16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics

Christine Tara Peterson, Vandana Sharma, Stanislav N. Iablokov, Levent Albayrak, Kamil Khanipov, Sasha Uchitel, Deepak Chopra, Paul J. Mills, Yuriy Fofanov, Dmitry A. Rodionov, Scott N. Peterson

Research output: Contribution to journalArticle

Abstract

10.1371/journal.pone.0213869

The prebiotic potential of nervine herbal medicines has been scarcely studied. We therefore used anaerobic human fecal cultivation to investigate whether medicinal herbs commonly used as treatment in neurological health and disease in Ayurveda and other traditional systems of medicine modulate gut microbiota. Profiling of fecal cultures supplemented with either Kapikacchu, Gotu Kola, Bacopa/Brahmi, Shankhapushpi, Boswellia/Frankincense, Jatamansi, Bhringaraj, Guduchi, Ashwagandha or Shatavari by 16S rRNA sequencing revealed profound changes in diverse taxa. Principal coordinate analysis highlights that each herb drives the formation of unique microbial communities predicted to display unique metabolic potential. The relative abundance of approximately one-third of the 243 enumerated species was altered by all herbs. Additional species were impacted in an herb-specific manner. In this study, we combine genome reconstruction of sugar utilization and short chain fatty acid (SCFA) pathways encoded in the genomes of 216 profiled taxa with monosaccharide composition analysis of each medicinal herb by quantitative mass spectrometry to enhance the interpretation of resulting microbial communities and discern potential drivers of microbiota restructuring. Collectively, our results indicate that gut microbiota engage in both protein and glycan catabolism, providing amino acid and sugar substrates that are consumed by fermentative species. We identified taxa that are efficient amino acid fermenters and those capable of both amino acid and sugar fermentation. Herb-induced microbial communities are predicted to alter the relative abundance of taxa encoding SCFA (butyrate and propionate) pathways. Co-occurrence network analyses identified a large number of taxa pairs in medicinal herb cultures. Some of these pairs displayed related culture growth relationships in replicate cultures highlighting potential functional interactions among medicinal herb-induced taxa.

Original languageEnglish (US)
Article numbere0213869
JournalPloS one
Volume14
Issue number3
DOIs
StatePublished - Mar 1 2019

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Neurodegenerative diseases
Nootropic Agents
Prebiotics
neurodegenerative diseases
prebiotics
Medicinal Plants
rRNA Genes
Neurodegenerative Diseases
Amino Sugars
medicinal plants
herbs
Volatile Fatty Acids
Genes
ribosomal RNA
Genome
microbial communities
Amino Acids
amino sugars
genome
short chain fatty acids

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics. / Peterson, Christine Tara; Sharma, Vandana; Iablokov, Stanislav N.; Albayrak, Levent; Khanipov, Kamil; Uchitel, Sasha; Chopra, Deepak; Mills, Paul J.; Fofanov, Yuriy; Rodionov, Dmitry A.; Peterson, Scott N.

In: PloS one, Vol. 14, No. 3, e0213869, 01.03.2019.

Research output: Contribution to journalArticle

Peterson, Christine Tara ; Sharma, Vandana ; Iablokov, Stanislav N. ; Albayrak, Levent ; Khanipov, Kamil ; Uchitel, Sasha ; Chopra, Deepak ; Mills, Paul J. ; Fofanov, Yuriy ; Rodionov, Dmitry A. ; Peterson, Scott N. / 16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics. In: PloS one. 2019 ; Vol. 14, No. 3.
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