Microplastics and human health - rapid literature review

Julian Flowers

20/01/2022

Search

Search for microplastics and human health

search <- "microplastics health human[mh] review[pt]"
n <- 153
start <- 1990
end <- 2021
key <- Sys.getenv("ncbi_key")

out <- pubmedAbstractR(search = search, n = n, start = start, end = end, ncbi_key = key)
## Please wait...Your query is (("microplastics"[MeSH Terms] OR "microplastics"[All Fields]) AND ("health"[MeSH Terms] OR "health"[All Fields]) AND "humans"[MeSH Terms]) AND review[pt] AND 1990[PDAT] : 2021[PDAT]. This returns 153 abstracts. By default 1000 abstracts are downloaded. You downloaded 153 abstracts. To retrieve more set 'n =' argument to the desired value
out$abstracts %>%
  select(year, title, journal, pmid) %>%
  flextable::flextable(cwidth = 6)

Abstract themes

Clustering

corpus <- out$abstracts %>%
  rename(absText = abstract) %>%
  create_abstract_corpus()

cluster <- create_abstract_cluster(corpus$corpus, minPts = 4)
## If there are a small number of abstracts, set perplexity value 
## to less than 30% of abstract count

## 0.393 sec elapsed
cluster$cluster_count
## [1] 7
labels <- create_cluster_labels(corpus$corpus, clustering = cluster$clustering)

unique(labels$labels)
## # A tibble: 7 × 2
## # Groups:   cluster [7]
##   cluster clus_names                                                            
##     <dbl> <chr>                                                                 
## 1       0 environ-microplast-review-human-health                                
## 2       1 mnp-micro-challeng-environ-review-health                              
## 3       2 np-mp-nanoplast-plastic-environment-effect-human-health-microplast    
## 4       3 gut-microbiota-effect-microplast-review-human-health                  
## 5       4 emerg-risk-marin-discuss-potenti-increas-contamin-microplast-review-h…
## 6       5 nanoplast-plastic-contamin-microplast-review-human-health             
## 7       6 environ-microplast-review-health-human

Topic modelling

corp <- quanteda::corpus(out$abstract$abstract)
dtm <- dfm(corp, remove = stopwords("en"), remove_punct = TRUE)


stm_c <- convert(dtm, to = "stm")

topics <- stm(documents = stm_c$documents, vocab = stm_c$vocab, data = stm_c$meta, K = 10, init.type = "Spectral")
## Beginning Spectral Initialization 
##   Calculating the gram matrix...
##   Finding anchor words...
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## Topic 1: mps, aquatic, environment, effects, microplastics 
##  Topic 2: human, health, aquatic, nmps, environment 
##  Topic 3: microplastics, human, food, exposure, potential 
##  Topic 4: marine, mps, environment, debris, microplastic 
##  Topic 5: microplastics, health, human, aquatic, water 
##  Topic 6: plastic, plastics, environment, waste, pollution 
##  Topic 7: mps, human, nps, health, can 
##  Topic 8: human, health, pollution, research, microplastics 
##  Topic 9: human, nanoplastics, effects, health, plastic 
##  Topic 10: microplastics, microplastic, research, marine, plastic 
## .........................................................................................................................................................
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## Topic 1: mps, aquatic, environment, microplastics, potential 
##  Topic 2: human, health, aquatic, effects, nmps 
##  Topic 3: microplastics, human, food, exposure, potential 
##  Topic 4: marine, mps, environment, debris, microplastic 
##  Topic 5: microplastics, health, human, aquatic, water 
##  Topic 6: plastic, plastics, waste, environment, pollution 
##  Topic 7: mps, nps, human, can, health 
##  Topic 8: human, health, pollution, research, effects 
##  Topic 9: human, effects, nanoplastics, health, plastic 
##  Topic 10: microplastics, microplastic, research, marine, plastic 
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## Topic 1: mps, aquatic, environment, microplastics, potential 
##  Topic 2: human, health, aquatic, effects, nmps 
##  Topic 3: microplastics, human, food, exposure, potential 
##  Topic 4: mps, marine, environment, debris, microplastic 
##  Topic 5: microplastics, health, human, aquatic, water 
##  Topic 6: plastic, plastics, waste, environment, pollution 
##  Topic 7: mps, nps, human, can, health 
##  Topic 8: human, health, pollution, research, effects 
##  Topic 9: human, effects, nanoplastics, health, plastic 
##  Topic 10: microplastics, microplastic, research, marine, plastic 
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## Topic 1: mps, aquatic, environment, microplastics, potential 
##  Topic 2: human, health, effects, aquatic, nmps 
##  Topic 3: microplastics, human, food, exposure, potential 
##  Topic 4: mps, marine, environment, debris, microplastic 
##  Topic 5: microplastics, health, human, aquatic, water 
##  Topic 6: plastic, plastics, waste, pollution, environment 
##  Topic 7: mps, nps, human, can, health 
##  Topic 8: human, health, pollution, research, effects 
##  Topic 9: human, effects, nanoplastics, health, plastic 
##  Topic 10: microplastics, microplastic, research, marine, plastic 
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## Model Converged
plot(topics, n = 7, text.cex = .5)

Sample article

Assessment of Human Health Risks Posed by Nano-and Microplastics Is Currently Not Feasible.

details <- europepmc::epmc_details(33261100)
d1 <- europepmc::epmc_details(33264963)

d1$basic
## # A tibble: 1 × 35
##   id       source pmid   doi    title authorString pubYear pageInfo abstractText
##   <chr>    <chr>  <chr>  <chr>  <chr> <chr>        <chr>   <chr>    <chr>       
## 1 33264963 MED    33264… 10.10… Envi… Rai PK, Lee… 2021    123910   In recent d…
## # … with 26 more variables: affiliation <chr>, publicationStatus <chr>,
## #   language <chr>, pubModel <chr>, isOpenAccess <chr>, inEPMC <chr>,
## #   inPMC <chr>, hasPDF <chr>, hasBook <chr>, hasSuppl <chr>,
## #   citedByCount <int>, hasData <chr>, hasReferences <chr>,
## #   hasTextMinedTerms <chr>, hasDbCrossReferences <chr>, hasLabsLinks <chr>,
## #   authMan <chr>, epmcAuthMan <chr>, nihAuthMan <chr>,
## #   hasTMAccessionNumbers <chr>, dateOfCompletion <chr>, …
ft_xml <- tidypmc::pmc_xml(details$basic$pmcid)
ft <- tidypmc::pmc_text(ft_xml)
ft_tables <- tidypmc::pmc_table(ft_xml)
ft_refs <- tidypmc::pmc_reference(ft_xml)

summary <- ft |>
  filter(section == "6. Concluding Remarks") %>%
  select(section, text) %>%
  mutate(text = paste(text, collapse = "\\.")) %>%
  distinct() %>%
  mutate(summ = map(text, ~myScrapers::text_summariser(.x, n = 4))) %>%
  unnest("summ")

tl;dr

Classification of microplastics. From Rai et al. (2021)

Potential human health impacts of mps. From Rai et al. (2021)

The facts that global plastics production has been growing exponentially since the 1950s, and that nearly the entire human population is nowadays permanently exposed to plastic-derived nmps, warrant a critical view of possible health risks posed by nmps, likely not arising from acute toxicity but maybe from long-term accumulation in the human body, or indirect effects caused by alterations in the gut microbiome. In past years the topic “microplastics pollution and possible health risks for humans” raised much attention in the public, and led to political discussions to limit or ban the industrial use of plastic microparticles in various products, although scientific data proving or disproving acute or long-term toxicity of nmps are scarce. Effects on human health remain elusive. Owing to the fact that it is extremely difficult to isolate and (chemically) identify micro- and, in particular, nanoparticles from environmental and biological samples, precise numbers about the human exposure towards nmps via the supposedly main uptake routes of ingestion and inhalation have not been determined yet.

References

Rai, Prabhat Kumar, Jechan Lee, Richard J. C. Brown, and Ki-Hyun Kim. 2021. “Environmental Fate, Ecotoxicity Biomarkers, and Potential Health Effects of Micro- and Nano-Scale Plastic Contamination.” Journal of Hazardous Materials 403 (February): 123910. https://doi.org/10.1016/j.jhazmat.2020.123910.