Camel milk affects serum metabolites by modulating the intestinal microflora

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Abstract

Gut microbes play a vital role in human health and are influenced by numerous factors including diet, genetics, and environment. (Fermented) Camel milk, which is abundant in nutrients and lacks allergenic proteins, has been consumed for its edible and medicinal properties for centuries. Research on camel milk’s impact on gut microbiota and host metabolism is still limited. The results found that sour camel milk contained various beneficial bacteria such as Lactobacillus helveticus, Acinetobacter lwoffii, Eubacterium coprostanoligenes group, Lachnospiraceae, which could be transported to the recipient’s intestines by diet. This study specified that the transportation of microbiome happened both intra- and inter-species and played a principal role in the formation of progeny gut microflora. An investigation on type 2 diabetic rats revealed that the composition of gut microflora and serum metabolites of those fed with high-dose camel whey was closer to that of the normal. Eubacterium limnetica , which can reduce the risk of diseases by producing MtcB protein, was found in the gut microflora of the ones taking camel milk. These results evidenced the high potential of camel milk as a functional food.

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    Reply to the reviewers

    We appreciate the time and effort that you and the reviewers have dedicated to providing your valuable feedback on our manuscript. Those comments are all valuable and very helpful for revising and improving our paper, as well as the importance guiding significance to our researches. We have highlighted the changes in yellow within the manuscript.

    *Here is a point-by-point response to the reviewers’ comments and concerns. *

    Comments from Reviewer #1 (Evidence, reproducibility and clarity (Required)):

    The provided document, titled "Camel Milk Affects Serum Metabolites by Modulating the Intestinal Microflora," is an extensive research paper. My summary covers the first 44 pages of the total 63 pages. The document begins with a standard review commons manuscript notice and provides contact information for the Review Commons office.

    The research focuses on the effects of camel milk on serum metabolites and the intestinal microflora. It starts with a detailed introduction to the topic, outlining the crucial role of gut microbes in human health and the influence of various factors like diet, genetics, and environment on these microbes. The paper emphasizes the nutritional richness of camel milk and its potential as a functional food, particularly its impact on gut microbiota and host metabolism.

    Initial sections of the paper discuss the research methodologies, including the study's keywords, abstract, and introduction. The abstract highlights the study's significant findings, such as the presence of various beneficial bacteria in sour camel milk, the inter- and intra-species transportation of microbiomes, and the impact of camel milk on the gut microflora and serum metabolites of type 2 diabetic rats.

    The introduction further delves into the composition of the human gut microbiota and the shaping factors of the adult gut microbiome. It also examines the role of diet in modulating gut microbiota and the potential health benefits of dairy products, with a particular focus on camel milk.

    Subsequent sections present detailed research findings, including the results of microbial composition and source analysis in camel milk, the composition and changes of rat gut microbiota under camel milk regulation, and the effects of camel milk-regulated gut microbiota on metabolism in rats. The research also explores the interspecies transfer of microbes using camel milk as a vector and analyzes the gut microbiota in people consuming camel milk.

    The paper further discusses the endophytic flora of camel edible desert plants and their possible influence on the camel's gut microbiota. The discussion section integrates the findings, offering insights into the potential health benefits of camel milk and its probiotic qualities. It also compares the effects of camel milk with other dairy products and discusses its role as a vector for beneficial microbes.

    Materials and methods used in the study are detailed towards the end of the summarized portion, describing sample collection and processing, the experimental setup for rats, and data processing and analysis techniques.

    Reviewer #1 (Significance (Required)):

    The paper continues with detailed research findings, including the microbial composition in camel milk, the impact on the gut microflora of rats and humans, and the serum metabolism effects.

    There's a focus on how camel milk, as a vector, can transfer beneficial microbes between species, influencing gut microbiota and host metabolism.

    The paper compares the effects of camel milk with other dairy products, emphasizing its unique health benefits and its role in transferring beneficial microbes.

    It discusses various bacteria found in camel milk and their potential health benefits.

    The research findings extend to understanding how camel milk affects human gut microbiota, with studies on pastoral herders who consume camel or bovine milk.

    Author response: We thank you for your approval and constructive and valuable feedback from you and other reviewers.

    Comments from Reviewer #2 (Evidence, reproducibility and clarity (Required)):

    summary:

    The authors introduce a study assessing the bacterial flora of sour fermented camel milk and its capability to introduce beneficial species into consumer's gut. They further tested the potential of its nutrients and species for beneficial effects on type 2 diabetic (t2d) rats. They claim that t2d rats fed with high-dose camel whey reveal a microbiota closer to that of healthy rats rather than that of other t2d rats not receiving the camel whey treatment. Further they claim that this effect is due to the presence of Eubacterium limnetica that was exclusively found in the gut microflora of rats taking camel milk and producing MtcB protein. They conclude that camel milk may have the potential to be functional food.

    Overall, I think the approach of looking into camel milk and its microbiota is of broad interest, as it is food consumed traditionally by many tribes and in several countries. However, to me the presentation of the findings, the data and the analysis is often unprecise and confusing.

    For example, the MtcB protein they claim to be the mechanism of reducing the risk for t2d in the abstract is mentioned only once in the whole study and there only as a finding of another study (cited). According to my understanding the abstract should contain the main findings of the study, rather than some side-finding from other studies happens to match with the study results. I assume the authors have plenty of results from their sequencing data and metabolomics that they could mention in the abstract.

    In the text the authors mention the analysis of the microbial composition and source analysis of camel milk, the analysis of the gut microbiota of young camels, the composition, and changes of rat gut microbiota under the regulation of camel milk, the structure and changes of gut microbiota in people taking camel milk and the analysis of the endophytic flora of camel edible desert plants. And this just quoting the headers in the results section. Why is that not represented/mentioned in the abstract? Instead the authors focus on the t2d rats and the MtcB mechanism they fail to present.

    Further the authors are sloppy when it comes to typos and preciseness. For example, in the abstract they talk first about sour camel milk, then whey and then milk again.

    I suggest a major restructuring/rewriting and if necessary partial reanalysing of the results and the conclusions.

    It would be good to have an overview figure combining the work done, also stating the number of samples for each experiment.

    __Author response: __Thank you very much for your nice suggestion on our manuscript, we applied some restructuring to our manuscript and the changes were highlighted in yellow.

    Major comments:

    1. Please make sure all raw data (sequences and filtering/assembly results) are deposited in public databases, like NCBI, ENA or else.

    __Author response: __The corresponding data is available as Mendeley Data, V1, https://doi.org/10. 17632/4w8n8n96tc.1, some datasets with bigger size uploaded failed owing to internet problem. The full version could be offered in other approaches if requested.

    1. Please state briefly for each dataset analysed, which sequencing method was used, how many samples were collected and how many were pooled for the sequencing runs:

    AmpliAeq, whole metagenome HiSeq, MiSeq?

    __Author response: __Sample and dataset information for sequence was supplied in Supplementary Table 9 and 12. Sequencing library was prepared following Illumina library preparation instructions, and sequenced using Illumina Miseq platform at Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China) with pair-end (PE) 150 bp reads.

    1. Page14 line283:

    F082? What is it? A strain, species or a sample?

    Please state clearly in the text.

    Also please avoid using abbreviations where possible and if you have to use them, please define.

    __Author response: __When applying diversity analysis at the specie level, a species annotated as unclassified_g_norank_f_F082 was found abundant in camel feces in Darbancheng.

    1. Page14 line307:

    "These evidenced that camel milk was a vector transferring microbes from the female camel to their cubs."

    Yes, that may be likely, but 16S amplicon-seq cannot provide evidence. Evidence would be strain similarity confirmed by SNP's or the like. So please state that this is speculative or show appropriate evidence.

    __Author response: __We completely agree that SNP’s is better evidence for this point and thank you. Microbial diversity analysis was a main part of initial design, and our limited sample couldn’t meet the needs of diversity and SNPs in the same time. There also were reports which used 16S based methods to trace the microbes source(Du et al., 2022; El-Mokdad, 2014; Wang et al., 2018).

    1. Page15 line322 ff:

    "Besides, using raw milk was not effective in type 2 diabetic rat model, so we chose camel whey and bovine whey as the diet of type 2 diabetic rats in follow-up experiments"

    Data/evidence? How is it different from whey on a nutrient perspective, as whey was more effective? Any explanation for this difference? And the bovine whey, what species did it contain? Can they be transferred regarding the processing of whey prior to application?

    __Author response: __This is an interesting and valuable question. We prepared raw milk and whey for the pre-test, then directly turned to validate the function of whey. Maybe we will investigate the composition difference in the future. The whey was prepared using the following protocol: Centrifuge fresh milk for 20 mins at 5000 r/min, discard the fat, and precipitate and obtain the middle layer of skim milk. After 20 mins in a 40 ℃ water bath, adjust the pH to 4.6 with 10% glacial acetic acid, and store in a 4°C refrigerator, overnight. Then, the skim milk was centrifuged at 8000 r/min for 20 min, repeated twice, and the middle whey fraction was collected. The centrifuged whey was poured into a petri dish and sealed. It was frozen at -80°C for 12 hours and then pierced with a sterile toothpick on the petri dish and then freeze-dried to get whey powders. A speculation was the preparing progress of whey played an important role in their functional difference. A comprehensive comparison of camel raw milk, camel whey, bovine raw milk, and whey will be an interesting point and we may investigate it shortly.

    1. Page17 line366ff:

    "Taking the number of microbes involved in this pathway, 8001 species were noted in the high-dose camel whey group, 3447 in the positive drug group, and only 1467 in the diabetics." How many species were present in the rats initially? Was species abundance different in the first place, or did they get lost, or came from the camel whey?

    __Author response: __The rats were fed with broad-spectrum antibiotics for 2 weeks, which ensured the same species abundance in the beginning.

    1. Page17 line369 ff:

    "It indicated that these microbes might resist the high glucose environment of the host through the synthesis and metabolism of their amino acids, and the effect of high-dose camel milk was more effective than that of metformin"

    -> How high was the glucose level in the rat gut? Or were there any obvious physiological changes in the t2d model rats that are characteristic for such a high-glucose environment? Please explain.

    __Author response: __This is an interesting and critical question. We didn’t measure the glucose level in the rat gut directly because we had to make sure other related characterizations worked properly. Besides, we thought camel milk could regulate microbial community, and further influence the blood sugar level, which was more representative in our sight. Blood sugar level is supplied in Fig.4O and Supplementary Table 11.

    1. The resolution/quality of the figures is low and the labelling often small. So not all text is readable.

    __Author response: __We adjusted the figures in the manuscript and offered additional independent picture files. Additionally, it seemed caused by the PDF merge progress, please check the pictures in .docx or .png files for details.

    1. Page19 line400 ff:

    What serum metabolites were analysed and why? Please write an intro-sentence to make it easier for the reader.

    Please write more precise what methods were used. Maybe I missed it, but I didn't find it in the methods part as well (Page40/41).

    __Author response: __The rats fed high-dose camel whey or metformin showed similar improvement in serum metabolite imbalance and were closer to normal. Caproylcarnitine, taurodeoxycholic acid, acetylcarnitine, creatinine, linoleic acid, and tridecanoic acid were detected as upregulated; 2-deoxyuridine, cyclohexylamine, L-pipecolic acid, LysoPC(18:0), uracil, caprylic acid, cholesterol sulfate, L-citrulline, pelargonic acid, and phenol downregulated. Carnitine supplementation, due to its key role in lipid metabolism and antioxidant effects, may effectively manage Type 2 Diabetes by addressing fatty acid metabolism dysregulation and oxidative stress(Bene, Hadzsiev, & Melegh, 2018). Studies have shown that taurodeoxycholic acid can enhance the effect of insulin and reduce blood sugar levels by regulating endoplasmic reticulum stress, and have potential in the treatment of diabetes(Xing, Zhou, Wang, & Xu, 2023). Low serum creatinine is associated with the development of T2D(Song, Hong, Sung, & Lee, 2022). Increased linoleic acid consumption was recommended for the prevention of T2D(Henderson, Crofts, & Schofield, 2018). The uridine is phosphorylated into uracil, which is converted to 2-deoxyuridine. Then 2-deoxyuridine is further converted to thymine with thymidine phosphorylase, the expression of thymidine phosphorylase was lost or considerably reduced when the organism suffered nephropathy and the high concentration of thymidine is a cause of DNA impairment, which is related to diabetes and diabetic nephropathy(Spinazzola et al., 2002; Szabo et al.; Xia, Hu, Liang, Zou, Wang, & Luo, 2010). L-Pipecolic acid are associated with higher incidence of T2D(Razquin et al., 2019). A research showed LysoPC(16:0) and (18:0) may mediated a fast progression of diabetic kidney disease(Yoshioka et al., 2022). Cholesterol sulfate is the most abundant known sterol sulfate in human plasma, and it plays a significant role in the control of glucose metabolism, which contribute to the pathogenesis of insulin resistance and the resultant development of diabetes(Shi et al., 2014; Zhang et al., 2022). L-citrulline supplementation might improve glucose homeostasis, some lipid factors and inflammatory markers in overweight and obese patients with T2D(Azizi, Mahdavi, Mobasseri, Aliasgharzadeh, Abbaszadeh, & Ebrahimi-Mameghani, 2021). T2D mellitus is associated with increased total plasma free fatty acid and modulating its concentration is the mechanism of some fibrates and statins drugs(I. S. Sobczak, A. Blindauer, & J. Stewart, 2019). Most of these metabolites have been reported as causes of T2D or consequences of T2D progress, some have been designed as therapeutic target.

    The serum metabolites were carried out using Agilent 1290 Infinity UHPLC system equipped with a HILIC column. The mobile phase of the optimized method consisted of (A) water with 25 mM ammonium acetate and 25 mM ammonia; and (B) acetonitrile (ACN). The following gradient elution was used: 5% A at 0-1min; 5-35% A at 1-14 min; 35-60% A at 14-16 min; 60% A at 16-18 min ; 60-5% A at 18-18.1 min and 5% A at 18.1-23 min. The flow rate was 0.3 mL/min, injection volume 2 μL, and column temperature was 25 ℃. Triple TOF 5600 mass spectrometer was applied for mass spectrometer analysis. The condition was used as following: Ion Source Gas1:60,Ion Source Gas2:60,Curtain gas:30,source temperature:600℃,IonSapary Voltage Floating ± 5500 V. TOF MS scan m/z range:60-1000 Da,product ion scan m/z range:25-1000 Da,TOF MS scan accumulation time 0.20 s/spectra, product ion scan accumulation time 0.05 s/spectra.MS/MS was gathered by information dependent acquisition (IDA) using high sensitivity mode, Declustering potential:±60 V, Collision Energy:35±15 eV, and IDA was set as Exclude isotope within 4 Da, Candidate ions to monito per cycle: 6. The methods part was complemented.

    Minor comments:

    1. Page1, line56-58 ff

    Please phrase more clearly:

    "This study specified that the transportation of microbiome happened both intra- and inter-species and played a principal role in the formation of progeny gut microflora."

    While the content is mostly comprehensible, there is a need for rephrasing and correction of language also in the following text.

    __Author response: __As suggested by the reviewer, we have rephrased and modified the abstract part.

    1. Page14 line300 ff:

    There is no need to show the OTU numbers in the text, please provide your results as a table in the supplements and refer to it in the text.

    Author response: We deleted OTU numbers in the manuscript and added the corresponding table in supplementary file.

    1. Page15 line328: Please check for typos, it is Shannon index, not Shanno.

    __Author response: __The corresponding correction was applied in the manuscript.

    1. Page16 line334:

    Please mention the number, age and sex of the rats used and how many groups you had in your experiments.

    __Author response: __SPF-grade male rats weighing 180-220 g were used for our related experiments. The detailed information is available in Supplementary Material (Supplementary Table 11-13).

    1. The headlines should logically structure the paper:

    For example, the authors have two very similar sections in the results part: "Composition and changes of rat gut microbiota under the regulation of camel milk" and "Analysis of the composition of gut microbiota in rats". Those can be combined or stated more concise.

    Also, other headlines improvement to make it easier for the reader to follow.

    __Author response: __We adjusted this part in the manuscript according to the reviewer’s suggestion.

    Reviewer #2 (Significance (Required)):

    I do think the study is of broad interest and relevance. However, the presentation of the analysis and data needs major revision. Especially it is lacking clarity on what was done for which samples and how the authors draw their conclusions. Also, I think that abstract and main text have a different focus. I would suggest to the authors to concentrate on their findings in abstract and text and state precisely what was done and what they found.

    __Author response: __Thank you very much for your recognition of our manuscript.

  2. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

    Learn more at Review Commons


    Referee #2

    Evidence, reproducibility and clarity

    Summary:

    The authors introduce a study assessing the bacterial flora of sour fermented camel milk and its capability to introduce beneficial species into consumer's gut. They further tested the potential of its nutrients and species for beneficial effects on type 2 diabetic (t2d) rats. They claim that t2d rats fed with high-dose camel whey reveal a microbiota closer to that of healthy rats rather than that of other t2d rats not receiving the camel whey treatment. Further they claim that this effect is due to the presence of Eubacterium limnetica that was exclusively found in the gut microflora of rats taking camel milk and producing MtcB protein. They conclude that camel milk may have the potential to be functional food.

    Overall, I think the approach of looking into camel milk and its microbiota is of broad interest, as it is food consumed traditionally by many tribes and in several countries. However, to me the presentation of the findings, the data and the analysis is often unprecise and confusing. For example, the MtcB protein they claim to be the mechanism of reducing the risk for t2d in the abstract is mentioned only once in the whole study and there only as a finding of another study (cited). According to my understanding the abstract should contain the main findings of the study, rather than some side-finding from other studies happens to match with the study results. I assume the authors have plenty of results from their sequencing data and metabolomics that they could mention in the abstract. In the text the authors mention the analysis of the microbial composition and source analysis of camel milk, the analysis of the gut microbiota of young camels, the composition, and changes of rat gut microbiota under the regulation of camel milk, the structure and changes of gut microbiota in people taking camel milk and the analysis of the endophytic flora of camel edible desert plants. And this just quoting the headers in the results section. Why is that not represented/mentioned in the abstract? Instead the authors focus on the t2d rats and the MtcB mechanism they fail to present. Further the authors are sloppy when it comes to typos and preciseness. For example, in the abstract they talk first about sour camel milk, then whey and then milk again.

    I suggest a major restructuring/rewriting and if necessary partial reanalysing of the results and the conclusions.

    It would be good to have an overview figure combining the work done, also stating the number of samples for each experiment.

    Major comments:

    1. Please make sure all raw data (sequences and filtering/assembly results) are deposited in public databases, like NCBI, ENA or else.
    2. Please state briefly for each dataset analysed, which sequencing method was used, how many samples were collected and how many were pooled for the sequencing runs: AmpliAeq, whole metagenome HiSeq, MiSeq?
    3. Page14 line283: F082? What is it? A strain, species or a sample? Please state clearly in the text. Also please avoid using abbreviations where possible and if you have to use them, please define.
    4. Page14 line307: "These evidenced that camel milk was a vector transferring microbes from the female camel to their cubs." Yes, that may be likely, but 16S amplicon-seq cannot provide evidence. Evidence would be strain similarity confirmed by SNP's or the like. So please state that this is speculative or show appropriate evidence.
    5. Page15 line322 ff: "Besides, using raw milk was not effective in type 2 diabetic rat model, so we chose camel whey and bovine whey as the diet of type 2 diabetic rats in follow-up experiments" Data/evidence? How is it different from whey on a nutrient perspective, as whey was more effective? Any explanation for this difference? And the bovine whey, what species did it contain? Can they be transferred regarding the processing of whey prior to application?
    6. Page17 line366ff: "Taking the number of microbes involved in this pathway, 8001 species were noted in the high-dose camel whey group, 3447 in the positive drug group, and only 1467 in the diabetics." How many species were present in the rats initially? Was species abundance different in the first place, or did they get lost, or came from the camel whey?
    7. Page17 line369 ff: "It indicated that these microbes might resist the high glucose environment of the host through the synthesis and metabolism of their amino acids, and the effect of high-dose camel milk was more effective than that of metformin"
    • How high was the glucose level in the rat gut? Or were there any obvious physiological changes in the t2d model rats that are characteristic for such a high-glucose environment? Please explain.
    1. The resolution/quality of the figures is low and the labelling often small. So not all text is readable.
    2. Page19 line400 ff: What serum metabolites were analysed and why? Please write an intro-sentence to make it easier for the reader. Please write more precise what methods were used. Maybe I missed it, but I didn't find it in the methods part as well (Page40/41).

    Minor comments:

    1. Page1, line56-58 ff Please phrase more clearly: "This study specified that the transportation of microbiome happened both intra- and inter-species and played a principal role in the formation of progeny gut microflora." While the content is mostly comprehensible, there is a need for rephrasing and correction of language also in the following text.
    2. Page14 line300 ff: There is no need to show the OTU numbers in the text, please provide your results as a table in the supplements and refer to it in the text.
    3. Page15 line328: Please check for typos, it is Shannon index, not Shanno.
    4. Page16 line334: Please mention the number, age and sex of the rats used and how many groups you had in your experiments.
    5. The headlines should logically structure the paper: For example, the authors have two very similar sections in the results part: "Composition and changes of rat gut microbiota under the regulation of camel milk" and "Analysis of the composition of gut microbiota in rats". Those can be combined or stated more concise. Also, other headlines improvement to make it easier for the reader to follow.

    Significance

    I do think the the study is of broad interest and relevance. However, the presentation of the analysis and data needs major revision. Especially it is lacking clarity on what was done for which samples and how the authors draw their conclusions. Also I think that abstract and main text have a different focus. I would suggest to the authors to concentrate on their findings in abstract and text and state precisely what was done and what they found.

  3. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

    Learn more at Review Commons


    Referee #1

    Evidence, reproducibility and clarity

    The provided document, titled "Camel Milk Affects Serum Metabolites by Modulating the Intestinal Microflora," is an extensive research paper. My summary covers the first 44 pages of the total 63 pages. The document begins with a standard review commons manuscript notice and provides contact information for the Review Commons office.

    The research focuses on the effects of camel milk on serum metabolites and the intestinal microflora. It starts with a detailed introduction to the topic, outlining the crucial role of gut microbes in human health and the influence of various factors like diet, genetics, and environment on these microbes. The paper emphasizes the nutritional richness of camel milk and its potential as a functional food, particularly its impact on gut microbiota and host metabolism.

    Initial sections of the paper discuss the research methodologies, including the study's keywords, abstract, and introduction. The abstract highlights the study's significant findings, such as the presence of various beneficial bacteria in sour camel milk, the inter- and intra-species transportation of microbiomes, and the impact of camel milk on the gut microflora and serum metabolites of type 2 diabetic rats.

    The introduction further delves into the composition of the human gut microbiota and the shaping factors of the adult gut microbiome. It also examines the role of diet in modulating gut microbiota and the potential health benefits of dairy products, with a particular focus on camel milk.

    Subsequent sections present detailed research findings, including the results of microbial composition and source analysis in camel milk, the composition and changes of rat gut microbiota under camel milk regulation, and the effects of camel milk-regulated gut microbiota on metabolism in rats. The research also explores the interspecies transfer of microbes using camel milk as a vector and analyzes the gut microbiota in people consuming camel milk.

    The paper further discusses the endophytic flora of camel edible desert plants and their possible influence on the camel's gut microbiota. The discussion section integrates the findings, offering insights into the potential health benefits of camel milk and its probiotic qualities. It also compares the effects of camel milk with other dairy products and discusses its role as a vector for beneficial microbes.

    Materials and methods used in the study are detailed towards the end of the summarized portion, describing sample collection and processing, the experimental setup for rats, and data processing and analysis techniques.

    Significance

    The paper continues with detailed research findings, including the microbial composition in camel milk, the impact on the gut microflora of rats and humans, and the serum metabolism effects. There's a focus on how camel milk, as a vector, can transfer beneficial microbes between species, influencing gut microbiota and host metabolism. The paper compares the effects of camel milk with other dairy products, emphasizing its unique health benefits and its role in transferring beneficial microbes. It discusses various bacteria found in camel milk and their potential health benefits. The research findings extend to understanding how camel milk affects human gut microbiota, with studies on pastoral herders who consume camel or bovine milk.