<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE article PUBLIC "-//NLM//DTD Journal Publishing DTD v3.0 20080202//EN" "http://dtd.nlm.nih.gov/publishing/3.0/journalpublishing3.dtd">
<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="3.0" xml:lang="en" article-type="research article">
 <front>
  <journal-meta>
   <journal-id journal-id-type="publisher-id">
    ajmb
   </journal-id>
   <journal-title-group>
    <journal-title>
     American Journal of Molecular Biology
    </journal-title>
   </journal-title-group>
   <issn pub-type="epub">
    2161-6620
   </issn>
   <issn publication-format="print">
    2161-6663
   </issn>
   <publisher>
    <publisher-name>
     Scientific Research Publishing
    </publisher-name>
   </publisher>
  </journal-meta>
  <article-meta>
   <article-id pub-id-type="doi">
    10.4236/ajmb.2025.154019
   </article-id>
   <article-id pub-id-type="publisher-id">
    ajmb-145836
   </article-id>
   <article-categories>
    <subj-group subj-group-type="heading">
     <subject>
      Articles
     </subject>
    </subj-group>
    <subj-group subj-group-type="Discipline-v2">
     <subject>
      Biomedical 
     </subject>
     <subject>
       Life Sciences
     </subject>
    </subj-group>
   </article-categories>
   <title-group>
    Alterations in Goat Microbiota Following Panax notoginseng Supplementation: Metagenomic Insights and Potential for Gastrointestinal Nematode Control
   </title-group>
   <contrib-group>
    <contrib contrib-type="author" xlink:type="simple">
     <name name-style="western">
      <surname>
       Yonathan
      </surname>
      <given-names>
       Tilahun
      </given-names>
     </name>
    </contrib>
    <contrib contrib-type="author" xlink:type="simple">
     <name name-style="western">
      <surname>
       Adekayode
      </surname>
      <given-names>
       Sonibare
      </given-names>
     </name>
    </contrib>
    <contrib contrib-type="author" xlink:type="simple">
     <name name-style="western">
      <surname>
       Zaisen
      </surname>
      <given-names>
       Wang
      </given-names>
     </name>
    </contrib>
   </contrib-group> 
   <aff id="affnull">
    <addr-line>
     aSherman Lewis School of Agriculture and Applied Sciences, Langston University, Langston, Oklahoma, USA
    </addr-line> 
   </aff> 
   <pub-date pub-type="epub">
    <day>
     22
    </day> 
    <month>
     09
    </month>
    <year>
     2025
    </year>
   </pub-date> 
   <volume>
    15
   </volume> 
   <issue>
    04
   </issue>
   <fpage>
    277
   </fpage>
   <lpage>
    282
   </lpage>
   <history>
    <date date-type="received">
     <day>
      4,
     </day>
     <month>
      August
     </month>
     <year>
      2025
     </year>
    </date>
    <date date-type="published">
     <day>
      19,
     </day>
     <month>
      August
     </month>
     <year>
      2025
     </year> 
    </date> 
    <date date-type="accepted">
     <day>
      19,
     </day>
     <month>
      September
     </month>
     <year>
      2025
     </year> 
    </date>
   </history>
   <permissions>
    <copyright-statement>
     © Copyright 2014 by authors and Scientific Research Publishing Inc. 
    </copyright-statement>
    <copyright-year>
     2014
    </copyright-year>
    <license>
     <license-p>
      This work is licensed under the Creative Commons Attribution International License (CC BY). http://creativecommons.org/licenses/by/4.0/
     </license-p>
    </license>
   </permissions>
   <abstract>
    Certain medicinal plants are known to have potent effects on egg hatching and larval motility of gastrointestinal nematodes (GIN) such as Haemonchus contortus (barber pole worm). In this study, we investigated the impact of Panax notoginseng (P. notoginseng) extracts on the gut microbiome of goats, in comparison to Syzygium aromaticum and Piper nigrum when used as treatments towards Haemonchus contortus (H. contortus). Using metagenomic analysis of rumen fluid and fecal samples, we observed significant alterations in the microbial community structure, specifically in the P. notoginseng treatment group. Notably, several microbial taxa were significantly upregulated in treated animals. These findings provide a foundation for further research to identify and harness microbiome-mediated resistance to gastrointestinal nematode (GIN) parasitism in goats.
   </abstract>
   <kwd-group> 
    <kwd>
     Medicinal Plants
    </kwd> 
    <kwd>
      Goats
    </kwd> 
    <kwd>
      Metagenomics
    </kwd> 
    <kwd>
      Panax notoginseng
    </kwd> 
    <kwd>
      Microbiome
    </kwd> 
    <kwd>
      Gastrointestinal Nematodes
    </kwd>
   </kwd-group>
  </article-meta>
 </front>
 <body>
  <sec id="s1">
   <title>1. Introduction</title>
   <p>Gastrointestinal parasitism poses major challenges to small ruminant production, especially in tropical, sub-tropical, and temperate regions worldwide, often resulting in substantial stock losses and economic hardship <xref ref-type="bibr" rid="scirp.145836-1">
     [1]
    </xref> <xref ref-type="bibr" rid="scirp.145836-2">
     [2]
    </xref>. Chemical anthelmintics, the current standard for parasite control, have led to widespread anthelmintic resistance due to overuse, and drug residues in food products pose additional public health concerns <xref ref-type="bibr" rid="scirp.145836-3">
     [3]
    </xref>-<xref ref-type="bibr" rid="scirp.145836-5">
     [5]
    </xref>. As such, research into alternative management options for helminth control is necessary.</p>
   <p>
    <xref ref-type="bibr" rid="scirp.145836-"></xref>Previous in-vitro studies from our laboratory (unpublished) have demonstrated potent inhibitory effects of Panax notoginseng (P. notoginseng) and other medicinal plants on helminth egg hatching and larval motility <xref ref-type="bibr" rid="scirp.145836-6">
     [6]
    </xref>. However, the in-vivo effects—particularly on host microbiome and related parasite resistance—remain unclear. The gut microbiome plays a critical role in host immunity and resistance to parasite infection <xref ref-type="bibr" rid="scirp.145836-7">
     [7]
    </xref>.</p>
  </sec><sec id="s2">
   <title>2. Objectives</title>
   <p>We report the effects of supplementation with Syzogium aromaticum, P. notoginseng (NOTOGINSENG), and Piper nigrum on the goat gut microbiome, aiming to identify microbial signatures associated with anti-parasitic benefits and to assess the potential for these botanicals in GIN parasite management programs.</p>
  </sec><sec id="s3">
   <title>3. Materials and Methods</title>
   <sec id="s3_1">
    <title>3.1. Animals and Housing</title>
    <p>Thirty adult Spanish goats (Fecal Egg Count [FEC] 500 - 3000 EPG) were selected from the flock maintained at Langston University. After cessation of Bioworma® and an acclimation period, goats were weighed, randomly assigned to five groups (n = 6 per group), and balanced for initial FEC. Animals were housed individually, with free access to water and provided Johnson grass hay (25 g/kg BW/day) and low protein concentrate pellets (15 g/kg BW/day).</p>
   </sec>
   <sec id="s3_2">
    <title>3.2. Treatments</title>
    <p>Dried plant materials (Syzygium aromaticum, Piper nigrum, and Panax notoginseng) were obtained commercially, ground into powder, and incorporated into molasses-based pellets and administered orally (50 g/animal/day) for 10 consecutive days (<xref ref-type="table" rid="table1">
      Table 1
     </xref>). Control animals received pellets without plant additives (<xref ref-type="table" rid="table1">
      Table 1
     </xref>). An additional group received a 1:1:1 mixture of the three botanicals (<xref ref-type="table" rid="table1">
      Table 1
     </xref>).</p>
    <table-wrap id="table1">
     <label>
      <xref ref-type="table" rid="table1">
       Table 1
      </xref></label>
     <caption>
      <title>
       <xref ref-type="bibr" rid="scirp.145836-"></xref>Table 1. The study was designed where group, number of subjects (goats), treatment types, the dose per animal per day of the total days of treatment are described.</title>
     </caption>
     <table class="MsoTableGrid custom-table" border="0" cellspacing="0" cellpadding="0"> 
      <tr> 
       <td class="custom-bottom-td custom-top-td acenter" width="10.27%"><p style="text-align:center">Group</p></td> 
       <td class="custom-bottom-td custom-top-td acenter" width="14.95%"><p style="text-align:center">No. goats</p></td> 
       <td class="custom-bottom-td custom-top-td acenter" width="29.92%"><p style="text-align:center">Treatment</p></td> 
       <td class="custom-bottom-td custom-top-td acenter" width="21.36%"><p style="text-align:center">Doses</p></td> 
       <td class="custom-bottom-td custom-top-td acenter" width="23.50%"><p style="text-align:center">Days of treatment</p></td> 
      </tr> 
      <tr> 
       <td class="custom-top-td acenter" width="10.27%"><p style="text-align:center">1</p></td> 
       <td class="custom-top-td acenter" width="14.95%"><p style="text-align:center">6</p></td> 
       <td class="custom-top-td acenter" width="29.92%"><p style="text-align:center">Control</p></td> 
       <td class="custom-top-td acenter" width="21.36%"><p style="text-align:center"></p></td> 
       <td class="custom-top-td acenter" width="23.50%"><p style="text-align:center"></p></td> 
      </tr> 
      <tr> 
       <td class="acenter" width="10.27%"><p style="text-align:center">2</p></td> 
       <td class="acenter" width="14.95%"><p style="text-align:center">6</p></td> 
       <td class="acenter" width="29.92%"><p style="text-align:center">Syzygium aromaticum</p></td> 
       <td class="acenter" width="21.36%"><p style="text-align:center">50 g/animal/day</p></td> 
       <td class="acenter" width="23.50%"><p style="text-align:center">10 days</p></td> 
      </tr> 
      <tr> 
       <td class="acenter" width="10.27%"><p style="text-align:center">3</p></td> 
       <td class="acenter" width="14.95%"><p style="text-align:center">6</p></td> 
       <td class="acenter" width="29.92%"><p style="text-align:center">Panax notoginseng</p></td> 
       <td class="acenter" width="21.36%"><p style="text-align:center">50 g/animal/day</p></td> 
       <td class="acenter" width="23.50%"><p style="text-align:center">10 days</p></td> 
      </tr> 
      <tr> 
       <td class="acenter" width="10.27%"><p style="text-align:center">4</p></td> 
       <td class="acenter" width="14.95%"><p style="text-align:center">6</p></td> 
       <td class="acenter" width="29.92%"><p style="text-align:center">Piper nigrum</p></td> 
       <td class="acenter" width="21.36%"><p style="text-align:center">50 g/animal/day</p></td> 
       <td class="acenter" width="23.50%"><p style="text-align:center">10 days</p></td> 
      </tr> 
      <tr> 
       <td class="custom-bottom-td acenter" width="10.27%"><p style="text-align:center">5</p></td> 
       <td class="custom-bottom-td acenter" width="14.95%"><p style="text-align:center">6</p></td> 
       <td class="custom-bottom-td acenter" width="29.92%"><p style="text-align:center">ANN (1:1:1)</p></td> 
       <td class="custom-bottom-td acenter" width="21.36%"><p style="text-align:center">50 g/animal/day</p></td> 
       <td class="custom-bottom-td acenter" width="23.50%"><p style="text-align:center">10 days</p></td> 
      </tr> 
     </table>
    </table-wrap>
   </sec>
   <sec id="s3_3">
    <title>3.3. Sampling and Laboratory Analyses</title>
    <p>Feed intake was assessed daily by subtracting orts from feed offered. Body weight was measured on days 0 and 10. Rumen fluid was collected by stomach tube on days 0 and 10 for microbiome analysis. Fecal samples were collected per rectum for FEC, egg hatching, and microbiome analyses. Parasitological methods included: Fecal Egg Counts (FEC) using the modified McMaster technique <xref ref-type="bibr" rid="scirp.145836-8">
      [8]
     </xref>-<xref ref-type="bibr" rid="scirp.145836-10">
      [10]
     </xref>. Egg hatching and larval recovery were completed using standard coproculture and baermannization <xref ref-type="bibr" rid="scirp.145836-11">
      [11]
     </xref>-<xref ref-type="bibr" rid="scirp.145836-13">
      [13]
     </xref>.</p>
    <p>Metagenomic DNA extraction was performed using Norgen Biotek Microbiome kits. DNA libraries were prepared (IDT xGen, NEB poly-A selection) and sequenced on an Illumina NovaSeq 6000 ([PE150], 20 M reads/sample). Bioinformatics and Statistical Analysis included sequence analysis with Partek® Flow® and MiniKraken, PCA and differential abundance analyses (Kruskal-Wallis test) were performed. Power analysis (SAS) confirmed the adequacy of n = 6/group for &gt; 89% statistical power.</p>
   </sec>
  </sec><sec id="s4">
   <title>4. Results</title>
   <sec id="s4_1">
    <title>4.1. Experimental Design and Power Analysis</title>
    <p>A sample size of 6 goats per treatment was found adequate (power &gt; 89%) to detect expected FEC difference based on prior studies.</p>
   </sec>
   <sec id="s4_2">
    <title>4.2. Microbiome Profiling</title>
    <p>When treatment controls were compared to those that were treated with NOTOGINSENG following infection with Haemonchus contortus. No significant overall change was observed when pooling treatment groups versus control, except when comparing the NOTOGINSENG treatment group versus the control. Comparison of treatment samples with the NOTOGINSENG group revealed significant microbiome shifts. Differential abundance showed Kruskal-Wallis testing of 1137 points between control and NOTOGINSENG groups revealing 33 significantly upregulated taxa, no downregulated taxa, 409 inconclusive, and 695 insignificant findings (<xref ref-type="fig" rid="fig1">
      Figure 1
     </xref>, <xref ref-type="table" rid="table2">
      Table 2
     </xref>).</p>
    <table-wrap id="table2">
     <label>
      <xref ref-type="table" rid="table2">
       Table 2
      </xref></label>
     <caption>
      <title>
       <xref ref-type="bibr" rid="scirp.145836-"></xref>Table 2. Significantly upregulated microbial flora when Control vs NOTOGENENG are compared.</title>
     </caption>
     <table class="MsoTableGrid custom-table" border="0" cellspacing="0" cellpadding="0"> 
      <tr> 
       <td class="custom-bottom-td custom-top-td acenter" width="54.27%"><p style="text-align:center">Feature ID</p></td> 
       <td class="custom-bottom-td custom-top-td acenter" width="17.65%"><p style="text-align:center">P-value</p></td> 
       <td class="custom-bottom-td custom-top-td acenter" width="22.99%"><p style="text-align:center">Fold change</p></td> 
      </tr> 
      <tr> 
       <td class="custom-top-td acenter" width="54.27%"><p style="text-align:center">Helicobacter sp. MIT 01-6242</p></td> 
       <td class="custom-top-td acenter" width="17.65%"><p style="text-align:center">0.000024</p></td> 
       <td class="custom-top-td acenter" width="22.99%"><p style="text-align:center">2</p></td> 
      </tr> 
      <tr> 
       <td class="acenter" width="54.27%"><p style="text-align:center">Fischerella sp NIES-4106</p></td> 
       <td class="acenter" width="17.65%"><p style="text-align:center">0.00078</p></td> 
       <td class="acenter" width="22.99%"><p style="text-align:center">2</p></td> 
      </tr> 
      <tr> 
       <td class="acenter" width="54.27%"><p style="text-align:center">Frischella perrara</p></td> 
       <td class="acenter" width="17.65%"><p style="text-align:center">0.00078</p></td> 
       <td class="acenter" width="22.99%"><p style="text-align:center">2</p></td> 
      </tr> 
      <tr> 
       <td class="acenter" width="54.27%"><p style="text-align:center">Spiroplasma apis</p></td> 
       <td class="acenter" width="17.65%"><p style="text-align:center">0.00078</p></td> 
       <td class="acenter" width="22.99%"><p style="text-align:center">2</p></td> 
      </tr> 
      <tr> 
       <td class="acenter" width="54.27%"><p style="text-align:center">Stenotrophomonas maltophilia</p></td> 
       <td class="acenter" width="17.65%"><p style="text-align:center">0.0029</p></td> 
       <td class="acenter" width="22.99%"><p style="text-align:center">16</p></td> 
      </tr> 
      <tr> 
       <td class="acenter" width="54.27%"><p style="text-align:center">Pseudodesulfovibrio piezophilu…</p></td> 
       <td class="acenter" width="17.65%"><p style="text-align:center">0.03</p></td> 
       <td class="acenter" width="22.99%"><p style="text-align:center">2</p></td> 
      </tr> 
      <tr> 
       <td class="custom-bottom-td acenter" width="54.27%"><p style="text-align:center">…(see full <xref ref-type="table" rid="table2">
          Table 2
         </xref> for additional taxa)</p></td> 
       <td class="custom-bottom-td acenter" width="17.65%"><p style="text-align:center"></p></td> 
       <td class="custom-bottom-td acenter" width="22.99%"><p style="text-align:center"></p></td> 
      </tr> 
     </table>
    </table-wrap>
    <fig id="fig1" position="float">
     <label>Figure 1</label>
     <caption>
      <title>
       <xref ref-type="bibr" rid="scirp.145836-"></xref>Figure 1. Volcano plot resulting from differential analyses using Kruskall-Wallis points of the presence of microbial organisms.</title>
     </caption>
     <graphic mimetype="image" position="float" xlink:type="simple" xlink:href="https://html.scirp.org/file/1070604-rId15.jpeg?20250922034331" />
    </fig>
   </sec>
  </sec><sec id="s5">
   <title>5. Discussion</title>
   <p>P.notoginseng supplementation resulted in significant changes to the microbiota not observed in goats treated with S. aromaticum or P.nigrum. Increased abundance of Helicobacter sp. MIT 01-6242 (an organism linked to ulceration in sea otters and known for antibiotic sensitivity) was recorded <xref ref-type="bibr" rid="scirp.145836-14">
     [14]
    </xref>. Fischerella sp NIES-4106 is a strain of cyanobactera that is not responsible for parasitic activity, but may be upregulated as a response to parasitic infection causing a range of symptoms caused by parasites <xref ref-type="bibr" rid="scirp.145836-15">
     [15]
    </xref>. Like Fischerella sp NIES-4106, Frischella perrara, is notably elevated in treated goats, it is known to be a dominant immunomodulator in honeybees, and may be involved in igniting the inflammation caused by GIN <xref ref-type="bibr" rid="scirp.145836-16">
     [16]
    </xref> <xref ref-type="bibr" rid="scirp.145836-17">
     [17]
    </xref>. Spiroplasma apis is another revealed microorganism that appears to be upregulated when a host is infected by a parasite such as H. contortus . The substantial modulation of microbial communities, points to P. notoginseng as a promising candidate for further study as a means of microbiome-mediated GIN control. The observed microbial communities are potentially conducive to anti-parasitic effects, possibly enhancing host immunity or antagonizing parasite establishment.</p>
  </sec><sec id="s6">
   <title>6. Conclusion</title>
   <p>P. notoginseng supplementation produced the most notable impact on goat gut microbiota among the botanicals studied. Several upregulated taxa have known or hypothetical roles in immunological and gastrointestinal health. These results suggest a microbiome-medited mechanism for parasite resistance and support the potential of P. notoginseng in sustainable parasite control programs for ruminants.</p>
  </sec><sec id="s7">
   <title>Author Contributions</title>
   <p>Conceptualization, Z.W. and A. S.; methodology, Z.W., A. S., and Y. T.; software, Z.W., A.S., and Y.T.; validation, Z.W., A. S., and Y. T.; formal analysis, Z.W., A. S., and Y. T.; investigation, Z.W., A. S., and Y. T.; resources, Z.W.; data curation, Y.T.; writing—original draft preparation, Z.W., A. S., and Y. T.; writing—review and editing, Z.W., A. S., and Y. T.; visualization, Z.W., A. S., and Y. T.; supervision, Z. W.; project administration, Z. W.; funding acquisition, Z. W. All authors have read and agreed to the published version of the manuscript.</p>
  </sec><sec id="s8">
   <title>Funding</title>
   <p>This work was supported partially by Capacity Building Program, Grant no. 2017-38821-26429/project accession no. 1012072 from the USDA National Institute of Food and Agriculture (ZW).</p>
  </sec><sec id="s9">
   <title>Acknowledgements</title>
   <p>The authors would like to acknowledge the assistance of faculty, staff, and students in the Sherman Lewis School of Agriculture and Applied Sciences at Langston University, Langston, OK.</p>
  </sec>
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