v24.09.0: Medieval Town of Toruń

Release v24.09.0 includes 4 new publications, representing 109 new ancient host-associated metagenome samples, 12 new ancient microbial genomes, and 11 new ancient environmental samples. This brings the repository to a total of 196 publications, 1540 ancient host-associated metagenome samples, 718 ancient microbial genomes, and 713 ancient environmental samples

Furthermore, this release adds 109 new ancient host-associated metagenome libraries, 6 new ancient microbial genome libraries, and 10 new ancient environmental libraries. This brings the repository to a total of 2670 ancient host-associated metagenome libraries, 3112 ancient microbial genomes libraries, and 822 ancient environmental libraries.

Added

Ancient Metagenome: Host Associated

• Austin 2024 10.1038/s41598-024-64818-7 (added by @alexhbnr and @jfy133)
• Bozzi 2024 10.1038/s41598-023-40246-x (added by @DavideBozzi and @alexhbnr)

Ancient Single Genome: Host Associated

• White 2021 10.3390/biology10121324 (added by @DianaSpurite, @jfy133, and @alexhbnr)

Ancient Metagenome: Environmental

• Zampirolo 2024 10.1016/j.cub.2024.08.047 (added by @GiuliaZ538)

Changed

• Fix archive sample accession codes for Liu 2024 10.1126/sciadv.adn8490 (@alexhbnr)
• Update the data_publication_doi of Lebrasseur 2024 10.1093/ve/vead087 (@alexhbnr)

Medieval Town of Toruń

Torun owes its origins to the Teutonic Order, which built a castle there in the mid-13th century as a base for the conquest and evangelization of Prussia. It soon developed a commercial role as part of the Hanseatic League. In the Old and New Town, the many imposing public and private buildings from the 14th and 15th centuries (among them the house of Copernicus) are striking evidence of Torun's importance.

Description is available under license CC-BY-SA IGO 3.0

v24.06: Su Nuraxi di Barumini

Release v24.06.0 includes 5 new publications, representing 4 new ancient host-associated metagenome samples, 39 new ancient microbial genomes, and 40 new ancient environmental samples. This brings the repository to a total of 192 publications, 1431 ancient host-associated metagenome samples, 706 ancient microbial genomes, and 702 ancient environmental samples

Furthermore, this release adds 4 new ancient host-associated metagenome libraries, 58 new ancient microbial genome libraries, and 58 new ancient environmental libraries. This brings the repository to a total of 2561 ancient host-associated metagenome libraries, 3106 ancient microbial genomes libraries, and 812 ancient environmental libraries.

Added

Ancient Metagenome: Host Associated

• Wright 2024 10.1016/j.jasrep.2024.104510 (added by @biancamariabonucci)

Ancient Single Genome: Host Associated

• Sun 2024 10.1038/s41467-024-47358-6 (added by @aidaanva)
• Urban 2024 10.1016/j.cub.2024.04.006 (added by @aidaanva)
• Lebrasseur 2024 10.1093/ve/vead087(added by @YuejiaoHuang)

Ancient Metagenome: Environmental

• Liu 2024 10.1126/sciadv.adn8490 (added by @rozwalak)

Su Nuraxi di Barumini

During the late 2nd millennium B.C. in the Bronze Age, a special type of defensive structure known as nuraghi (for which no parallel exists anywhere else in the world) developed on the island of Sardinia. The complex consists of circular defensive towers in the form of truncated cones built of dressed stone, with corbel-vaulted internal chambers. The complex at Barumini, which was extended and reinforced in the first half of the 1st millennium under Carthaginian pressure, is the finest and most complete example of this remarkable form of prehistoric architecture.

Description is available under license CC-BY-SA IGO 3.0

v24.03: Monticello

Release v24.03.0 includes 8 new publications, representing 15 new ancient host-associated metagenome samples, 8 new ancient microbial genomes, and 50 new ancient environmental samples. This brings the repository to a total of 187 publications, 1427 ancient host-associated metagenome samples, 667 ancient microbial genomes, and 662 ancient environmental samples

Furthermore, this release adds 146 new ancient host-associated metagenome libraries, 58 new ancient microbial genome libraries, and 50 new ancient environmental libraries. This brings the repository to a total of 2557 ancient host-associated metagenome libraries, 3048 ancient microbial genomes libraries, and 754 ancient environmental libraries.

Added

Ancient Metagenome: Host Associated

• Nishimura 2024 10.1371/journal.pone.0295924 (added by @alexhbnr)
• Kirdok 2023 10.1038/s41598-023-48762-6 (added by @AnnaEWhite)
• Fiorin 2024 10.1038/s41598-024-52422-8 (added by @jfy133)
• Jackson 2024 10.1093/molbev/msae017(added by @iseultj)

Ancient Single Genome: Host Associated

• Majander 2024 10.1038/s41586-023-06965-x (added by @ilight1542)
• Rozwalak 2024 10.1038/s41467-023-44370-0 (added by @rozwalak)
• Jackson 2024 10.1093/molbev/msae017(added by @iseultj)

Ancient Metagenome: Environmental

• Buchwald 2024 10.1093/ismejo/wrad006 (added by @Darcy220606)
• Murchie 2023 10.1038/s41467-021-27439-6 (added by @ktozdogan)

Monticello and the University of Virginia in Charlottesville

Thomas Jefferson (1743–1826), author of the American Declaration of Independence and third president of the United States, was also a talented architect of neoclassical buildings. He designed Monticello (1769–1809), his plantation home, and his ideal 'academical village' (1817–26), which is still the heart of the University of Virginia. Jefferson's use of an architectural vocabulary based upon classical antiquity symbolizes both the aspirations of the new American republic as the inheritor of European tradition and the cultural experimentation that could be expected as the country matured.

Description is available under license CC-BY-SA IGO 3.0

v23.12: Cathedral, Alcázar and Archivo de Indias

Release v23.12.0 includes 3 new publications, representing 11 new ancient host-associated metagenome samples, 38 new ancient microbial genomes, and 30 new ancient environmental samples. This brings the repository to a total of 179 publications, 1412 ancient host-associated metagenome samples, 659 ancient microbial genomes, and 612 ancient environmental samples

Furthermore, this release adds 11 new ancient host-associated metagenome libraries, 124 new ancient microbial genome libraries, and 30 new ancient environmental libraries. This brings the repository to a total of 2411 ancient host-associated metagenome libraries, 2990 ancient microbial genomes libraries, and 704 ancient environmental libraries.

v23.09: Historic Centre of Cienfuegos

Release v23.09.0 includes 7 new publications, representing 2 new ancient host-associated metagenome samples, 35 new ancient microbial genomes, and 0 new ancient environmental samples. This brings the repository to a total of 176 publications, 1401 ancient host-associated metagenome samples, 621 ancient microbial genomes, and 582 ancient environmental samples

Furthermore, this release adds 2 new ancient host-associated metagenome libraries, 564 new ancient microbial genome libraries, and 0 new ancient environmental libraries. This brings the repository to a total of 2400 ancient host-associated metagenome libraries, 2866 ancient microbial genomes libraries, and 674 ancient environmental libraries.

Added

Ancient Metagenome: Host Associated

• Fontani 2023 10.1038/s41598-023-39250-y (added by @Darcy220606)

Ancient Single Genome: Host Associated

• Neumann 2023 10.1553/archaeologia107 (added by @DianaSpurite)
• Bonczarowska 2023 10.1098/rspb.2023.0622 (added by @DianaSpurite)
• Long 2023 10.1371/journal.ppat.1011538 (added by @DianaSpurite)
• Campos 2023 10.1038/s41467-023-39950-z (added by @DianaSpurite)
• Parker2023 10.1371/journal.ppat.1011404 (added by @DianaSpurite)
• Clavel 2023 10.1016/j.isci.2023.106787 (added by @DianaSpurite/@theHatIsBack)

Historic Centre of Cienfuegos

The colonial town of Cienfuegos was founded in 1819 in the Spanish territory but was initially settled by immigrants of French origin. It became a trading place for sugar cane, tobacco and coffee. Situated on the Caribbean coast of southern-central Cuba at the heart of the country’s sugar cane, mango, tobacco and coffee production area, the town first developed in the neoclassical style. It later became more eclectic but retained a harmonious overall townscape. Among buildings of particular interest are the Government Palace (City Hall), San Lorenzo School, the Bishopric, the Ferrer Palace, the former lyceum, and some residential houses. Cienfuegos is the first, and an outstanding example of an architectural ensemble representing the new ideas of modernity, hygiene and order in urban planning as developed in Latin America from the 19th century.

Description is available under license CC-BY-SA IGO 3.0

v23.06.0: Aachen Cathedral

Release v23.06.0 includes 8 new publications, representing 41 new ancient host-associated metagenome samples, 3 new ancient microbial genomes, and 46 new ancient environmental samples. This brings the repository to a total of 169 publications, 1399 ancient host-associated metagenome samples, 586 ancient microbial genomes, and 582 ancient environmental samples

Furthermore, this release adds 66 new ancient host-associated metagenome libraries, 24 new ancient microbial genome libraries, and 47 new ancient environmental libraries. This brings the repository to a total of 2398 ancient host-associated metagenome libraries, 2302 ancient microbial genomes libraries, and 674 ancient environmental libraries.

Added

Ancient Metagenome: Host Associated

• Kimsis 2023 10.1111/1758-2229.13157 (added by @maxibor)
• Honap 2023 10.1002/ajpa.24735 (added by @schummax/ @tomrichtermeier/ @Frederik-Lutz)
• Klapper 2023 10.1126/science.adf5300 (added by @alexhbnr)

Ancient Single Genome: Host Associated

• Swali 2023 10.1038/s41467-023-38393-w (added by @DianaSpurite)

Ancient Metagenome: Environmental

• Rigou 2022 10.1093/femsml/uqac003 (added by @schummax, @tomrichtermeier, @Frederik-Lutz, and @alexhbnr)
• Armbrecht 2021, 10.1038/s43705-021-00070-8 (added by @ktozdogan)
• Vassallo 2023 10.1128/spectrum.04374-22 (added by @jfy133)
• Klapper 2023 10.1126/science.adf5300 (added by @alexhbnr)
• Zimmermann 2023 10.1038/s41467-023-36845-x (added by @ktozdogan)

Aachen Cathedral

Construction of this palatine chapel, with its octagonal basilica and cupola, began c. 790–800 under the Emperor Charlemagne. Originally inspired by the churches of the Eastern part of the Holy Roman Empire, it was splendidly enlarged in the Middle Ages.

Description is available under license CC-BY-SA IGO 3.0

v23.03.0: Rocky Necropolis of Pantalica

Release v23.03.0 includes 8 new publications, representing 110 new ancient host-associated metagenome samples, 23 new ancient microbial genomes, and 52 new ancient environmental samples. This brings the repository to a total of 161 publications, 1358 ancient host-associated metagenome samples, 583 ancient microbial genomes, and 536 ancient environmental samples

Furthermore, this release adds 180 new ancient host-associated metagenome libraries, 98 new ancient microbial genome libraries, and 64 new ancient environmental libraries. This brings the repository to a total of 2332 ancient host-associated metagenome libraries, 2278 ancient microbial genomes libraries, and 627 ancient environmental libraries.

Corrections were made to 3 publications.

Added

Ancient Metagenome: Host Associated

• Moraitou 2022 10.1093/molbev/msac263 (added by @alexhbnr)
• Quagliariello 2022 10.1038/s41467-022-34416-0 (added by @alexhbnr)
• Sarhan 2023 10.1186/s12915-022-01509-7 (added by @msabrysarhan)

Ancient Single Genome: Host Associated

• Braun 2020 10.3390/microorganisms8020298 (added by @jfy133)
• Quagliariello 2022 10.1038/s41467-022-34416-0 (added by @DianaSpurite)
• Bonczarowska 2022 10.1186/s13059-022-02806-8 (added by @DianaSpurite)
• Eaton 2023 10.1016/j.cub.2023.01.064 (added by @DianaSpurite)
• Rifkin 2023 10.1038/s42003-023-04582-y (added by @mibr30)
• Sarhan 2023 10.1186/s12915-022-01509-7 (added by @msabrysarhan)

Ancient Metagenome: Environmental

• Kjaer 2022 10.1038/s41586-022-05453-y (added by @ktozdogan)
• Nwosu 2023,10.1038/s42003-023-04430-z (added by @ktozdogan)

Changed

• Fixed md5sum hash error of a Ozga2019 sample
• Fixed md5sum hash error of a Granehall2021 sample
• Replace URLs of Velsko2022 with the ones from the column "fastq_ftp" instead of the column "submitted_ftp" from ENA

Rocky Necropolis of Pantalica

The site consists of two separate elements, containing outstanding vestiges dating back to Greek and Roman times: The Necropolis of Pantalica contains over 5,000 tombs cut into the rock near open stone quarries, most of them dating from the 13th to 7th centuries BC. Vestiges of the Byzantine era also remain in the area, notably the foundations of the Anaktoron (Prince’s Palace). The other part of the property, Ancient Syracuse, includes the nucleus of the city’s foundation as Ortygia by Greeks from Corinth in the 8th century BC. The site of the city, which Cicero described as ‘the greatest Greek city and the most beautiful of all’, retains vestiges such as the Temple of Athena (5th century BC, later transformed to serve as a cathedral), a Greek theatre, a Roman amphitheatre, a fort and more. Many remains bear witness to the troubled history of Sicily, from the Byzantines to the Bourbons, interspersed with the Arabo-Muslims, the Normans, Frederick II of the Hohenstaufen dynasty (1197–1250), the Aragons and the Kingdom of the Two Sicilies. Historic Syracuse offers a unique testimony to the development of Mediterranean civilization over three millennia.

Description is available under license CC-BY-SA IGO 3.0

v22.12: Joya de Cerén

Release v22.12 includes 21 new publications, representing 187 new ancient host-associated metagenome samples, 27 new ancient microbial genomes, and 102 new ancient environmental samples. This brings the repository to a total of 153 publications, 1248 ancient host-associated metagenome samples, 560 ancient microbial genomes, and 484 ancient environmental samples

Furthermore, this release adds 323 new ancient host-associated metagenome libraries, 84 new ancient microbial genome libraries, and 123 new ancient environmental libraries. This brings the repository to a total of 2152 ancient host-associated metagenome libraries, 2180 ancient microbial genomes libraries, and 563 ancient environmental libraries.

A correction was made to 1 publication.

New Contributors

• @DianaSpurite made their first contribution in #981
• @ktozdogan made their first contribution in #1020

CHANGELOG

Added

Ancient Metagenome: Host Associated

• Modi 2021 10.1016/j.quaint.2021.12.003 (added by @jfy133)
• Scorrano 2022 10.1038/s42003-022-04190-2 (added by @ktozdogan)
• Fagernäs 2022 10.1093/femsmc/xtac006 (added by @jfy133)
• Velsko 2022 10.1093/pnasnexus/pgac148 (added by @bbartholdy)

Ancient Single Genome: Host Associated

• Jäger 2022 10.1016/j.tube.2022.102181 (added by @DianaSpurite)
• Rieux 2021 10.1038/s41598-021-00518-w (added by @DianaSpurite)
• Guellil 2021 10.1038/s41598- 021- 98214-2 (added by @DianaSpurite)
• Guellil 2022 10.1186/s13059-021-02580-z (added by @DianaSpurite)
• Spyrou 2022 10.1038/s41586-022-04800-3 (added by @DianaSpurite)
• Neumann 2022 10.1016/j.cub.2022.06.094 (added by @DianaSpurite)
• Vågene 2022 10.1038/s41467-022-28562-8 (added by @DianaSpurite)
• Austin 2022 10.1038/s42003-022-03890-z (added by @DianaSpurite)
• Guellil 2022 10.1126/sciadv.abo4435 (added by @DianaSpurite)
• Long 2022 10.1038/s42003-022-03527-1 (added by @jfy133 )
• Quagliariello 2022 10.1038/s41467-022-34416-0 (added by @DianaSpurite)

Ancient Metagenome: Environmental

• Armbrecht 2022 10.1038/s41467-022-33494-4 (added by @ilight1542)
• Courtin 2022 10.1002/edn3.336 (added by @ktozdogan)
• Iwańska 2022 10.1038/s41598-022-12761-w (added by @ktozdogan)
• Gelabert 2021 10.1016/j.cub.2021.06.023 (added by @ktozdogan)
• Moore 2020 10.1002/ece3.6082 (added by @ktozdogan)
• Perez 2022 10.3390/microorganisms10081623 (added by @Darcy220606)

Changed

• Synchronised site location name of PattersonRoss2018 with Long2022

Joya de Cerén Archaeological Site

Joya de Cerén was a pre-Hispanic farming community that, like Pompeii and Herculaneum in Italy, was buried under an eruption of the Laguna Caldera volcano c. AD 600. Because of the exceptional condition of the remains, they provide an insight into the daily lives of the Central American populations who worked the land at that time.

Description is available under license CC-BY-SA IGO 3.0

v22.09.2

Patch release: upload correct release ZIP update

Sixth (and long-awaited) major release of AncientMetagenomeDir.

This release includes a significant update to the repository, with an extension to DNA sequencing library level metadata! You can now use these tables to directly download sequencing data, with knowledge of their construction to help with informed processing of public data. The release also sees the deprecation of the 'Anthropgenic' metagenome table due to a lack of interest. This will be reinstated in the future if of interest to the community.

Release v22.09 includes 6 new publications and 3 removed publications, representing 23 new ancient host-associated metagenome samples, 165 new ancient microbial genomes, and 7 new (previously missed) ancient environmental samples.

It adds 1829 new ancient host-associated metagenome libraries, 2096 new ancient microbial genome libraries, and 440 new ancient environmental libraries.

This brings the repository to a total of 126 publications, 1061 new ancient host-associated metagenome samples, 533 ancient microbial genomes, and 382 new ancient environmental samples. It also includes 1829 new ancient host-associated metagenome libraries, 2096 new ancient microbial genome libraries, and 440 new ancient environmental libraries.

Corrections were made to 29 publications.

New Contributors

• @jasmezz made their first contribution in #443
• @SalWas1 made their first contribution in #631
• @bbartholdy made their first contribution in #670
• @Darcy220606 made their first contribution in #684
• @EisenRa made their first contribution in #653
• @AdrianForsythe made their first contribution in #709
• @meganemichel made their first contribution in #686
• @GUNeumann made their first contribution in #689
• @ossmith made their first contribution in #715
• @iseultj made their first contribution in #747
• @ArchaeOphelie made their first contribution in #753
• @yaxalponce made their first contribution in #756
• @Kelzor made their first contribution in #757
• @Xevkin made their first contribution in #764
• @AndreaQ7 made their first contribution in #769
• @Micro-IT made their first contribution in #794
• @mlo89 made their first contribution in #777
• @Anna-palaeome made their first contribution in #755
• @nihandilsad made their first contribution in #759
• @arthurKocher made their first contribution in #775
• @ilight1542 made their first contribution in #781
• @valentinavan made their first contribution in #839
• @jgserr made their first contribution in #858

CHANGELOG

Added

• Extended repository to include library level metadata for all existing samples

Ancient Metagenome: Host Associated

• Granehäll 2021 10.1186/s40168-021-01132-8
• Maixner 2021 10.1016/j.cub.2021.09.031
• Kazarina 2021b 10.1016/j.jasrep.2021.103213

Ancient Single Genome: Host Associated

• Granehäll 2021 10.1186/s40168-021-01132-8
• Pfrengle 2021 10.1186/s12915-021-01120-2
• Kocher 2021 10.1126/science.abi5658
• Andrades Valtueña 2022 10.1073/pnas.2116722119

Ancient Metagenome: Environmental

Ancient Metagenome: Anthropogenic

• Due to the lack of community interest, this table has now been deprecated and will not be included in future releases of AncientMetagenomeDir. However it will be reinstated in the future if interest returns.

Misc

• Added library metadata for FASTQ and BAM level data
• Changed the missing value from NA to Unknown for archive_project for the samples tsv
• Removed 'sampling date' columns from host-associated metagenome and single-genome sample tables as this is almost never reported

Changed

• Changed archive_project from NA to Unknown for Taubenberger2005, PattersonRoss2018, Worobey2016
• Fixed Susat2021 DOIs (excel dragging error)
• Fixed Kazarina2021 Project/Sample accessions (column flip error)
• Fixed Morozova2020 DOIs (excel dragging error)
• Fixed Bieker2020 DOIs (paper partly reused previous data for new purpose and earlier had the other publication DOI. Now made all DOIs and dates consistent for the publication where metagenomics was performed)
• Fixed Bieker2020 sample USNH-39 into two separate 'artifical samples' due to upload of two libraries to two difference archives.
• Fixed Bieker2020 missing sample accession codes (due to later re-sequencing and non-reused SRS/ERS code)
• Fixed Muhlemann2018 Project ID (now available)
• Fixed FellowsYates2021 corrected typo in longitude 85.53 > -85.53
• Fixed Velsko2018 project name to Velsko2019 (wrong publication year)
• Fixed Schuenemann2011 Put the accession ID of the full plasmid sequence not partial
• Fixed Martin2013 corrected archive name (incorrectly reported in publication)
• Fixed Seersholm2016 archive ENA (from incorrectly specified as SRA)
• Fixed Eisenhofer2020 date rounding error (originally added 230 rather than 200)
• Fixed BravoLopez2020 typo in site name (Inmaculate -> Immaculate)
• Fixed Willmann2018 project_name (originally missing the second 'n')
• Fixed DeDios2020, DeDios2019, DeDios2021 project_names (originally had lowercase leading d)
• Fixed DeDios2020 sample_name from Jean-Paul Marat to Marat to make it consistent with the libraries uploaded in the ENA
• Fixed Campos2021 sample accession column had run accession
• Fixed Philips2017 fixed incorrect DOI (from later publication that reused same data)
• Fixed Wagner2014 incorrect archive in the samples tsv
• Fixed Eerkens2018 sample name from an individual name to the specific calculus sample name
• Fixed Zhou2018 by switching sample name to a clearer one based on the file name rather than just the project_archive ID
• Fixed Zhou2018 in ancientsinglegenome-hostassociated archive_project and archive_accession to be more explicit as of which files have been use to reconstruct the genome
• Fixed Campos2021 sample_name to HERB_1937 to make it consistent with the libraries uploaded in the ENA
• Fixed Borry2020 sample_name to match archaeological ID from paper (as opposed to laboratory ID which was in sample.tsv table)
• Fixed Velsko2019 accidental inclusion of old sample accessions to keep 'correct' sample accession of correct data
• Fixed Liang2021 sample names to be more specific to allow association with library names
• Fixed GuzmanSolis2021 archive_project and archive_accession to include the Dryad doi and the specific ids from the download links
• Fixed Ardelean2020 sample_name incorrect in samples tsv, replaced with sample_name from libraries tsv
• Fixed Morozova2020 typo in - Azov37 -> Axov38
• Fixed Morozova2020 accidental ERS code duplication across two samples

Removed

• Removed Mendum2014 sample SK27 due to TreeBASE repository not being accessible any more
• Removed SantiagoRodriguez2016 and SantiagoRodridguez2016 samples as raw data is no longer publicly accessible on MG-RAST
• Removed Braadbaart2020 as uploaded data was not shotgun data as required for inclusion in environmental table
• Removed Worobey2016 samples SF74 and SF73 as not in final consensus sequences
• Removed Schulte2021 sample accessions of targeted capture libraries (which were different from the shotgun libraries)
• Removed Schuenemann2018 libraries (Jørgen_*) that were originally published in tandem with and already included in KrauseKyora2018b

Pyu Ancient Cities

Pyu Ancient Cities includes the remains of three brick, walled and moated cities of Halin, Beikthano and Sri Ksetra located in vast irrigated landscapes in the dry zone of the Ayeyarwady (Irrawaddy) River basin. They reflect the Pyu Kingdoms that flourished for over 1,000 years between 200 BC and AD 900. The three cities are partly excavated archaeological sites. Remains include excavated palace citadels, burial grounds and manufacture sites, as well as monumental brick Buddhist stupas, partly standing walls and water management features – some still in use – that underpinned the organized intensive agriculture.

Description used under license CC-BY-SA IGO 3.0

v22.09: Pyu Ancient Cities

Sixth (and long-awaited) major release of AncientMetagenomeDir.

This release includes a significant update to the repository, with an extension to DNA sequencing library level metadata! You can now use these tables to directly download sequencing data, with knowledge of their construction to help with informed processing of public data. The release also sees the deprecation of the 'Anthropgenic' metagenome table due to a lack of interest. This will be reinstated in the future if of interest to the community.

Release v22.09 includes 6 new publications and 3 removed publications, representing 23 new ancient host-associated metagenome samples, 165 new ancient microbial genomes, and 7 new (previously missed) ancient environmental samples.

It adds 1829 new ancient host-associated metagenome libraries, 2096 new ancient microbial genome libraries, and 440 new ancient environmental libraries.

This brings the repository to a total of 126 publications, 1061 new ancient host-associated metagenome samples, 533 ancient microbial genomes, and 382 new ancient environmental samples. It also includes 1829 new ancient host-associated metagenome libraries, 2096 new ancient microbial genome libraries, and 440 new ancient environmental libraries.

Corrections were made to 29 publications.

New Contributors

• @jasmezz made their first contribution in #443
• @SalWas1 made their first contribution in #631
• @bbartholdy made their first contribution in #670
• @Darcy220606 made their first contribution in #684
• @EisenRa made their first contribution in #653
• @AdrianForsythe made their first contribution in #709
• @meganemichel made their first contribution in #686
• @GUNeumann made their first contribution in #689
• @ossmith made their first contribution in #715
• @iseultj made their first contribution in #747
• @ArchaeOphelie made their first contribution in #753
• @yaxalponce made their first contribution in #756
• @Kelzor made their first contribution in #757
• @Xevkin made their first contribution in #764
• @AndreaQ7 made their first contribution in #769
• @Micro-IT made their first contribution in #794
• @mlo89 made their first contribution in #777
• @Anna-palaeome made their first contribution in #755
• @nihandilsad made their first contribution in #759
• @arthurKocher made their first contribution in #775
• @ilight1542 made their first contribution in #781
• @valentinavan made their first contribution in #839
• @jgserr made their first contribution in #858

CHANGELOG

Added

• Extended repository to include library level metadata for all existing samples

Ancient Metagenome: Host Associated

• Granehäll 2021 10.1186/s40168-021-01132-8
• Maixner 2021 10.1016/j.cub.2021.09.031
• Kazarina 2021b 10.1016/j.jasrep.2021.103213

Ancient Single Genome: Host Associated

• Granehäll 2021 10.1186/s40168-021-01132-8
• Pfrengle 2021 10.1186/s12915-021-01120-2
• Kocher 2021 10.1126/science.abi5658
• Andrades Valtueña 2022 10.1073/pnas.2116722119

Ancient Metagenome: Environmental

Ancient Metagenome: Anthropogenic

• Due to the lack of community interest, this table has now been deprecated and will not be included in future releases of AncientMetagenomeDir. However it will be reinstated in the future if interest returns.

Misc

• Added library metadata for FASTQ and BAM level data
• Changed the missing value from NA to Unknown for archive_project for the samples tsv
• Removed 'sampling date' columns from host-associated metagenome and single-genome sample tables as this is almost never reported

Changed

• Changed archive_project from NA to Unknown for Taubenberger2005, PattersonRoss2018, Worobey2016
• Fixed Susat2021 DOIs (excel dragging error)
• Fixed Kazarina2021 Project/Sample accessions (column flip error)
• Fixed Morozova2020 DOIs (excel dragging error)
• Fixed Bieker2020 DOIs (paper partly reused previous data for new purpose and earlier had the other publication DOI. Now made all DOIs and dates consistent for the publication where metagenomics was performed)
• Fixed Bieker2020 sample USNH-39 into two separate 'artifical samples' due to upload of two libraries to two difference archives.
• Fixed Bieker2020 missing sample accession codes (due to later re-sequencing and non-reused SRS/ERS code)
• Fixed Muhlemann2018 Project ID (now available)
• Fixed FellowsYates2021 corrected typo in longitude 85.53 > -85.53
• Fixed Velsko2018 project name to Velsko2019 (wrong publication year)
• Fixed Schuenemann2011 Put the accession ID of the full plasmid sequence not partial
• Fixed Martin2013 corrected archive name (incorrectly reported in publication)
• Fixed Seersholm2016 archive ENA (from incorrectly specified as SRA)
• Fixed Eisenhofer2020 date rounding error (originally added 230 rather than 200)
• Fixed BravoLopez2020 typo in site name (Inmaculate -> Immaculate)
• Fixed Willmann2018 project_name (originally missing the second 'n')
• Fixed DeDios2020, DeDios2019, DeDios2021 project_names (originally had lowercase leading d)
• Fixed DeDios2020 sample_name from Jean-Paul Marat to Marat to make it consistent with the libraries uploaded in the ENA
• Fixed Campos2021 sample accession column had run accession
• Fixed Philips2017 fixed incorrect DOI (from later publication that reused same data)
• Fixed Wagner2014 incorrect archive in the samples tsv
• Fixed Eerkens2018 sample name from an individual name to the specific calculus sample name
• Fixed Zhou2018 by switching sample name to a clearer one based on the file name rather than just the project_archive ID
• Fixed Zhou2018 in ancientsinglegenome-hostassociated archive_project and archive_accession to be more explicit as of which files have been use to reconstruct the genome
• Fixed Campos2021 sample_name to HERB_1937 to make it consistent with the libraries uploaded in the ENA
• Fixed Borry2020 sample_name to match archaeological ID from paper (as opposed to laboratory ID which was in sample.tsv table)
• Fixed Velsko2019 accidental inclusion of old sample accessions to keep 'correct' sample accession of correct data
• Fixed Liang2021 sample names to be more specific to allow association with library names
• Fixed GuzmanSolis2021 archive_project and archive_accession to include the Dryad doi and the specific ids from the download links
• Fixed Ardelean2020 sample_name incorrect in samples tsv, replaced with sample_name from libraries tsv
• Fixed Morozova2020 typo in - Azov37 -> Axov38
• Fixed Morozova2020 accidental ERS code duplication across two samples

Removed

• Removed Mendum2014 sample SK27 due to TreeBASE repository not being accessible any more
• Removed SantiagoRodriguez2016 and SantiagoRodridguez2016 samples as raw data is no longer publicly accessible on MG-RAST
• Removed Braadbaart2020 as uploaded data was not shotgun data as required for inclusion in environmental table
• Removed Worobey2016 samples SF74 and SF73 as not in final consensus sequences
• Removed Schulte2021 sample accessions of targeted capture libraries (which were different from the shotgun libraries)
• Removed Schuenemann2018 libraries (Jørgen_*) that were originally published in tandem with and already included in KrauseKyora2018b

Pyu Ancient Cities

Pyu Ancient Cities includes the remains of three brick, walled and moated cities of Halin, Beikthano and Sri Ksetra located in vast irrigated landscapes in the dry zone of the Ayeyarwady (Irrawaddy) River basin. They reflect the Pyu Kingdoms that flourished for over 1,000 years between 200 BC and AD 900. The three cities are partly excavated archaeological sites. Remains include excavated palace citadels, burial grounds and manufacture sites, as well as monumental brick Buddhist stupas, partly standing walls and water management features – some still in use – that underpinned the organized intensive agriculture.

Description used under license CC-BY-SA IGO 3.0