An atlas of the tissue and blood metagenome in cancer reveals novel links between bacteria, viruses and cancer

Borchmann, Sven

doi:10.1101/773200

Cited by 5 publications

(6 citation statements)

References 73 publications

(101 reference statements)

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“…In terms of species level annotation, compared with other methods, Kraken 2 has a relatively low false positive rate, and the accuracy is relatively high [44,36]. Kraken 2 has also been used in many studies to identify viruses from metagenomic sequencing data (e.g., [4,56,57]. Although BatCoV BM48-31 belongs to the same lineage B betacoronaviruses with SARS-CoV-2, there is still a considerable amount of phylogenetic distance between them.…”

Section: Discussionmentioning

confidence: 99%

The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2

2022

Microb Ecol

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The microbiome of upper respiratory tract (URT) acts as a gatekeeper to respiratory health of the host. However, little is still known about the impacts of SARS-CoV-2 infection on the microbial species composition and co-occurrence correlations of the URT microbiome, especially the relationships between SARS-CoV-2 and other microbes. Here, we characterized the URT microbiome based on RNA metagenomic-sequencing datasets from 1737 nasopharyngeal samples collected from COVID-19 patients. The URT-microbiome network consisting of bacteria, archaea, and RNA viruses was built and analyzed from aspects of core/periphery species, cluster composition, and balance between positive and negative interactions. It is discovered that the URT microbiome in the COVID-19 patients is enriched with Enterobacteriaceae , a gut associated family containing many pathogens. These pathogens formed a dense cooperative guild that seemed to suppress beneficial microbes collectively. Besides bacteria and archaea, 72 eukaryotic RNA viruses were identified in the URT microbiome of COVID-19 patients. Only five of these viruses were present in more than 10% of all samples, including SARS-CoV-2 and a bat coronavirus (i.e., BatCoV BM48-31) not detected in humans by routine means. SARS-CoV-2 was inhibited by a cooperative alliance of 89 species, but seems to cooperate with BatCoV BM48-31 given their statistically significant, positive correlations. The presence of cooperative bat-coronavirus partner of SARS-CoV-2 (BatCoV BM48-31), which was previously discovered in bat but not in humans to the best of our knowledge, is puzzling and deserves further investigation given their obvious implications. Possible microbial translocation mechanism from gut to URT also deserves future studies. Supplementary Information The online version contains supplementary material available at 10.1007/s00248-022-02148-9.

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Section: Discussionmentioning

confidence: 99%

The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2

2022

Microb Ecol

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“…These approaches allowed us to conclude that microbial compositions were distinct between and within cancer types, and that trace amounts of their DNA were detectable in human blood and plasma samples, thereby suggesting a novel diagnostic approach 1 . Moreover, these conclusions were later validated and extended by numerous papers 2,[5][6][7][8][9][10][11][12][13] .…”

Section: Mainmentioning

confidence: 67%

Reply to: Caution Regarding the Specificities of Pan-Cancer Microbial Structure

Sepich‐Poore

Kopylova

Zhu

et al. 2023

Preprint

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The cancer microbiome field tremendously accelerated following the release of our manuscript nearly three years ago, including direct validation of our cancer type-specific conclusions in independent, international cohorts and the tumor microbiome's adoption into the hallmarks of cancer. Disentangling contamination signals from biological signals is an important consideration for this research field. Therefore, despite numerous, high-impact, peer-reviewed research papers that either validated our conclusions or extended them using data we released, we carefully considered criticism raised by Gihawiet al. about potential mishandling of contaminants, batch effects, and machine learning approaches—all of which were central topics in our manuscript. Nonetheless, a close examination of each concern alongside the original manuscript and re-analyses of our published data strongly demonstrates the robustness of the original findings. To remove all doubt, however, we have reproduced all key conclusions from the original manuscript using only overlapping bacterial genera identified in a highly decontaminated, multi-cancer, international cohort (Weizmann Institute of Science, WIS), with or without batch correction, and with multiclass machine learning analyses to mitigate class imbalances. Our published pan-cancer mycobiome manuscript also affirms these findings using updated, state-of-the-art methods. We also note that every analysis shown here was possible using public data and code that we had already provided.

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“…13) CHINA: Fujian? (Borchmann 1941, Hua 2002), Yunnan (Pic 1911, Borchmann 1917, Hua 2002; MNHN), SE Xizang (HBUM). INDIA: Uttarakhand (BMNH).…”

Section: Taxonomymentioning

confidence: 99%

Longizonitis, a new nemognathine genus from the Himalayas (Coleoptera, Meloidae)

Pan

Ren

Bologna

2018

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The new blister beetle genus Longizonitis Pan and Bologna is described. The genus is referred to the tribe Nemognathini, subfamily Nemognathinae, and its relationships are briefly discussed. It is distributed in southern China (Yunnan, SE Xizang, and probably Fujian) and India (Uttarakhand), in a transitional area between the Palaearctic and Oriental regions. The type species, Longizonitis semirubra (Pic, 1911), comb. n., is re-described and illustrated.

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An atlas of the tissue and blood metagenome in cancer reveals novel links between bacteria, viruses and cancer

Abstract: Bacterial

Cited by 5 publications

References 73 publications

The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2

The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2

Reply to: Caution Regarding the Specificities of Pan-Cancer Microbial Structure

Longizonitis, a new nemognathine genus from the Himalayas (Coleoptera, Meloidae)

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