8. Looking for a professor

Student 1 100

First of all, you need to enter https://pubmed.ncbi.nlm.nih.gov/ and click to the advanced sarch option. Then, from the click list on the left, choose Publication Type as ‘review’ click to the button on the right side to add an ‘AND’. After that step, you can add another filter to your search. Choose Title/Abstract and write ‘metagenomics’ and add an ‘AND’ again. Now, click to the add list again and choose Date – Publication to write ‘’2017/01/01’’ to the left one and you can left the right one empty to get the results until today. Finally, choose Affiliation and type ‘france’ to obtain the studies in the affiliations in France.

(((review[Publication Type]) AND (metagenomics[Title/Abstract]) ) AND
(("2017/01/01"[Date - Publication] : "3000"[Date - Publication]))) AND
(france[Affiliation])

The number of results is 74.

First few rows of the table:

1: Aron-Wisnewsky J Vigliotti C, Witjes J, Le P, Holleboom AG, Verheij J, Nieuwdorp M Clément K. Gut microbiota and human NAFLD: disentangling microbial signatures from metabolic disorders. Nat Rev Gastroenterol Hepatol. 2020 May;17(5):279-297. doi: 10.1038/s41575-020-0269-9. Epub 2020 Mar 9. PMID: 32152478.

2: Lagier JC Dubourg G, Million M, Cadoret F, Bilen M, Fenollar F, Levasseur A, Rolain JM Fournier PE, Raoult D. Culturing the human microbiota and culturomics. Nat Rev Microbiol. 2018 May 1;16:540-550. doi: 10.1038/s41579-018-0041-0. PMID: 29937540.

3: Françoise A Héry-Arnaud G. The Microbiome in Cystic Fibrosis Pulmonary Disease. Genes (Basel). 2020 May 11;11(5):536. doi: 10.3390/genes11050536. PMID: 32403302; PMCID: PMC7288443.

4: Jagadeesan B Gerner-Smidt P, Allard MW, Leuillet S, Winkler A, Xiao Y, Chaffron S Van Der Vossen J, Tang S, Katase M, McClure P, Kimura B, Ching Chai L Chapman J, Grant K. The use of next generation sequencing for improving food safety: Translation into practice. Food Microbiol. 2019 Jun;79:96-115. doi: 10.1016/j.fm.2018.11.005. Epub 2018 Nov 17. PMID: 30621881; PMCID: PMC6492263.

5: Debédat J Clément K, Aron-Wisnewsky J. Gut Microbiota Dysbiosis in Human Obesity: Impact of Bariatric Surgery. Curr Obes Rep. 2019 Sep;8(3):229-242. doi: 10.1007/s13679-019-00351-3. PMID: 31197613.

Student 2 99

1. To answer that question we should use pubmed section from NCBI. Then we should choose the specific interest we want. The year of publication, affiliation, title etc.

2. The query looks like this;

    (((France[Affiliation]) AND (("2018"[Date - Publication] : "3000"[Date - Publication])))
    AND (metagenomics[MeSH Terms]) ) AND (review[Filter])

There are 34 results. some of them are;

1. Culturing the human microbiota and culturomics.

2. Enterotypes in the landscape of gut microbial community composition.

3. The Microbiome in Cystic Fibrosis Pulmonary Disease.

Student 3 90

1. I will suggest to my friend that we can search on NCBI databases includes France, Metagenomic etc. And we can find some researches about this topic and this location. And my friend can choose one of them to contact.

2. If I write a query like this: “((France[Affiliation]) AND ((”2017/11/03”[Date - Publication] : “2022/11/03”[Date - Publication]))) AND (“metagenomics”[MeSH Major Topic])”

I can find some French researches working in a project related to Metagenomics.

The result of this query is: 149. (In PubMed database)

If I want to be more specific I write a query includes author publishing date, affiliation to see that a specific researcher’s publishes.

For example

I choose one the researcher to find his publishes; Blasco-Baque V. And if a write a query like this: (((France[Affiliation]) AND ((“2017/11/03”[Date - Publication] : “2022/11/03”[Date - Publication]))) AND (Metagenomics[Title])) AND (blasco baque v[Author]) in PubMed database (Result is 2), I can reach his papers related with Metagenomics. By this way, my friend can make her/his own decision.

Student 4 90

1. We can do the search for this situation in NCBI. We will use Advanced search. To achieve all the informations you want, we can write this:

   ((France[Affiliation]) AND ((“2017”[Date - Publication] : “3000”[Date - Publication]))) AND (Metagenomics[Affiliation]) AND review[filter]

2. I got only 2 results. To create the list of papers

I selected Save, then Selection: All Results and Format: CSV. I got these:

35136384, “Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications”, “Moore KJM, Cahill J, Aidelberg G, Aronoff R, Bektaş A, Bezdan D, Butler DJ, Chittur SV, Codyre M, Federici F, Tanner NA, Tighe SW, True R, Ware SB, Wyllie AL, Afshin EE, Bendesky A, Chang CB, Dela Rosa R 2nd, Elhaik E, Erickson D, Goldsborough AS, Grills G, Hadasch K, Hayden A, Her SY, Karl JA, Kim CH, Kriegel AJ, Kunstman T, Landau Z, Land K, Langhorst BW, Lindner AB, Mayer BE, McLaughlin LA, McLaughlin MT, Molloy J, Mozsary C, Nadler JL, D’Silva M, Ng D, O’Connor DH, Ongerth JE, Osuolale O, Pinharanda A, Plenker D, Ranjan R, Rosbash M, Rotem A, Segarra J, Schürer S, Sherrill-Mix S, Solo-Gabriele H, To S, Vogt MC, Yu AD, Mason CE

35335666, “Type Strains of Entomopathogenic Nematode-Symbiotic Bacterium Species, Xenorhabdus szentirmaii (EMC) and X. budapestensis (EMA), Are Exceptional Sources of Non-Ribosomal Templated, Large-Target-Spectral, Thermotolerant-Antimicrobial Peptides (by Both), and Iodinin (by EMC)”, “Fodor A, Gualtieri M, Zeller M, Tarasco E, Klein MG, Fodor AM, Haynes L, Lengyel K, Forst SA, Furgani GM, Karaffa L, Vellai T.”, “Pathogens. 2022 Mar 11

Student 5 90

1. I found some article about your wishes. I searched in NCBI PUBMED about metagenomics works in France last 5 years. First of all in NCBI, I chose our database is PUBMED, then click the advance. I entred as this:

   ((Metagenomics[Title]) AND (France[Affiliation])) AND ((“2017/11/04”[Date - Publication] : “2022/11/04”[Date - Publication]))

2. The answer is 87.

Student 6 100

a- For this question i use pubmed ncbi search. I entrez a advanced query:

("France"[Affiliation] AND "metagenomics"[MeSH Major Topic] AND
2017/01/01:3000/12/31[Date - Publication]) AND (review[Filter])

and search with it.

b- It shows 15 results. 1- Paleomicrobiology of the human digestive tract: A review. 2- STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies.3- A Robust Framework for Microbial Archaeology.

Student 7 100

Firstly you should enter to pubmed advanced search. Then click to Afilliation button and write “France”, click AND button. After that choose “Date-Publication” button and write 2017-2022, click AND button. Then choose “MeSH Major Topic” and write metagenomics, click AND button. At the end, click “Publication Type” button and write review, click AND button. Click Search button and you will see the papers. Click on the “save” button on the result page. Select all results on this page, csv file and download. You can open this file with excel.

Query: ((("2017"[Date - Publication] : "2022"[Date - Publication]))) AND
(Metagenomics[MeSH Major Topic]) AND (Review[Publication Type]) AND
(France[Affiliation])

b.) I found 15 articles and you can see the table from the link. https://docs.google.com/spreadsheets/d/1VgS1MnB7IjB9uiSvLYYVcNK6lmJ2X_GrgkqWl5BR6Tc/edit?usp=sharing

Student 8 90

Go pubmed and click the advanced. ((metagenomics[MeSH Terms]) AND (("2017"[Date - Create] : "2022"[Date - Create]))) AND (france[Affiliation]). For a research on a topic which has been interested by someone , I use mesh term to search. Then I choose the date for last 5 yeras and finally I choose the affiliation as France. Usually many papers are published with some collaboration from different institutes and countries so for affiliation I choose france just in case. It will give us 423 results.

1. Culturing the human microbiota and culturomics.( title)-Jean-Christophe Lagier -Aix Marseille Université-2018 May

2. The Microbiome in Cystic Fibrosis Pulmonary Disease-Alice Françoise - University of Brest, I-2020

3. Protection of the Human Gut Microbiome From Antibiotics-Jean de Gunzburg-Da Volterra, Paris, France.

2 Metagenopolis Institut National de la Recherche Agronomique, Jouy-en-Josas, France.-2018

Student 9 99

1. I would suggest her to use NCBI’s advanced search tool and create a query that fulfills all her criteria to obtain a list she can choose from.

2. Here is the query I have created:

   (((“france”[Affiliation]) AND (“review”[Publication Type])) AND (“metagenomics”[All Fields])) AND ((“2017/11/4”[Date - Publication] : “2022/11/4”[Date - Publication])).

The number of results is 83. There is a Save option on the upper left corner of the results page. I clicked Save/Selection-All results/Format-CSV and an excel file with a .csv (comma-separated value) extension is created for further use. Here are the first 3 rows of the file. I will also send the file that I have obtained called FranceMetagenomics, through e-mail.

PMID Title,Authors,Citation,First Author,Journal/Book,Publication Year,Create Date,PMCID,NIHMS ID,DOI

“29937540”Culturing the human microbiota and culturomics”, “Lagier JC, Dubourg G, Million M, Cadoret F, Bilen M, Fenollar F, Levasseur A, Rolain JM, Fournier PE, Raoult D.”, “Nat Rev Microbiol. 2018 May 1” “16:540-550. doi: 10.1038/s41579-018-0041-0.”, “Lagier JC”, “Nat Rev Microbiol”, “2018”, “2018/06/26”, ““,”“,”10.1038/s41579-018-0041-0”

“32152478”Gut microbiota and human NAFLD: disentangling microbial signatures from metabolic disorders”, “Aron-Wisnewsky J, Vigliotti C, Witjes J, Le P, Holleboom AG, Verheij J, Nieuwdorp M, Clément K.”, “Nat Rev Gastroenterol Hepatol. 2020 May” “17(5):279-297. doi: 10.1038/s41575-020-0269-9. Epub 2020 Mar 9.”, “Aron-Wisnewsky J”, “Nat Rev Gastroenterol Hepatol”, “2020”, “2020/03/11”, ““,”“,”10.1038/s41575-020-0269-9”

Student 10 99

The query is

((France[Affiliation]) AND (metagenomics[Title]) OR metagenomic[Title]) AND (("2017/01/01"[Date - Publication] : "2022/11/04"[Date - Publication])) AND (review[Filter])

and 111 results.

Student 11 90

1. For this kind of specific search, I’ll use PubMed’s Advanced Search. I will filter the described wishes of my friend in the entrez part.

2. Query:

   (((Metagenomics[Title/Abstract]) AND (France[Affiliation])) AND ((“2017/01/01”[Date - Publication] : “3000”[Date - Publication]))) AND (Review[Filter])

Resulted in 74 review papers.

Student 12 100

1. I think it would be best if she search about it in PubMed. First, she should go to NCBI/PubMed advanced search page. Then, she should use these filters to get what she needs to learn: MeSH major topic (which we use to filter our topic that is metagenomics), publication type ( which we use for just getting review papers), publication date ( which we filter papers that published last 5 years) and affiliation ( which we use for filtering papers related at least one affiliation in france)

2. The query in PubMed is:

   (((“metagenomics”[MeSH Major Topic]) AND (“review”[Publication Type])) AND ((“2017/11/04”[Date - Publication] : “2023/11/04”[Date - Publication]))) AND (“france”[Affiliation])

No of results: 12

* I sent the table via e-mail because I didn’t know how to add it here.

Student 13 90

1. I would go NCBI website. Get in PubMed database. Search for papers has the features my friend wanted. And by looking the authors of these papers or places of these papers my friend can found somewhere to study or someone two study with.

2. I search

   ((Metagenomics[Title]) AND ((“2017”[Date - Publication] : “3000”[Date - Publication]))) AND (France[Affiliation])

in the PubMed database. I found 98 results. I press to “Save” button and save as CSV.

First row (title row):PMID Title,Authors,Citation,First Author,Journal/Book,Publication Year,Create Date,PMCID,NIHMS ID,DOI

Second row: 29942096 “Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women”, “Hoyles L, Fernández-Real JM, Federici M, Serino M, Abbott J, Charpentier J, Heymes C, Luque JL, Anthony E, Barton RH, Chilloux J, Myridakis A, Martinez-Gili L, Moreno-Navarrete JM, Benhamed F, Azalbert V, Blasco-Baque V, Puig J, Xifra G, Ricart W, Tomlinson C, Woodbridge M, Cardellini M, Davato F, Cardolini I, Porzio O, Gentileschi P, Lopez F, Foufelle F, Butcher SA, Holmes E, Nicholson JK, Postic C, Burcelin R, Dumas ME.”, “Nat Med. 2018 Jul 24(7):1070-1080. doi: 10.1038/s41591-018-0061-3. Epub 2018 Jun 25.”, “Hoyles L”, “Nat Med”, “2018”, “2018/06/27”, “PMC6140997”, “EMS77125”, “10.1038/s41591-018-0061-3”

Third row: 28750650 “Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis”, “Wen C, Zheng Z, Shao T, Liu L, Xie Z, Le Chatelier E, He Z, Zhong W, Fan Y, Zhang L, Li H, Wu C, Hu C, Xu Q, Zhou J, Cai S, Wang D, Huang Y, Breban M, Qin N, Ehrlich SD.”, “Genome Biol. 2017 Jul 27 18(1):142. doi: 10.1186/s13059-017-1271-6.”, “Wen C”, “Genome Biol”, “2017”, “2017/07/29”, “PMC5530561”, ““,”10.1186/s13059-017-1271-6”

Student 14 99

I would go to the PubMed database and use advanced search. I would filter article type as review, search for metagenomics in all fields, for the last 5 years I would use Date-Completion and for the affiliation of the authors in France I would use Affiliation search. The search would look like this:

"review"[Filter] AND "metagenomics"[All Fields] AND 2017:2022[Date - Completion] AND "France"[Affiliation]

There are 87 answers for this search. I couldn’t paste the list. Here is the first three answers from text file:

1: Lagier JC Dubourg G, Million M, Cadoret F, Bilen M, Fenollar F, Levasseur A, Rolain JM Fournier PE, Raoult D. Culturing the human microbiota and culturomics. Nat Rev Microbiol. 2018 May 1;16:540-550. doi: 10.1038/s41579-018-0041-0. PMID: 29937540.

2: Costea PI Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD Ley RE, Ochman H, O’Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P. Enterotypes in the landscape of gut microbial community composition. Nat Microbiol. 2018 Jan;3(1):8-16. doi: 10.1038/s41564-017-0072-8. Epub 2017 Dec 18. Erratum in: Nat Microbiol. 2018 Feb 13;: PMID: 29255284; PMCID: PMC5832044.

3: Aron-Wisnewsky J Vigliotti C, Witjes J, Le P, Holleboom AG, Verheij J, Nieuwdorp M Clément K. Gut microbiota and human NAFLD: disentangling microbial signatures from metabolic disorders. Nat Rev Gastroenterol Hepatol. 2020 May;17(5):279-297. doi: 10.1038/s41575-020-0269-9. Epub 2020 Mar 9. PMID: 32152478.