CoChat
Sign Up
Cited by 63Reproductive tract infections researchGut microbiota and healthBacteriophages and microbial interactions

Bacterial amylases enable glycogen degradation by the vaginal microbiome

Open access
Jenkins, Dominick J., Woolston, Benjamin M., Hood-Pishchany, M. Indriati, Pelayo, Paula, Konopaski, Alyssa N., Quinn Peters, M., France, Michael T., Ravel, Jacques +4 more·2023·Nature Microbiology
DOI 10.1038/s41564-023-01447-2PMC PMC10465358
Open this paper in CoChat — free accountOpen PDF

Abstract

The human vaginal microbiota is frequently dominated by lactobacilli and transition to a more diverse community of anaerobic microbes is associated with health risks. Glycogen released by lysed epithelial cells is believed to be an important nutrient source in the vagina. However, the mechanism by which vaginal bacteria metabolize glycogen is unclear, with evidence implicating both bacterial and human enzymes. Here we biochemically characterize six glycogen-degrading enzymes (GDEs), all of which are pullanases (PulA homologues), from vaginal bacteria that support the growth of amylase-deficient Lactobacillus crispatus on glycogen. We reveal variations in their pH tolerance, substrate preferences, breakdown products and susceptibility to inhibition. Analysis of vaginal microbiome datasets shows that these enzymes are expressed in all community state types. Finally, we confirm the presence and activity of bacterial and human GDEs in cervicovaginal fluid. This work establishes that bacterial GDEs can participate in the breakdown of glycogen, providing insight into metabolism that may shape the vaginal microbiota.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41564-023-01447-2

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Estrogen increases glycogen production in vaginal epithelial cells, and bacterial amylases enable glycogen breakdown, promoting Lactobacillus persistence.

    “Estrogen increases the production of glycogen in vaginal epithelial cells, and bacterial amylases enable glycogen breakdown, promoting Lactobacillus persistence [4, 41].”

    From Feasibility, safety and tolerability of estrogen and/or probiotics for improving vaginal health in Canadian African, Caribbean, and Black women: A pilot phase 1 clinical trial (2025) · cites this paper as [41]

    The Abstract and Results report that bacterial glycogen-degrading enzymes support Lactobacillus growth on glycogen, while the Main section links vaginal glycogen to Lactobacillus colonization. The paper does not establish that estrogen increases glycogen production in vaginal epithelial cells, and describes a contribution to Lactobacillus dominance as potential rather than demonstrated persistence. No page numbers are provided in our copy. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 66

  1. [1]Kalia N Singh J Kaur M Microbiota in vaginal health and pathogenesis of recurrent vulvovaginal infections: a critical review Ann. Clin. Microbiol. Antimicrob. 2020 19 5 31992328 PMC6986042
  2. [2]Ravel J Vaginal microbiome of reproductive-age women Proc. Natl Acad. Sci. USA 2011 108 4680 4687 20534435 PMC3063603
  3. [3]Anahtar MN Inflammatory responses in the female genital tract Immunity 2016 42 965 976 PMC4461369 25992865
  4. [4]Gosmann C Lactobacillus-deficient cervicovaginal bacterial communities are associated with increased HIV acquisition in young South African women Immunity 2017 46 29 37 28087240 PMC5270628
  5. [5]Dols JAM Microarray-based identification of clinically relevant vaginal bacteria in relation to bacterial vaginosis Am. J. Obstet. Gynecol. 2011 204 305.e1 305.e7 21272848
  6. [6]Hočevar K Vaginal microbiome signature is associated with spontaneous preterm delivery Front. Med. 2019 6 201 PMC6746969 31552254
  7. [7]Gajer P Temporal dynamics of the human vaginal microbiota Sci. Transl. Med. 2012 4 132ra52 22553250 PMC3722878
  8. [8]Foster KR Schluter J Coyte KZ Rakoff-Nahoum S The evolution of the host microbiome as an ecosystem on a leash Nature 2017 548 43 51 28770836 PMC5749636
  9. [9]Rakoff-Nahoum S Foster KR Comstock LE The evolution of cooperation within the gut microbiota Nature 2016 533 255 259 27111508 PMC4978124
  10. [10]Porter NT Martens EC The critical roles of polysaccharides in gut microbial ecology and physiology Annu. Rev. Microbiol. 2017 71 349 369 28657886
  11. [11]Rakoff-Nahoum S Coyne MJ Comstock LE An ecological network of polysaccharide utilization among human intestinal symbionts Curr. Biol. 2014 24 40 49 24332541 PMC3924574
  12. [13]Amabebe E Anumba DOC The vaginal microenvironment: the physiologic role of Lactobacilli Front. Med. 2018 5 181 PMC6008313 29951482
  13. [14]Mirmonsef P Free glycogen in vaginal fluids is associated with Lactobacillus colonization and low vaginal pH PLoS ONE 2014 9 26 29 PMC4102502 25033265
  14. [15]Stewart-Tull DES Evidence that vaginal lactobacilli do not ferment glycogen Am. J. Obstet. Gynecol. 1964 88 676 679 14128200
  15. [16]Wylie JG Henderson A Identity and glycogen-fermenting ability of lactobacilli isolated from the vagina of pregnant women J. Med. Microbiol. 1969 2 363 366 4996481
  16. [17]Spear GT Human α-amylase present in lower-genital-tract mucosal fluid processes glycogen to support vaginal colonization by Lactobacillus J. Infect. Dis. 2014 210 1019 1028 24737800 PMC4168305
  17. [18]Spear GT Effect of pH on cleavage of glycogen by vaginal enzymes PLoS ONE 2015 10 e0132646 26171967 PMC4501710
  18. [19]Huffman RD Nawrocki LD Wilson WA Brittingham A Digestion of glycogen by a glucosidase released by Trichomonas vaginalis Exp. Parasitol. J. 2015 159 151 159 26420465
  19. [20]Smith RW Brittingham A Wilson WA Purification and identification of amylases released by the human pathogen Trichomonas vaginalis that are active towards glycogen Mol. Biochem. Parasitol. 2016 210 22 31 27506885
  20. [21]Nunn, K. L. et al. Amylases in the human vagina. mSphere10.1128/msphere.00943-20 (2020). PMC7729256 33298571
  21. [22]van der Veer C Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota Microbiome 2019 7 49 30925932 PMC6441167
  22. [23]Hertzberger R Genetic elements orchestrating Lactobacillus crispatus glycogen metabolism in the vagina Int. J. Mol. Sci. 2022 23 5590 35628398 PMC9141943
  23. [24]Qiao Y Gene cloning and enzymatic characterization of alkali-tolerant type I pullulanase from Exiguobacterium acetylicum Lett. Appl. Microbiol. 2015 60 52 59 25273816
  24. [25]Ma B A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina Nat. Commun. 2020 11 940 32103005 PMC7044274
  25. [26]Chen Y Activity-based protein profiling of retaining α-amylases in complex biological samples J. Am. Chem. Soc. 2021 143 2423 2432 33497208 PMC7883350
  26. [27]von Heijne G The signal peptide J. Membr. Biol. 1990 115 195 201 2197415
  27. [28]Bhandari P Tingley JP Palmer DRJ Abbott DW Hill JE Characterization of an a-glucosidase enzyme conserved in Gardnerella spp. isolated from the human vaginal microbiome J. Bacteriol. 2021 203 e0021321 34124938 PMC8351627
  28. [29]Boot HJ Kolen CPAM Pouwels PH Identification, cloning, and nucleotide sequence of a silent S-layer protein gene of Lactobacillus acidophilus ATCC 4356 which has extensive similarity with the S-layer protein gene of this species J. Bacteriol. 1995 177 7222 7230 8522531 PMC177603
  29. [30]Willing SE Clostridium difficile surface proteins are anchored to the cell wall using CWB2 motifs that recognise the anionic polymer PSII Mol. Microbiol. 2015 96 596 608 25649385 PMC4973711
  30. [31]Krogh A Larsson B von Heijne G Sonnhammer ELL Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes J. Mol. Biol. 2001 305 567 580 11152613
  31. [32]Cantarel BI The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics Nucleic Acids Res. 2009 37 20894 PMC2686590 18838391
  32. [33]El-Gebali S The Pfam protein families database in 2019 Nucleic Acids Res. 2019 47 D427 D432 30357350 PMC6324024
  33. [34]Boraston AB A structural and functional analysis of α-glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition J. Biol. Chem. 2006 281 587 598 16230347
  34. [35]Wiatrowski HA Mutations in the Gal83 glycogen-binding domain activate the Snf1/Gal83 kinase pathway by a glycogen-independent mechanism Mol. Cell. Biol. 2004 24 352 361 14673168 PMC303368
  35. [36]Michelin M Purification and biochemical characterization of a thermostable extracellular glucoamylase produced by the thermotolerant fungus Paecilomyces variotii J. Ind. Microbiol. Biotechnol. 2008 35 17 25 17938981
  36. [37]da Silva TM Purification and biochemical characterization of a novel α-glucosidase from Aspergillus niveus Int. J. Gen. Mol. Microbiol. 2009 96 569 578 19757138
  37. [38]Li Y Zhang L Ding Z Gu Z Shi G Engineering of isoamylase: improvement of protein stability and catalytic efficiency through semi-rational design J. Ind. Microbiol. Biotechnol. 2016 43 3 12 26597030
  38. [39]Jung JH Characterization of a novel extracellular α-amylase from Ruminococcus bromii ATCC 27255 with neopullulanase-like activity Int. J. Biol. Macromol. 2019 130 605 614 30836186
  39. [40]Lee HW Characterization and application of BiLA, a psychrophilic α-amylase from Bifidobacterium longum J. Agric. Food Chem. 2016 64 2709 2718 26979859
  40. [41]Marie S. Møller A An extracellular cell-attached pullulanase confers branched α-glucan utilization in human gut Lactobacillus acidophilus Appl. Environ. Microbiol. 2017 83 e00402-17 28411221 PMC5452828
  41. [42]Amsel R Nonspecific vaginitis. Diagnostic criteria and microbial and epidemiologic associations Am. J. Med. 1983 74 14 22 6600371
  42. [43]Lin FP Leu KL Cloning, expression, and characterization of thermostable region of amylopullulanase gene from Thermoanaerobacter ethanolicus 39E Appl. Biochem. Biotechnol. 2002 97 33 44 11900114
  43. [44]Nisha M Satyanarayana T Characterization of recombinant amylopullulanase (gt-apu) and truncated amylopullulanase (gt-apuT) of the extreme thermophile Geobacillus thermoleovorans NP33 and their action in starch saccharification Appl. Microbiol. Biotechnol. 2013 97 6279 6292 23132347
  44. [45]Nisha, M. & Satyanarayana, T. Recombinant bacterial amylopullulanases: developments and perspectives. 4, 388–400 (2013). PMC3937200 23645215
  45. [46]Wang M Discovery of a new microbial origin cold-active neopullulanase capable for effective conversion of pullulan to panose Int. J. Mol. Sci. 2022 23 6928 35805929 PMC9267027
  46. [47]Hii SL Tan JS Ling TC Ariff ABin Pullulanase: role in starch hydrolysis and potential industrial applications Enzym. Res. 2012 2012 921362 PMC3443597 22991654
  47. [48]France MT Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data Genome Biol. 2022 23 66 35232471 PMC8886902
  48. [49]Kaminski J Structure, function, and diversity of the healthy human microbiome with ShortBRED Nature 2012 486 207 214 22699609 PMC3564958
  49. [50]Garcia WL Profiling how the gut microbiome modulates host xenobiotic metabolism in response to benzo[a]pyrene and 1-nitropyrene exposure Chem. Res. Toxicol. 2022 35 585 596 35347982 PMC9878584
  50. [51]Bhandari P Tingley J Abbott DW Hill JE Glycogen-degrading activities of catalytic domains of a-amylase and a-amylase-pullulanase enzymes conserved in Gardnerella spp. from the vaginal microbiome J. Bacteriol. 2023 205 e0039322 36744900 PMC9945562
  51. [52]Andersch-Björkman Y Thomsson KA Holmén Larsson JM Ekerhovd E Hansson GC Large-scale identification of proteins, mucins and their O-glycosylation in the endocervical mucus during the menstrual cycle Mol. Cell. Proteom. 2007 6 708 716 17220477
  52. [53]Pereira L Identification of novel protein biomarkers of preterm birth in human cervical−vaginal fluid J. Proteome Res. 2007 6 1269 1276 17373840
  53. [54]Kim YE Quantitative proteomic profiling of cervicovaginal fluid from pregnant women with term and preterm birth Proteome Sci. 2021 19 3 33588889 PMC7885372
  54. [55]Zhang, J., Li, L., Zhang, T. & Zhong, J. Characterization of a novel type of glycogen‑degrading amylopullulanase from Lactobacillus crispatus. Appl. Microbiol. Biotechnol. 106, 4053–4064 (2022). 35612627
  55. [57]Lithgow, K. V, Cochinamogulos, A., Muirhead, K. & Oluoch, L. M. Resolving glycogen and related enzymes reveals correlates of Lactobacillus crispatus dominance in a cohort of young African women. Preprint at Res. Square10.21203/rs.3.rs-1679828/v1 (2022).
  56. [58]Markowitz VM IMG: the integrated microbial genomes database and comparative analysis system Nucleic Acids Res. 2012 40 115 122 PMC3245086 22194640
  57. [59]Almagro Armenteros JJ SignalP 5.0 improves signal peptide predictions using deep neural networks Nat. Biotechnol. 2019 37 420 423 30778233
  58. [60]Nayfach S Pollard KS Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome Genome Biol. 2015 16 51 25853934 PMC4389708
  59. [61]Levin BJ A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-L-proline Science 2017 355 eaai8386 28183913 PMC5705181
  60. [62]Jiang J Detection of active mammalian GH31 α-glucosidases in health and disease using in-class, broad-spectrum activity-based probes ACS Cent. Sci. 2016 2 351 358 27280170 PMC4882745
  61. [63]Yu F Haynes SE Nesvizhskii AI IonQuant enables accurate and sensitive label-free quantification with FDR-controlled match-between-runs Mol. Cell. Proteom. 2021 20 100077 PMC8131922 33813065
  62. [64]Keller A Nesvizhskii AI Kolker E Aebersold R Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal. Chem. 2002 74 5383 5392 12403597
  63. [65]Nesvizhskii AI Keller A Kolker E Aebersold R A statistical model for identifying proteins by tandem mass spectrometry Anal. Chem. 2003 75 4646 4658 14632076
  64. [66]Kong AT Leprevost FV Avtonomov DM Mellacheruvu D Nesvizhskii AI MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics Nat. Methods 2017 14 513 520 28394336 PMC5409104
  65. [67]Tyanova S The Perseus computational platform for comprehensive analysis of (prote)omics data Nat. Methods 2016 13 731 740 27348712
  66. [68]Zhang H DbCAN2: a meta server for automated carbohydrate-active enzyme annotation Nucleic Acids Res. 2018 46 W95 W101 29771380 PMC6031026

Cited by

Sorted by citations

Authors
Jenkins, D. J., Woolston, B. M., Hood-Pishchany, M. I., Pelayo, P., Konopaski, A. N., Quinn Peters, M., France, M. T., Ravel, J., Mitchell, C. M., Rakoff-Nahoum, S., Whidbey, C., & Balskus, E. P.
Affiliations
  • Harvard University (US)
  • Northeastern University (US)
  • Boston Children's Hospital (US)
  • Seattle University (US)
  • University of Maryland, Baltimore (US)
  • Howard Hughes Medical Institute (US)
Corresponding author
  • Rakoff-Nahoum, Seth
  • Whidbey, Christopher
  • Balskus, Emily P.
ORCID
Venue
Nature Microbiology
Publisher
Springer Science and Business Media LLC
Published
2023-08-10
Volume
8
Issue
9
Pages
1641-1652
ISSN
2058-5276 (ISSN-L)
DOI
10.1038/s41564-023-01447-2
PMC
PMC10465358
OpenAlex
W4385741861
Cited by
63
References
1
Citations by year
2026: 24 · 2025: 27 · 2024: 11 · 2023: 1
FWCI
11.57
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Microbiology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Bill and Melinda Gates Foundation (OPP1189211, OPP1189217)
  • Howard Hughes Medical Institute
  • U.S. Department of Health and Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD000850)
  • Doris Duke Charitable Foundation (2019129)
  • National Science Foundation
  • Burroughs Wellcome Fund
  • Pew Charitable Trusts
  • March of Dimes Foundation
  • U.S. Department of Health and Human Services (1K08AI130392-01)
  • U.S. Department of Health and Human Services | NIH | National Institute of General Medical Sciences (DP2GM136652)
  • M.J. Murdock Charitable Trust (NS‐201913756)
Topics
  • Life Sciences › Immunology and Microbiology › Microbiology › Reproductive tract infections research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
Keywords
bacterial amylase, glycogenolysis, vaginal microbiota, Lactobacillus crispatus, cervicovaginal fluid, pH tolerance, substrate specificity, enzyme inhibition, community state types, vaginal dysbiosis
MeSH terms
Amylases, Bacteria, Female, Glycogen, Humans, Vagina, Microbiota

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review