Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population

May combine two claims.

Among the 376 SGBs, 116 were kSGBs and 260 were uSGBs (comprising 751 MAGs).

“Among all SGBs, 116 were classified as “known” (kSGBs) as they included reference genomes available in public databases and 260 as “unknown” (uSGBs, comprising 751 MAGs) lacking reference genomes (Data S2A).”

May combine two claims.

Eubacterium rectale SGB4933 and Prevotella copri Clade A SGB1626 were the most prevalent kSGBs in the Ethiopian cohort (72% and 30%, respectively).

“Among them, Eubacterium rectale SGB4933 (36 MAGs in Ethiopian cohort) and Prevotella copri Clade A SGB1626 (15 MAGs26) were the most prevalent kSGBs in the Ethiopian cohort (72% and 30%, respectively).”

May combine two claims.

A core of 50 SGBs (31 kSGBs, 19 uSGBs) was present at least once in all five cohorts, representing 25.6% ± 2.7% of MAGs per cohort.

“we found a “core” of 50 SGBs (31 kSGBs and 19 uSGBs) present at least once in all five cohorts (representing 25.6% ± 2.7% of the MAGs of each single cohort).”

May combine two claims.

Blastocystis sp. was never detected in Ethiopian newborns; the youngest positive child was 21 months old.

“In concordance with previous findings,48 we confirmed that Blastocystis sp. was never detected in Ethiopian newborns (the youngest positive child was 21 months old)”

May combine two claims.

ST2 was the only ST shared at the strain level in all cases in which it was present both in the mother and the infant, and also in one case of two siblings sharing the same ST.

“ST2 was also the only ST shared at the strain level in all cases in which it was present both in the mother and the infant, and also in one case of two siblings sharing the same ST (Figure S2B).”

May combine two claims.

90 uSGBs were uniquely found in non-westernized and Ethiopian infants' metagenomes, compared with only 24 SGBs found in both Ethiopian and westernized infants but not non-westernized.

“This microbial under-characterization in non-westernized populations was confirmed by the detection of 90 uSGBs that were uniquely found in non-westernized and Ethiopian infants’ metagenomes (in comparison, only 24 SGBs were found in both Ethiopian and westernized infants but not in non-westernized ones; Figure 1C).”

May combine two claims.

Both Italian and Swedish cohorts had a higher strain-sharing rate than Ethiopian, Ghanaian, and Tanzanian populations, opposite to the reduction effect of C-section samples in the Swedish cohort.

“For instance, both the Italian and Swedish cohorts had a higher strain-sharing rate than the Ethiopian, Ghanaian, and Tanzanian populations, which is the opposite effect exerted by C-section samples in the Swedish cohort (i.e., reduction of the strain-sharing rate; Figure S2A).”

May combine two claims.

Lacticaseibacillus paracasei subsp. paracasei SGB7142 and Lactiplantibacillus xiangfangensis SGB7204 were the most abundant microbes in both injera samples, representing 92.7% and 81.5% of the microbial community.

“Lacticaseibacillus paracasei subsp. paracasei SGB7142 (previously Lactobacillus paracasei) and Lactiplantibacillus xiangfangensis SGB7204 (previously Lactobacillus xiangfangensis) were the most abundant microbes in both samples, where they represented 92.7% and 81.5% of the microbial community (Table 1).”

• AssumptionRests on an assumption: Teff is a cereal typically grown in the tropics and especially in Ethiopia, where it represents a major food grain.

May combine two claims.

Selenomonadaceae uSGB6973 was highly prevalent in Ethiopian mother-infant pairs (42.9%) and highly shared (17.9% of positive pairs), while present only in one individual and never shared in Ghana and Tanzania.

“Among these, the Selenomonadaceae uSGB6973 was not only highly prevalent in Ethiopian mother-infant pairs (42.9%) but also highly shared (17.9% of positive pairs), while being present only in one individual and never shared in both Ghana and Tanzania (Figure 2C).”

May combine two claims.

In cases where both mother and infant were colonized by Blastocystis spp., infants of non-westernized cohorts shared the same ST with their mothers only in 3 out of 5 cases, with siblings carrying different STs.

“In cases in which both the mother and the infant were colonized by Blastocystis spp., infants of non-westernized cohorts shared the same ST with their mothers only in 3 out of 5 cases (Figure 3B), as already observed in the Ethiopian cohort, with siblings belonging to the same family carrying different STs.”

May combine two claims.

In the Ethiopian cohort, taxa from which mother-infant strain sharing was inferred belonged to uSGBs, in contrast with the Swedish cohort where infants shared an extremely limited fraction of uSGs with mothers.

“In the Ethiopian cohort, the taxa from which mother-infant strain sharing was inferred belonged to uncharacterized SGBs (i.e., uSGBs; Figure 2B), in stark contrast with what was observed in the Swedish cohort, where infants shared an extremely limited fraction of uSGs with their own mothers (Figure 2B).”

May combine two claims.

In westernized cohorts, Blastocystis sp. was present in only 8% of samples and with three additional STs (ST4, ST6, ST7).

“On the contrary, in the westernized cohorts, Blastocystis sp. was present in only 8% of the samples and with three additional STs (i.e., ST4, ST6, and ST7; Figure 3A).”

May combine two claims.

For 3 of 5 colonized Ethiopian infants, the mother was colonized as well, but only one case had the same ST (ST1 in family D07).

“For 3 of the 5 colonized Ethiopian infants, we found that the mother was colonized as well but in only one case with the same ST (namely ST1 in family D07; Figure 3B; Table S2).”

May combine two claims.

Ethiopian infants shared with their mothers a median of 4.9% of SGBs at strain level, in line with other non-westernized cohorts (median 7.6%) but substantially lower than westernized infants (median 28.6%, Fisher p < 2.2E-16).

“We found that Ethiopian infants shared with their mothers a median of 4.9% of the SGBs found in their microbiome at the stain level, in line with other non-westernized cohorts (median 7.6%) but substantially lower than westernized infants (median 28.6%, Fisher test p value < 2.2E−16; Figure 2A).”

May combine two claims.

Non-westernized infants, including Ethiopian ones, had a higher prevalence (29%) but a very similar median age (6 years).

“Non-westernized infants, including Ethiopian ones, had instead a higher prevalence (29%) but a very similar median age (6 years)”

May combine two claims.

Ethiopian and non-westernized infants had on average 35.6 SGBs profiled at strain level, higher than westernized infants (24.3 SGBs).

“Of note, Ethiopian and non-westernized infants had on average 35.6 SGBs that could be profiled at the strain level, which is higher than that for westernized infants (24.3 SGBs)”

May combine two claims.

All four SGBs (3 uSGBs) shared only in Ethiopian and other non-westernized cohorts belonged to Prevotellaceae, present on average in 37.7% and shared in 14.3% of non-westernized mother-infant pairs, absent in Italian and Swedish.

“Similarly, all the four SGBs (3 uSGBs) that were only shared in the Ethiopian and in the other non-westernized cohorts belonged to the Prevotellaceae family, and they were present on average in 37.7% and shared in 14.3% of the non-westernized mother-infant pairs while completely absent in Italian and Swedish ones (Figure 2C).”

May combine two claims.

Westernized infants had a much lower prevalence of Blastocystis spp. (3%) with a median age of 4 years 7 months for positive individuals.

“Overall, westernized infants had a much lower prevalence of Blastocystis spp. (3%) with a median age of 4 years and 7 months for the positive individuals.”

May combine two claims.

In non-westernized populations, Blastocystis sp. was present at a similar average prevalence (37%) and with the same three STs (ST1, ST2, ST3).

“We then extended our analysis also to the other mother-infant cohorts and found that in the non-westernized populations Blastocystis sp. was present at a similar average prevalence (37%) and with the same three STs (i.e., ST1, ST2, and ST3; Figure 3A).”

May combine two claims.

Blastocystis sp. was detected in 30% of samples with three distinct STs (ST1, ST2, ST3).

“Blastocystis sp. was detected in 30% of the samples with three distinct sequence types (STs), namely ST1, ST2, and ST3.”

May combine two claims.

Of the 13 SGBs specifically shared only in the Ethiopian cohort, 4 were kSGBs and 9 were uSGBs (unassigned at species n=1, genus n=5, class n=3).

“Indeed, of the 13 SGBs that were specifically shared only in the Ethiopian cohort, only 4 were kSGBs, whereas the other 9 were uSGBs taxonomically unassigned at the species (n = 1), genus (n = 5), and class (n = 3) levels (Figure 2C).”

May combine two claims.

This clustering was particularly clear for R. bromii SGB4285, F. prausnitzii SGBs 15316 and 15318, E. rectale SGB4933, and Eubacterium uSGB4290, but not for Parabacteroides distasonis SGB1934 and Phocaeicola vulgatus SGB1814.

“This was particularly clear for R. bromii SGB4285, F. prausnitzii SGBs 15316 and 15318, and E. rectale SGB4933 and the related Eubacterium uSGB4290 (Figures 1D and S1C) but not for two of the most prevalent SGBs in infants, namely Parabacteroides distasonis SGB1934 and Phocaeicola vulgatus SGB1814, which showed no specific lifestyle-dependent strain similarity pattern (Figure S1C).”

May combine two claims.

Of these 19 SGBs, 10 were assigned to Prevotellaceae and 5 were unassigned at phylum level.

“Of these, 10 SGBs were assigned to the Prevotellaceae family and 5 were unassigned at the phylum level (Data S2C)”

May combine two claims.

The eight other species included three previously Lactobacillus species (Fructilactobacillus sanfranciscensis, Latilactobacillus curvatus, and Secundilactobacillus silagei), three Gluconobacter species (G. oxydans, G. cerinus, and G. japonicus), Acetobacter orientalis, and Pediococcus parvulus.

“These included three previously Lactobacillus species (Fructilactobacillus sanfranciscensis, Latilactobacillus curvatus, and Secundilactobacillus silagei), three Gluconobacter species (G. oxydans, G. cerinus, and G. japonicus), Acetobacter orientalis, and Pediococcus parvulus.”

May combine two claims.

The dough MAGs exhibited the highest breadth of coverage for 50% of the Ethiopian samples, whereas the remaining ones mapped better against other reference genomes (GCA_009496975 in 6 cases and GCA_000225325 in 1 case).

“The dough MAGs exhibited the highest breadth of coverage (thus likely best match) for 50% of the Ethiopian samples, whereas the remaining ones mapped better against other reference genomes (i.e., GCA_009496975 in 6 cases and GCA_000225325 in 1 case; Table S3).”

May combine two claims.

When other genomes were the best match for the Ethiopian strains, the dough MAGs were on median the second and fourth closest references and only the 21st and 24th closest to the only strain of F. sanfranciscensis from westernized populations.

“However, also when these other genomes were the best match for the Ethiopian strains, the dough MAGs were on median the second and fourth closest references and only the 21st and 24th closest to the only strain of F. sanfranciscensis from westernized populations (Table S3).”

May combine two claims.

Only four out of the ten species found in the teff dough were also present in Ethiopian individuals (three previously Lactobacillus species and Pediococcus parvulus), although their relative abundance was always <0.05%.

“Only four out of the ten species found in the dough were also present in Ethiopian individuals (i.e., three previously Lactobacillusspecies and Pediococcus parvulus; Table 1), although their relative abundance was always <0.05%.”

• AssumptionRests on an assumption: Teff-based porridges and gruels (genfo) are traditionally eaten by new mothers and weaning infants in the Ethiopian community.

May combine two claims.

Injera samples had a higher presence of LAB, mainly belonging to the former genus Lactobacillus and to Pediococcus species, but also AAB which are commonly described in other fermented products.

“As was expected, we found a higher presence of LAB, mainly belonging to the former genus Lactobacillus and to Pediococcus species, in the injera but also AAB which are commonly described in other fermented products.”

Probably not a substantial claim: may not pass S3 (load-bearing).

The metagenomic assembly and binning approach produced 11,250 medium- and high-quality MAGs with CheckM completeness >50% and contamination <5%, as defined in Bowers et al.

“This approach produced 11,250 medium- and high-quality MAGs with CheckM 1.0.767 completeness >50% and contamination <5%, as defined in Bowers et al.90”

• cites Bowers et al.90 Bowers R.M. Kyrpides N.C. Stepanauskas R. Harmon-Smith M. Doud D. Reddy T.B.K. Schulz F. Jarett J. Rivers A.R. Eloe-Fadrosh E.A. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Nat. Biotechnol. 35 2017 725 731 28787424 PMC6436528Not checked yet

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Classified as probably not a substantial claim.

Metagenomic assembly can partially mitigate the underrepresentation of non-westernized microbiome members in genomic catalogs.

“Recent efforts showed that metagenomic assembly can partially mitigate this problem,23,25,33,34”

• cites [23] Pasolli E. Asnicar F. Manara S. Zolfo M. Karcher N. Armanini F. Beghini F. Manghi P. Tett A. Ghensi P. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle Cell 176 2019 649.e20–662.e20 PMC6349461 30661755 sourceNot checked yet

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• cites [25] Nayfach S. Shi Z.J. Seshadri R. Pollard K.S. Kyrpides N.C. New insights from uncultivated genomes of the global human gut microbiome Nature 568 2019 505 510 30867587 PMC6784871 sourceNot checked yet

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• cites [33] Almeida A. Mitchell A.L. Boland M. Forster S.C. Gloor G.B. Tarkowska A. Lawley T.D. Finn R.D. A new genomic blueprint of the human gut microbiota Nature 568 2019 499 504 30745586 PMC6784870 sourceNot checked yet

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• cites [34] Almeida A. Nayfach S. Boland M. Strozzi F. Beracochea M. Shi Z.J. Pollard K.S. Sakharova E. Parks D.H. Hugenholtz P. A unified catalog of 204,938 reference genomes from the human gut microbiome Nat. Biotechnol. 39 2021 105 114 32690973 PMC7801254 sourceNot checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing).

LAB belonging to the former genus Lactobacillus and genus Pediococcus are commonly found in different teff sourdoughs.

“While lactic acid bacteria (LAB) belonging to the former genus Lactobacillus and genus Pediococcus are commonly found in different teff sourdoughs,50,51”

• cites [50] Moroni A.V. Arendt E.K. Dal Bello F. Biodiversity of lactic acid bacteria and yeasts in spontaneously-fermented buckwheat and teff sourdoughs Food Microbiol. 28 2011 497 502 21356457 sourceNot checked yet

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• cites [51] Tilahun B. Tesfaye A. Muleta D. Bahiru A. Terefework Z. Wessel G. Isolation and Molecular Identification of lactic acid Bacteria Using 16S rRNA Genes from Fermented Teff (Eragrostis tef (Zucc.)) Dough Int. J. Food Sci. 2018 2018 8510620 30155476 PMC6098851 sourceNot checked yet

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May combine two claims.

The lower fraction of microbes shared in non-westernized microbiomes is not due to technical artifacts and may be partly explained by higher microbiome richness, possibly due to increased acquisition from other environmental or family sources.

“suggesting the lower fraction of microbes shared in non-westernized microbiomes is not due to technical artifacts and may be in part explained by a much higher microbiome richness, possibly due to increased acquisition of microbiome members from other environmental or family sources.42,43”

• cites [42] Brooks B. Olm M.R. Firek B.A. Baker R. Thomas B.C. Morowitz M.J. Banfield J.F. Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome Nat. Commun. 8 2017 1814 29180750 PMC5703836 sourceNot checked yet

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• cites [43] Brito I.L. Yilmaz S. Huang K. Xu L. Jupiter S.D. Jenkins A.P. Naisilisili W. Tamminen M. Smillie C.S. Wortman J.R. Mobile genes in the human microbiome are structured from global to individual scales Nature 535 2016 435 439 27409808 PMC4983458 sourceNot checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing).

Teff is commonly used in Ethiopia to make injera and other fermented products such as soups and alcoholic beverages.

“Teff is commonly used in Ethiopia to make injera, a typical fermented bread-like food, but also other fermented products, such as soups and alcoholic beverages.49”

• cites [49] Gebremariam M.M. Zarnkow M. Becker T. Teff (Eragrostis tef) as a raw material for malting, brewing and manufacturing of gluten-free foods and beverages: a review J. Food Sci. Technol. 51 2014 2881 2895 26396284 PMC4571201 sourceNot checked yet

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• AssumptionRests on an assumption: Teff is a cereal typically grown in the tropics and especially in Ethiopia, where it represents a major food grain.

Probably not a substantial claim: may not pass S3 (load-bearing).

Teff is traditionally naturally fermented by saving part of the liquid that forms at the top of the fermentation vessel (ersho) to start a new fermentation process driven by both prokaryotic and eukaryotic microbes.

“Teff is traditionally naturally fermented by saving part of the liquid that forms at the top of the fermentation vessel (ersho) to start a new fermentation process driven by both prokaryotic and eukaryotic microbes.50,51,52”

• cites [50] Moroni A.V. Arendt E.K. Dal Bello F. Biodiversity of lactic acid bacteria and yeasts in spontaneously-fermented buckwheat and teff sourdoughs Food Microbiol. 28 2011 497 502 21356457 sourceNot checked yet

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• cites [51] Tilahun B. Tesfaye A. Muleta D. Bahiru A. Terefework Z. Wessel G. Isolation and Molecular Identification of lactic acid Bacteria Using 16S rRNA Genes from Fermented Teff (Eragrostis tef (Zucc.)) Dough Int. J. Food Sci. 2018 2018 8510620 30155476 PMC6098851 sourceNot checked yet

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• cites [52] Tadesse B.T. Abera A.B. Tefera A.T. Muleta D. Alemu Z.T. Wessel G. Molecular characterization of fermenting yeast species from fermented Teff dough during preparation of injera using ITS DNA sequence Int. J. Food Sci. 2019 2019 1291863 31355246 PMC6633962 sourceNot checked yet

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• AssumptionRests on an assumption: Teff is a cereal typically grown in the tropics and especially in Ethiopia, where it represents a major food grain.

May combine two claims.

Not only non-westernized adults but also infants harbor a large amount of uncharacterized microbial diversity in their gut.

“suggesting that not only non-westernized adults22,24,40 but also infants, which are still poorly sampled in studies focusing on non-westernized communities, harbor a large amount of uncharacterized microbial diversity in their gut.”

May combine two claims.

Acquisition of Blastocystis sp. occurs later in life independently of lifestyle.

“which again suggests that acquisition of Blastocystis sp. occurs later in life independently of lifestyle.”

Probably not a substantial claim: may not pass S3 (load-bearing).

AAB Gluconobacter and Acetobacter spp. are commonly found in other fermented foods, such as kombucha and kefir, cocoa bean and buckwheat fermentation, and the sourdough fermentation starter jiaozi.

“the acetic acid bacteria (AAB) Gluconobacter and Acetobacter spp. were not described in fermented teff products before, even if they are commonly found in other fermented foods, such as kombucha and kefir, but also in the cocoa bean and buckwheat fermentation, and the sourdough fermentation starter jiaozi.53,54,55”

• cites [53] Ua-Arak T. Jakob F. Vogel R.F. Characterization of growth and exopolysaccharide production of selected acetic acid bacteria in buckwheat sourdoughs Int. J. Food Microbiol. 239 2016 103 112 27118673 sourceNot checked yet

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• cites [54] De Vuyst L. Van Kerrebroeck S. Leroy F. Microbial ecology and process technology of sourdough fermentation Adv. Appl. Microbiol. 100 2017 49 160 28732554 sourceNot checked yet

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• cites [55] Tamang J.P. Cotter P.D. Endo A. Han N.S. Kort R. Liu S.Q. Mayo B. Westerik N. Hutkins R. Fermented foods in a global age: east meets West Compr. Rev. Food Sci. Food Saf. 19 2020 184 217 33319517 sourceNot checked yet

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May combine two claims.

This is the first study addressing mother-infant strain sharing in non-westernized communities and reporting how environmental conditions affect not only infant microbiome composition but also its acquisition.

“To our knowledge, this is the first study addressing mother-infant strain sharing in non-westernized communities and reporting how environmental conditions affect not only infant microbiome composition but also its acquisition.”

• AssumptionRests on an assumption: Most studies about infant microbial colonization have been conducted in westernized populations, and the effect of different lifestyles on bacterial seeding has been largely underexplored.

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Previous studies in adults described differential microbiota patterns in non-westernized populations, including Prevotella spp. as a marker for non-westernized microbiomes.

“Previous studies in adults have described differential microbiota patterns in non-westernized populations, highlighting, for example, Prevotella spp. as a marker for non-westernized microbiomes.26,57”

• cites [26] Tett A. Huang K.D. Asnicar F. Fehlner-Peach H. Pasolli E. Karcher N. Armanini F. Manghi P. Bonham K. Zolfo M. The Prevotella copri complex comprises four distinct clades underrepresented in westernized populations Cell Host Microbe 26 2019 666.e7–679.e7 PMC6854460 31607556 sourceNot checked yet

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• cites [57] Tamburini F.B. Maghini D. Oduaran O.H. Brewster R. Hulley M.R. Sahibdeen V. Norris S.A. Tollman S. Kahn K. Wagner R.G. Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa Nat. Commun. 13 2022 926 35194028 PMC8863827 sourceNot checked yet

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May combine two claims.

A study based on 16S rRNA gene sequencing confirmed in children from a non-westernized Gambian community that P. copri, F. prausnitzii, and P. stercorea were the most abundant species in the infant gut microbiome and increased gradually with age.

“Recently, a study based on 16S rRNA gene sequencing confirmed these results in children from a non-westernized Gambian community, where P. copri, F. prausnitzii, and P. stercorea were the most abundant species in the infant gut microbiome,58 and they increased gradually with age.”

• cites [58] de Goffau M.C. Jallow A.T. Sanyang C. Prentice A.M. Meagher N. Price D.J. Revill P.A. Parkhill J. Pereira D.I.A. Wagner J. Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network Nat. Microbiol. 7 2022 132 144 34972822 PMC8727306 sourceNot checked yet

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May combine two claims.

Similar, albeit less marked, patterns of microbiome composition differences by lifestyle were already observed for adults but were never investigated in younger individuals.

“Similar, albeit less marked, patterns were already observed for adults22,23,24,25 with different lifestyles but were never investigated in younger individuals.”

• cites [22] Yatsunenko T. Rey F.E. Manary M.J. Trehan I. Dominguez-Bello M.G. Contreras M. Magris M. Hidalgo G. Baldassano R.N. Anokhin A.P. Human gut microbiome viewed across age and geography Nature 486 2012 222 227 22699611 PMC3376388 sourceNot checked yet

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• cites [23] Pasolli E. Asnicar F. Manara S. Zolfo M. Karcher N. Armanini F. Beghini F. Manghi P. Tett A. Ghensi P. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle Cell 176 2019 649.e20–662.e20 PMC6349461 30661755 sourceNot checked yet

  Not checked in the free run.

• cites [24] De Filippo C. Cavalieri D. Di Paola M. Ramazzotti M. Poullet J.B. Massart S. Collini S. Pieraccini G. Lionetti P. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa Proc. Natl. Acad. Sci. USA 107 2010 14691 14696 20679230 PMC2930426 sourceNot checked yet

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• cites [25] Nayfach S. Shi Z.J. Seshadri R. Pollard K.S. Kyrpides N.C. New insights from uncultivated genomes of the global human gut microbiome Nature 568 2019 505 510 30867587 PMC6784871 sourceNot checked yet

  Not checked in the free run.

May combine two claims.

The locally produced teff-based fermented sourdough newly sequenced in this study proved to be a source of microbial strains uniquely present in the Ethiopian cohort, albeit probably only transiently.

“An example is the locally produced teff-based fermented sourdough that we newly sequenced in this study and that proved to be a source of microbial strains uniquely present in the Ethiopian cohort, albeit probably only transiently.”

• AssumptionRests on an assumption: Teff-based porridges and gruels (genfo) are traditionally eaten by new mothers and weaning infants in the Ethiopian community.

Probably not a substantial claim: may not pass S3 (load-bearing).

Escherichia coli and Bifidobacterium spp. are the most shared within European mother-infant pairs.

“While Escherichia coli and Bifidobacterium spp. are the most shared within the European pairs, as previously described,10,15,16,17,41”

• cites [10] Bäckhed F. Roswall J. Peng Y. Feng Q. Jia H. Kovatcheva-Datchary P. Li Y. Xia Y. Xie H. Zhong H. Dynamics and stabilization of the human gut microbiome during the first year of life Cell Host Microbe 17 2015 852 26308884 sourceNot checked yet

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• cites [15] Asnicar F. Manara S. Zolfo M. Truong D.T. Scholz M. Armanini F. Ferretti P. Gorfer V. Pedrotti A. Tett A. Segata N. Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling mSystems 2 2017 10.1128/mSystems.00164-16 PMC5264247 28144631 sourceNot checked yet

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• cites [16] Ferretti P. Pasolli E. Tett A. Asnicar F. Gorfer V. Fedi S. Armanini F. Truong D.T. Manara S. Zolfo M. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome Cell Host Microbe 24 2018 133.e5–145.e5 PMC6716579 30001516 sourceNot checked yet

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• cites [17] Yassour M. Jason E. Hogstrom L.J. Arthur T.D. Tripathi S. Siljander H. Selvenius J. Oikarinen S. Hyöty H. Virtanen S.M. Strain-level analysis of mother-to-child bacterial transmission during the first few months of life Cell Host Microbe 24 2018 146.e4–154.e4 PMC6091882 30001517 sourceNot checked yet

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• cites [41] Duranti S. Lugli G.A. Mancabelli L. Armanini F. Turroni F. James K. Ferretti P. Gorfer V. Ferrario C. Milani C. Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission Microbiome 5 2017 66 28651630 PMC5485682 sourceNot checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Cinek et al. reported that the prevalence and subtypes of Blastocystis varied among six different geographical locations and would be related to the bacterial fraction of the infant microbiome.

“Cinek et al. reported that the prevalence and subtypes of Blastocystis varied among six different geographical locations and it would be also related to the bacterial fraction of the infant microbiome.61”

• cites [61] Cinek O. Polackova K. Odeh R. Alassaf A. Kramná L. Ibekwe M.U. Majaliwa E.S. Ahmadov G. Elmahi B.M.E. Mekki H. Blastocystis in the faeces of children from six distant countries: prevalence, quantity, subtypes and the relation to the gut bacteriome Parasit. Vectors 14 2021 399 34384477 PMC8359624 sourceNot checked yet

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Classified as probably not a substantial claim.

Because of the different age distribution between Ethiopian and Westernized infants, Westernized infants were randomly picked to get a similar age distribution with respect to Ethiopian ones before performing statistical tests.

“Because of the different age distribution between Ethiopian and Westernized infants, we randomly picked Westernized infants aged 0–6 months, 6-12 months, and 1-12 years to get a similar age distribution with respect to Ethiopian ones before performing statistical tests.”

Classified as probably not a substantial claim. May combine two claims.

Infants were vaginally delivered with no perinatal antibiotic prophylaxis exposure, except for some C-section delivered Italian (15/156 Italian samples) and Swedish newborns (30/300 Swedish samples).

“Infants were vaginally delivered with no perinatal antibiotic prophylaxis exposure, except for some C-section delivered Italian (15/156 Italian samples) and Swedish newborns (30/300 Swedish samples).”

Classified as probably not a substantial claim.

Each test was repeated 10 times with 10 different random pickings.

“Each test was repeated 10 times with 10 different random pickings, with each test comparing the microbiome composition of 127 Westernized and 20 Ethiopian infants (0-6 mo.: 55 West. and 12 Eth.; 6-12 mo.: 27 West. and 6 Eth.; 12-36 mo.: 9 West. and 2 Eth.).”

Classified as probably not a substantial claim.

Core genes never found in more than 1% of the sequences included in any other SGBs were selected as marker genes.

“Core genes never found in more than 1% of the sequences included in any other SGBs were selected as marker genes.”

Classified as probably not a substantial claim.

Traditional fermented food has the capacity to modulate gut microbiota.

“traditional fermented food due to its capacity to modulate gut microbiota,62,63”

• cites [62] Milani C. Duranti S. Napoli S. Alessandri G. Mancabelli L. Anzalone R. Longhi G. Viappiani A. Mangifesta M. Lugli G.A. Colonization of the human gut by bovine bacteria present in Parmesan cheese Nat. Commun. 10 2019 1286 30894548 PMC6426854 sourceNot checked yet

  Not checked in the free run.

• cites [63] Peluzio M.d.C.G. Dias M.d.M.E. Martinez J.A. Milagro F.I. Kefir and intestinal microbiota modulation: implications in human health Front. Nutr. 8 2021 638740 10.3389/fnut.2021.638740 33693024 PMC7938729 sourceNot checked yet

  Not checked in the free run.

May combine two claims.

The highly consumed fermented food would be a source of LAB for the gut microbiome, contributing to the difference in the microbial patterns observed in this population.

“our results suggest that the highly consumed fermented food would be a source of LAB for the gut microbiome, contributing to the difference in the microbial patterns observed in this population.”

• AssumptionRests on an assumption: Teff-based porridges and gruels (genfo) are traditionally eaten by new mothers and weaning infants in the Ethiopian community.

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Protocols were approved by the Ethics Committee of the University of Trento and the Ethics Committee of Santa Chiara Hospital (Trento, Italy, EC ref number: 51082283 - 30/07/2014).

“Protocols were approved by the Ethics Committee of the University of Trento and the Ethics Committee of Santa Chiara Hospital (Trento, Italy, EC ref number: 51082283 - 30/07/2014), as previously reported.16”

• cites [16] Ferretti P. Pasolli E. Tett A. Asnicar F. Gorfer V. Fedi S. Armanini F. Truong D.T. Manara S. Zolfo M. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome Cell Host Microbe 24 2018 133.e5–145.e5 PMC6716579 30001516 sourceNot checked yet

  Not checked in the free run.

Probably not a substantial claim: may not pass S3 (load-bearing).

Unknown SGBs with fewer than 5 MAGs overall, including MAGs external to the study cohorts, were excluded because the authors cannot ensure they are not populated with assembly artifacts or chimeric genomes.

“Unknown SGBs with less than 5 MAGs overall (including MAGs external from the study cohorts) were excluded, as we cannot ensure they are not populated with assembly artifacts or chimeric genomes.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Only samples with a breadth of coverage >10% for a specific ST reference genome were considered positive for Blastocystis sp. and for that specific ST.

“Only samples with a breadth of coverage >10% for a specific ST reference genome were considered positive for Blastocystis sp. and for that specific ST (Table S2).”

Probably not a substantial claim: may not pass S3 (load-bearing).

Blastocystis sp. was identified by applying previously validated methods and thresholds.

“We identified Blastocystis sp. by applying previously validated methods and thresholds.47”

• cites [47] Beghini F. Pasolli E. Truong T.D. Putignani L. Cacciò S.M. Segata N. Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome ISME J. 11 2017 2848 2863 28837129 PMC5702742 sourceNot checked yet

  Not checked in the free run.

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

These analyses are limited by the small sample size and by the lack of metagenomes of fermented food items consumed by new mothers and weaning infants from the other surveyed westernized and non-westernized cohorts.

“These analyses are limited by the small sample size and by the lack of metagenomes of fermented food items consumed by new mothers and weaning infants from the other surveyed westernized and non-westernized cohorts”

May combine two claims.

Injera is a highly consumed food made of teff sourdough fermented for 24-96 h, depending on the optimum temperature, and contains higher counts of LAB and yeast (LAB to yeast ratio of 10:1 to 100:1).

“we included in the metagenomic analysis two samples of injera, a highly consumed food made of teff sourdough fermented for 24–96 h, depending on the optimum temperature, which contain higher counts of LAB and yeast (LAB to yeast ratio of 10:1 to 100:1).64”

• cites [64] Mengesha Y. Tebeje A. Tilahun B. A review on factors influencing the fermentation process of teff (eragrostis teff) and other cereal-based ethiopian injera Int. J. Food Sci. 2022 2022 4419955 35368804 PMC8970856 sourceNot checked yet

  Not checked in the free run.

May combine two claims.

Lifestyle can impact microbiome composition not only through different food sources, drug availability, and environmental factors but potentially also through different patterns of mother-to-infant sharing of microbiome strains that strongly differ between westernized and non-westernized lifestyles.

“Overall, the work presented here highlights how lifestyle can impact microbiome composition not only through the different food sources, drug availability, and environmental factors but potentially also through different patterns of mother-to-infant sharing of microbiome strains that strongly differ between westernized and non-westernized lifestyles.”

• AssumptionRests on an assumption: Most studies about infant microbial colonization have been conducted in westernized populations, and the effect of different lifestyles on bacterial seeding has been largely underexplored.

Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

Non-Westernized cohorts already had an age distribution similar to the Ethiopian one.

“Non-Westernized cohorts already had an age distribution similar to the Ethiopian one.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Benjamini-Hochberg FDR corrections were performed to account for multiple hypothesis testing.

“Statistical significance was assessed through Fisher, Wilcoxon or Mann-Whitney U’s tests with multiple hypothesis testing Benjamini-Hochberg FDR corrections, as reported in the text.”

• Also stated in: § Quantification and statistical analysis · plain

  “Benjamini-Hochberg FDR corrections were performed to account for multiple hypothesis testing.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Metagenome-assembled genomes (MAGs) were reconstructed through single-sample metagenomic assembly and contig binning, an approach validated elsewhere.

“Metagenome-assembled genomes (MAGs) were reconstructed through single-sample metagenomic assembly and contig binning as validated elsewhere.23”

• cites [23] Pasolli E. Asnicar F. Manara S. Zolfo M. Karcher N. Armanini F. Beghini F. Manghi P. Tett A. Ghensi P. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle Cell 176 2019 649.e20–662.e20 PMC6349461 30661755 sourceNot checked yet

  Not checked in the free run.

May combine two claims.

Mother-infant sharing of Blastocystis spp. would be relevant in westernized countries but much less in non-westernized communities, where the environment may be the main source for these species.

“our results suggest that the mother-infant sharing of Blastocystis spp. would be relevant in the case of westernized countries but much less in non-westernized communities where the environment may be the main source for these species.”

Classified as probably not a substantial claim.

Strain consensus sequences were reconstructed using CMSeq with criteria: mapping quality >= 30, coverage >= 5 folds, minimum identity of reads >= 97%, aligned read length >= 30nt, and minimum dominant allele frequency >= 80%.

“with following criteria: (1) mapping quality >= 30, (2) coverage >= 5 folds, (3) minimum identity of reads >= 97%, (4) aligned read length >= 30nt, (5) minimum dominant allele frequency >= 80%.”

Classified as probably not a substantial claim.

The threshold defining identical strains was inferred by selecting the first percentile of the distribution of the non-related-samples distances.

“Using the StrainPhlAn's phylogenetic trees, this script generates a pairwise distance matrix normalized by the total branch length of the tree and infers a threshold defining identical strains by selecting the first percentile of the distribution of the non-related-samples distances.”