached the maximum (2026 ± 77 μg kg−1 DM h−1) at 72 h. Comparatively, household kitchen waste (HKW) reached the maximum emission rate (10,396 ± 363 μg kg−1 DM h−1) at 16 h. Sulfide and aldehydes ketones were identified as dominant odor contributor to UFW and CFW, respectively. While aldehydes ketones and sulfides were both dominant odor contributor to HKW. Moreover, the microbial diversity analysis suggests that Acinetobacter was the dominant genus in UFW, and Lactobacillus was the dominant genus in CFW and HKW. In addition, it was evident that each odorous pollutant was significantly associated with two or more bacterial genera, and most bacterial genera such as Acinetobacter, were also significantly associated with multiple odorous pollutants. The variation of odorants composition kept consistent with microbial composition. The present study could provide essential evidence for a comprehensive understanding of odorant generation in the initial decomposition stage of municipal biowaste. It could contribute to setting out strategies for odor control and abatement in municipal biowaste management systems.

The highest emission was observed in household kitchen waste with alcohol esters.

The highest total odor activity values were observed in uncooked food waste.

Lactobacillus was the dominant genus in household kitchen waste and cooked food waste.

Acinetobacter was the dominant genus in uncooked food waste. 

The variation of odorants composition kept consistent with microbial composition.




REFERENCES

Lee J, Kim HJ, Lee SS, Kim KW, Kim DK, Lee SH, Lee ED, Choi BH, Barido FH, Jang A. Effects of diet and castration on fatty acid composition and volatile compounds in the meat of Korean native black goats. Anim Biosci. 2023 Jan 11. doi: 10.5713/ab.22.0378. Epub ahead of print. PMID: 36634653. download pdf

Zou S, Ni M, Liu M, Xu Q, Zhou D, Gu Z, Yuan J. Starvation alters gut microbiome and mitigates off-flavors in largemouth bass (Micropterus salmoides). Folia Microbiologica. 2023 Jan 13:1-2.

Lülf RH, Selg-Mann K, Hoffmann T, Zheng T, Schirmer M, Ehrmann MA. Carbohydrate Sources Influence the Microbiota and Flavour Profile of a Lupine-Based Moromi Fermentation. Foods. 2023 Jan 2;12(1):197. doi: 10.3390/foods12010197. PMID: 36613413; PMCID: PMC9818829.

Nie E, Wang W, Duan H, Zhang H, He P, Lü F. Emission of odor pollutants and variation in microbial community during the initial decomposition stage of municipal biowaste. Sci Total Environ. 2023 Feb 25;861:160612. doi: 10.1016/j.scitotenv.2022.160612. Epub 2022 Nov 29. PMID: 36455726.

Shi Q, Tang X, Liu BQ, Liu WH, Li H, Luo YY. Correlation between microbial communities and key odourants in fermented capsicum inoculated with Pediococcus pentosaceus and Cyberlindnera rhodanensis. J Sci Food Agric. 2023 Feb;103(3):1139-1151. doi: 10.1002/jsfa.12321. Epub 2022 Nov 24. PMID: 36349455.

Gabashvili IS Cutaneous Bacteria in the Gut Microbiome as Biomarkers of Systemic Malodor and People Are Allergic to Me (PATM) Conditions: Insights From a Virtually Conducted Clinical Trial JMIR Dermatol 2020;3(1):e10508 doi:  10.2196/10508

Search Odors (cdc.gov) - database of toxic chemicals

OdorDB: Home (yale.edu)